Living Tradition
Editor: Msgr. John F. McCarthy, J.C.D., S.T.D.Distributed several times a year to interested members.
Associate Editor: Rev. Brian W. Harrison, O.S., M.A., S.T.D.  Not to be republished without permission.
Please address all correspondence    e-mail:
Living Tradition, Oblates of Wisdom, P.O. Box 13230, St. Louis, MO 63157, USA

No. 124 Roman Theological Forum | Article Index | Study Program July 2006


reviewed by John F. McCarthy

[Francis S. Collins, The Language of God: A Scientist Presents Evidence for Belief
(New York: Free Press – Simon and Schuster, 2006
– viii plus 294 pages – available also from ]

Part I.  Random Change Versus Intelligent Design

1. Francis Collins’ The Language of God: A Scientist Presents Evidence for Belief is a powerfully written and challenging defense of the Darwinian theory of evolution that is bound to have considerable impact on the reading public.  Dr. Collins is qualified in physics and biochemistry and is a doctor of medicine as well.  He is a leading geneticist who headed the highly successful Human Genome Project, concluded in April 2003, which for the first time mapped the human genome.  He has also made discoveries relating to the causes of cystic fibrosis, neurofibromatosis, and Huntington’s disease.  The principal aim of his book is to show that the evolution of all living species has undeniably come about through random change and natural selection, and thus to convince Christians to accept the theory of evolution and bring it into synthesis with their faith.  He aims also to convince atheists to abandon their lack of belief in God.  In fact, the title, The Language of God,  refers to the idea that the genome is “the language in which God created life” (p. 2).  But a three-page article on the book which appeared in the 17 July 2006 issue of Time magazine has suggested that scientists who do not admit to believing in a God who answers prayers would probably be less drawn by the book to believe in a loving God than would Christian believers who are at present opposed to the theory of evolution probably be drawn to accept it.

2. Collins notes that all of us have arrived at a certain worldview (p. 6).  He grew up as an agnostic or non-believer, was converted to atheism by his schoolmates in college, and some time afterwards began his odyssey through belief in the existence of God to a final acceptance of the divinity of Christ as a non-Catholic evangelical Christian, which he has been now for over twenty-eight years.  The story of his conversion is impressive and even at times moving (narrated especially in the first and the last chapters of the book).  He has not only given himself to belief in Jesus Christ, but he has also dedicated himself to the service of his fellow man, in such ways as spending time as a volunteer medical doctor in Africa.  His intention in writing this book is one of genuine concern for peace and harmony between scientists and Christian believers.  He considers himself to be a theistic evolutionist, and he avers that “theistic evolution is the dominant position of serious biologists who are also serious believers” (p. 199).

3. Collins describes his position as a theistic evolutionist in the following terms:

   ·   The universe began to exist from nothingness about fourteen billion years ago.

   ·   The properties of the universe appear to be finely tuned for biological life.

   ·   The precise mechanism by which life arose on Earth is unknown, but after life once existed, without the need of any other supernatural intervention, evolution and natural selection permitted all of the succeeding biological diversification that came over very long periods of time.

   ·   Humans are part of this process, but they also have characteristics, such as awareness of the Moral Law and the universal search for God, that defy evolutionary explanation and point to our spiritual nature (p. 200).

4. Collins calls this version of theistic evolution “Biologos,” (“life through word” – that is, life through the divine Word of God) in that, while it accepts the Darwinian theory of evolution, it also expresses the belief “that God is the source of all life and that life expresses the will of God” (p. 203).  But Biologos is not conceived of as a scientific theory; it is tested only by “the spiritual logic of the heart, the mind, and the soul” (p. 204).  This combined outlook, he points out, cannot prove that God is real, since a leap of faith is always required for belief in God, but it has provided for very many scientist-believers a satisfying perspective that allows both the scientific and the religious worldviews to coexist happily within us (p. 201).  But, on the other hand, he says, belief in the existence of God is “intensely plausible,” as Augustine, Aquinas, and C.S. Lewis have made clear (p. 164). The Big Bang demands a divine explanation, because nature could not have created itself (p. 67).  And the Anthropic Principle (that the laws of the universe, such as the fifteen physical constants, seem set up to accommodate a stable universe able to sustain complex forms of life [p. 74]) provides a significant argument in favor of a Creator (p. 78).  How does the Darwinian theory of evolution allow Collins to see that God is the source of life?  Perhaps as the Creator of the first living biological form, and then, not because God has actively shaped biological life to be what it is, but because God, in his infinite knowledge, knew how every one of an infinite number of possible universes would turn out after the evolutionary throw of the dice, and He chose to create that deposit of initial matter/energy which, by a random and undirected process of change, would end up as the universe and the biological species that in fact arose, so that what necessarily appears to us in linear time as a universe and a biosphere produced by random and undirected change is actually, from the viewpoint of eternity, God’s plan (p. 205).

5. Collins hesitates in this presentation to go beyond a general sense of the existence of God, because the discussion tends to become emotional as soon as one begins to express a specific set of beliefs (p. 219). However, certain of his beliefs appear.  At a certain point he became aware that his own pride and sinfulness were blocking his desire to draw closer to God (pp. 220-222).  He was led by the writing of C.S. Lewis to believe that Jesus is the Son of God, and then the sight of a beautiful frozen waterfall caused him to surrender to Jesus (p. 225).  He saw that Jesus, by his Cross and Resurrection, has freed us from the bondage of sin and has thus assured us “that He no longer judges us by our actions, but sees us as having been washed clean” (pp. 222-223).  And he came to reflect seriously on the reality of God, the meaning of human existence, the possibility of an afterlife, and other spiritual ideas that are beyond the reach of the “scientific method” (p. 228).  How does this new synthesis of science and faith stand up under criticism?

6. In response to the obvious design of the universe and of living species, whose possibility of having come about by sheer chance is virtually nil, some atheistic evolutionists have advanced the idea that, if there are an infinite number of universes, this one could have happened by chance.  Francis Collins theistically modifies this idea with the notion that God could have chosen this chance universe and biosphere from an infinite number of possible universes.  One could combine these two notions by speculating that God did, in fact, institute an infinite number of randomly developing universes, either simultaneously or successively at intervals of thirty or forty billion years for each Big Bang, and then watched serenely for almost an infinite length of time until this universe and biosphere finally came about, and here we are.  The problem with all four of these hypotheses is that there is not a shred of evidence to support them, so the common experience of there being only one universe remains in possession.  And it stands to reason that, if God had the power to create from nothing the original substance of the universe, He would also have the power and the interest to shape its development.  Collins, although he denies any divine guidance in the rise of living species after the possible creation of the very first form, nevertheless, in theistically arguing that God must have created the laws of physics and chemistry as fine-tuned to produce an environment supportive of biological and human life, is admitting some intelligent design of the universe without suggesting when or how.  But the Bible seems to tell us in veiled language that God ignited the prime elements of the universe on the first day of creation, when He said, “Let there be light” (Gen 1:3).  And then God created the laws of physics and chemistry on the second day of creation, when he said, “Let there be a firmament in the midst of the waters [that is, let there be a structure of the universe], and let it separate the waters from the waters [that is, the swirling gases and other liquids in outer space from the swirling ball of gas that was becoming the Earth]” (Gen 1:6).  To say this is not making the Bible into a textbook of empirical science; it is reading a subtle message written under a simplified, “eye-witness” account of two successive historical events that took place at the beginning of time.

7. According to Francis Collins, science reveals that the universe, including the planet Earth, and life itself are engaged in a process of evolution.  He doesn’t exclude all miracles, but he maintains that frequent miraculous interventions by God would be as chaotic in the realm of physical nature as they would be disrupting in the action of human free will (p. 45).  And so, he says, believers should be cautious in invoking divine intervention in areas which are currently mysterious, lest they formulate an unnecessary theological argument that is doomed to later refutation (p. 93).  In particular he is opposed to the idea of assuming multiple acts of special creation of each living species on Earth (p. 26), but he also questions the absolutely proven need of a divine intervention even for the emergence of the first living species, from which all other living species are claimed to have descended (pp. 92-93).  In sum, Collins rejects the observation of common experience that all living biological species are intelligently designed works of art, and he is particularly opposed to the Intelligent Design Movement, which argues on a molecular level that the complex functions of living organisms cannot have arisen by chance (pp. 182, 187). 

8. Collins finds that intelligent design falls short as a viable scientific theory in its inability either to predict other findings or to suggest other approaches for further experimental verification (p. 187).  For instance, the human blood-clotting cascade, with its dozen or more proteins, can be visualized as a gradual accession of the elements of the cascade, beginning from a very simple mechanism serviceable for a “low-pressure, low-flow hemodynamic system,” and evolving over a long period of time into the more complicated structure needed by mammals for a high-pressure cardiovascular system (p. 189).  Ancient gene duplications could have allowed a new  copy of a protein not needed for the original function gradually to evolve so as to take on a new function, propelled by the force of natural selection.  Thus, “Darwinism predicts that plausible intermediate steps must have existed, and some have indeed already been found” (p. 190).  I am not skilled in empirical science and am not, therefore, qualified to comment directly on the accuracy of these data, which I assume to be correct, but I am qualified to comment on the logic of the explanation, using, as available, the data of other empirical scientists, such as Michael Behe, whose theory Francis Collins is criticizing in this place.  Behe, in his challenging book Darwin’s Black Box, dedicates eighteen pages to a very detailed and thoroughgoing analysis of the human blood-clotting cascade.  He notes that of itself the hypothesis of gene duplication and shuffling says nothing about how any particular protein or protein system was first produced (Behe, p. 90). 

9. Thus, in an attempt at an evolutionary explanation of blood clotting, Professor Russell Doolittle, while he imagines a series of steps in which clotting proteins appear one after another, gives no reason for the appearance of the proteins and does not even try to calculate the probability of their appearance in a random duplication and recombination of gene pieces (Behe, pp. 91-93).  Behe does make the calculation of probability for random duplication and recombination, and he finds the odds of lining up the required proteins to be beyond imagination (Behe, 93-96). And this horrendous improbability includes the protein duplication that Collins proposes as an answer. In my estimation as an unskilled observer of this discussion, the random evolving of the first two or three steps of the cascade that Collins visualizes is not as unreal as are the later steps, when the cascade is in need of new kinds of proteins and is hanging out there all on its own with no functionability.  Thus, the idea of evolving over a long period of time into a complicated system seems to be making the mere length of time supply for a causation that is otherwise lacking. And intelligent design does predict that, if the blood-clotting cascade or any other irreducibly complex system was designed in advance, the mutations being controlled accordingly, each respective system would emerge as it was designed to emerge.  Collins rejoins that the central premise of intelligent design theory is that “the entire blood-clotting cascade had to emerge fully functional from prior DNA gibberish,” but ID theory can allow with high statistical improbability that the first two or three steps of a longer cascade could be taken at random, while the later steps, requiring new kinds of proteins, are beyond statistical probability.

10. Michael Behe presents the bacterial flagellum as an example of irreducible complexity.  Francis Collins counters that several components of the bacterial flagellum could have been received by transfer, since they are related to an entirely different mechanism used by certain kinds of bacteria to inject toxins into bacteria that they are attacking (p. 192).  Collins says that each of these pieces presents a natural explanation for a step that intelligent design attributes to supernatural forces and leaves the proponents of intelligent design with constantly smaller ground to stand on (p. 193).  However, Behe had pointed out that the flagellum, a whip-like rotary propeller used by some bacteria for swimming, has no structural counterpart in more complex cells and it generates energy from a flow of acid through the bacterial membrane (Behe, pp. 71-72).  Because it is necessarily composed of three parts, a paddle, a rotor, and a motor, it is irreducibly complex.  The cilium (paddle) itself contains over two hundred different kinds of proteins.  The bacterial flagellum needs about forty additional kinds of proteins in order to be able to function.  Biochemists have discovered “staggering complexity” in the cilium alone and more in the bacterial flagellum, with dozens or even hundreds of precisely tailored parts (Behe, pp. 72-73).  “As the number of required parts increases, the difficulty of gradually putting the system together skyrockets, and the likelihood of indirect scenarios plummets” (Behe, p. 73).  A general point to be gathered from these statistics is that the enormous increase in the complexity of living cells that has been discovered by microbiologists has made the plausibility of Darwinian evolution dramatically less.  For instance, DNA “was previously considered to be little more than nuclear packing material, of no particular interest” (Collins, p. 101), but now the “elegance” of DNA, RNA, and protein “continues to be a source of awe and wonder” (p. 104). 

11. In reflecting on the fact that molecular biology has now revealed how amazing and complex life turns out to be,  Collins draws the conclusion that evolution, therefore, as a mechanism, can be and must be true (p. 107).  “No serious biologist today,”  he remarks, “doubts the theory of evolution to explain the marvelous complexity and diversity of life.”  He finds that the recognition of the inter-relatedness of all species through the mechanism of evolution is to such a degree the foundation of all biology that it is hard to imagine how one could study life without it (p. 99).  What he means is that it is almost impossible to imagine how to correlate the huge amounts of data emerging from the studies of genomes without the use of Darwin’s theory (p. 141).  As Theodosius Dobzhansky has expressed it, “Nothing in biology makes sense except in the light of evolution.”1  On the contrary, many serious scientists today are questioning the Darwinian theory of evolution.  Philosopher of science Stephen Meyer, in an extensive essay published in August 2004 in the Proceedings of the Biological Society of Washington, a peer-reviewed biology journal sponsored by the National Museum of Natural History of the Smithsonian Institution in Washington, D.C., entitled “Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories,” proposed intelligent design as an explanation alternative to Darwinian evolution for the origin of biological information and the higher categories of living species.  Meyer notes that “in the last decade or so a host of scientific essays and books have questioned the efficacy of selection and mutation as a mechanism for generating morphological novelty, as even a brief literature survey will establish” (Meyer, under “Introduction”).2  He goes on to say that “many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins” and that “such skepticism often derives from consideration of the extreme improbability (and specificity) of functional genes and proteins” (Meyer, under “Novel Genes and Proteins”).  Meyer points out that there are good reasons “why the issue of teleology or design has reemerged within the scientific discussion of biological origins”  and “why some scientists and philosophers of science have considered teleological explanations for the origin of form and information despite strong methodological prohibitions against design as a scientific hypothesis,” and he lists, by way of example, twelve prominent biologists who have published books and essays in English from 1992 to 2004 supporting the intelligent design theory (Meyer, under “Convergence and Teleological Evolution”).

12. Biologists seek the origins of proteins, organs, and whole animal and vegetable forms.  Even regarding the rise of new kinds of proteins, many biologists question the Darwinian and neo-Darwinian theories of evolution.  Meyer notes that cassette mutagenesis experiments carried out during the early 1990s suggest that the probability of attaining at random the correct sequencing of a short protein molecule only 100 amino acids long is about one in ten to the sixty-fifth power.  Based on these experiments, Axe has estimated that the probability for a protein 150 amino acids long is one in ten to the seventy-seventh power.  Meyer claims that this chance is “so small as to make appeals to chance absurd, even granting the duration of the entire universe” (Meyer, under “Novel Genes and Proteins”).  Collins admits that, before the advent of microbiology, Darwin did not know and had no way of knowing what the mechanism of evolution by natural selection might be, but now we know that this variation is fostered “by naturally occurring mutations in DNA.”  He admits also that most of the mutations that take place naturally in essential or vulnerable parts of the genome are harmful and are rapidly culled out of the population, because they reduce reproductive fitness, so that only on rare occasions will a mutation take place by chance that offers a slight amount of selective advantage, but over a very long period of time these favorable changes can result in major changes in biological function  (p. 131).  Is this reasoning up-to-date?  Collins offers no statistical study of the probability of the mechanism that he is describing, while Meyer points to statistical studies that show that to synthesize even one new kind of protein by the method proposed by Collins would take longer than the duration of the entire universe.  And this is just for one new protein.  But the basic discussion here has to do with macroevolution, with changes ending up in new living species, possessing thousands or millions of new and different codes and characteristics in and around the genomes. Collins sees the distinction between microevolution and macroevolution to be rather arbitrary, inasmuch as “larger changes that result in new species are a result of a succession of smaller incremental steps” (p. 132). Is this just wishful thinking?

13. Over the years, many advocates of intelligent design have pointed to the human eye as displaying a complexity beyond the scope of random change and natural selection.  Collins observes that Darwin himself recognized this problem as a formidable one, but he also suggested some steps by which this could have been accomplished according to his theory.  Darwin observed that even some very simple organisms have light sensitivity, while others progressed to a simple pigmented pit containing light-sensitive cells, and in others this pit has been converted into a cavity with just a pinhole to admit light.  The addition of an overlying jellylike substance in other organisms has enabled some focusing of the light.  Hence, “given hundreds of millions of years,” this system could have evolved into the modern mammalian eye (Collins, pp. 190-191).  But this is an enormous jump, and the immense number of missing steps is filled only by an immense length of time which was not available in the first place.  It is not the first anatomical steps that so defy the probability of the random process as it is the more specialized steps that come afterward.  And Behe points out that “each of the anatomical steps and structures that Darwin thought were so simple actually involves staggeringly complicated biochemical processes that cannot be papered over with rhetoric” (Behe, p. 22).

14. New higher animal forms have appeared.  Collins critically notes that certain theists have tried to present the Cambrian explosion of new life forms as evidence of supernatural intervention, in that about 400 million years ago plants appeared on dry land and a mere 30 million years later animals also had moved onto land.  In addition, there appeared to be in the fossil record few transitional forms between sea creatures and land-dwelling four-legged animals.  But, he says, recent discoveries have documented “compelling examples of just this kind of transition” (p. 95).  In fact, he adds, “many of the previous gaps in understanding of the history of life on Earth are now being filled by the discovery of extinct species” (pp. 93-94).  Thus, he says, in the last few years, intermediate fossil forms have been found for such new species as birds, turtles, elephants, and whales (p. 173).  And so, “the overwhelming weight of scientific data” supports the view of the interrelatedness of all living things, including ourselves (p. 141), so much so that, from the viewpoint of a biologist the evidence in favor of evolution is “utterly compelling,” and “the predictions of evolution have been borne out in more ways than Darwin could have possibly imagined” (p. 146).

15. Collins does not himself expand at this point upon the new discoveries of intermediate fossil forms, but he rather refers the reader (p. 174) to Darrel Falk’s Coming to Peace with Science.3  In his book Falk compares three possibilities to explain the fossil record regarding the origin of biological species: a)creation out of nothing by God of each individual living species; b)creation by God of the basic types of living organisms followed by microevolution of the more numerous related species; c)gradual evolution of all species “under the control of God’s Presence” and “according to God’s will and God’s command” (Falk, p. 87).  Regarding the possibility of creation from nothing of all species, in addition to offering evidence from genetics, Falk excludes the creation of each individual species as a non-problem for Christian believers, on the ground that the Bible does not say that God uttered a long series of unique commands to achieve this purpose (Falk, p. 102).  The idea that God was the engineer-designer of every species one by one “has come from our own minds and not from God’s holy Word” (p. 168).  Regarding the possibility of creation of the basic types only, Falk points out that large categories of organisms, such as insects, crabs, spiders, birds, dogs, whales, etc. did not yet appear during the Cambrian explosion, and those forms that did appear had  bodily forms that were very different from what we see today (p. 95).  And so Falk concentrates on the notion of the gradual evolution of all species.  When it comes to the recently discovered intermediate fossil forms mentioned above by Collins, Falk gives several examples.

16. Elephants have a highly distinctive form among mammals.  In the fossil record there are 164 different elephant-related species, of which only two remain in existence today (Falk, p. 98).  In the earliest forms, dating from about fifty million years ago, “they were the size of a small pig and did not have a trunk”.  As they grew larger, they developed a longer and longer trunk (Falk, p. 99).  Whales are also highly distinctive mammals.  They now have a fat pad for detecting sound, but 52 million years ago they were the size of wolves and they had a terrestrial hearing mechanism with no sign of a place for a fat-pad apparatus (Falk, p. 107).  Then about 42 million years ago a species of whales had an 18-inch hind leg with a foot that “was almost certainly a residual structure that had not yet been eliminated” (Falk, p. 109).  Turtles are highly distinctive among reptiles.  The development of the backs of turtles to the present form is shown in the fossil record to have taken place between 255 million and 210 million years ago (Falk, p. 103).  Regarding the evolution of fish to four-legged animals, beginning around 370 million years ago, the first land animals were very fish-like in appearance (Falk, p. 115).  Mammals are highly distinct from reptiles.  Reptiles appeared about 260 million years ago, and by about 245 million years ago some were becoming increasingly like mammals (Falk, p. 116).  At the time of the transition, reptile cynodonts had a double hinge in their jaws: one was like the dentary-squamosal junction found in mammals, while the other was the quadrate-articular junction typical of reptiles .  Biologists believe that, over hundreds of thousands of years, “the quadrate-articular bones were freed up to become the famous incus/malleus of the middle ear” of mammals (Falk, p. 117).  Birds are quite distinct from reptiles.  It seems that some of the birds that existed 100 million years ago still had teeth, longer tails and fingers with claws emerging slightly out of the wings (Falk, p. 123).  To the question how a reptile could turn into a bird, Falk, in favoring the idea of a gradual transition from species to species as “an extremely likely alternative” (Falk, p. 170), gives two responses: “anything is possible in response to the command of God’s Word and the Presence of God’s Spirit;” and we need also to understand the immense amount of time that was involved in the process (p. 132). 

17. Against the thesis that God created each new species from scratch, Falk points out that the “wording” in the genomes is almost identical in closely related species, somewhat different in species that are less closely related, and very different in species that are distantly related (Falk, p. 182).  A piece of “floating gibberish” called a retroposon can insert itself into a gene, and, once it has been inserted, there is no natural mechanism by which it can be removed.  It has been discovered that a retroposon called SINE CHR-1 occurs (randomly) in the same place in the whale and the dolphin as well as in all even-toed ungulates, such as the hippopotamus, the cow, the sheep, the deer, the giraffe, but does not occur in the same place in more distantly related species, such as the pig and the camel.  Again, to show the lack of a common ancestor, the same genes are arranged in one order in the chimpanzee and the orangutan and in reverse order in the gorilla.  But monkeys, chimps, and gorillas have certain gene arrangements in common that cats do not have, and, going further back, cats share with monkeys, chimps, and gorillas certain genetic arrangements that less similar species do not have.  Falk finds that “the only good interpretation” of these and similar findings is that all along the line some species share various common ancestors that other species do not have.  The same argument for determining common ancestors, he says, holds for silenced viruses in the genes (Falk, pp. 191-194; 197-198).  Falk is not as clear as Collins about accepting the dominant role of random mutations and natural selection, but he leans this way where he says that God willed freedom for his creation, and “in that freedom gene sequences shuffle, change, and become rearranged” (Falk, p. 195).  And from the study of gene sequences, he finds it to be obvious that God did not create each new species “from the dirt of the ground or with the snap of his fingers” (Falk, p. 198).  Granted that God can move suddenly by performing nature miracles, he can also work subtlely in a manner that cannot be detected “except through the lens of faith” (Falk, pp. 195-196).  Hence, God can use natural forces to accomplish overall purposes that cannot be detected by empirical scientists looking only at small details of the finished work (Falk, p. 206).

18. On the other side, Meyer’s information-based analysis of the Cambrian explosion supports the claim of recent authors like Muller and Newman that the mechanism of selection and genetic mutation considered to be sufficient by Darwinian evolutionists, “does not constitute an adequate causal explanation of the origination of biological form in the higher taxonomic groups” (Meyer, under “Introduction”), that is, of the appearance of new and higher living species.  In the Cambrian explosion, Meyer notes, between 19 and 35 phyla out of a total of 40 appeared for the first time within a time-window of only five to ten million years, and, in almost all cases, the new species had “no clear morphological antecedents in earlier Vendian or pre-Cambrian fauna” (Meyer, under “The Cambrian Explosion”).  And, as Valentine and Erwin noted in 1987, the fossil record fails to document a large pool of species prior to the Cambrian era (Meyer, under “Punctuated Equilibrium”).  Curiously for Darwinian theory, Meyer adds, in the Cambrian explosion, the higher new species seem to have appeared earlier than the lower new species (Meyer, under “Self-Organizational Models”).  S. Ohno also concluded in 1996 that “the mutational divergence of preexisting genes cannot explain the origin of the Cambrian forms in the time allowed” (ten million years) (Meyer, under “Novel Genes and Proteins”). 

19. The Darwinian evolutionary theory held by Francis Collins affirms that, once the first life form arose, evolution and natural selection were sufficient for all of the following biological diversification that came about over very long periods of time (no. 3 above).  But, regarding new animal species in general, Meyer argues that no current theory of evolution can account for the origin of the information necessary to build novel animal forms, since no adequate source of new form and structure has been identified by evolutionary theorists (Meyer, under “Introduction”).  By “form” he means “the four-dimensional topological relations of anatomical parts” (Meyer, under “Defining Biological Form and Information”).  According to Meyer, “DNA alone cannot account for the morphological changes required to build a new body plan”.  McDonald points out that genes observed to vary within natural populations do not lead to major adaptive changes, while genes that could lead to major changes, as in the notion of macroevolution, do not vary.  Indeed, there is no evidence from developmental genetics that the favorable body-plan mutations required by neo-Darwinism ever occur (Meyer, under “Novel Body Plans”).  Hence, Darwinian theory does not provide a way for the rise of new body plans.  “Neither structural proteins alone, nor the genes that code for them, are sufficient to determine the three-dimensional shape and structure of the entities they form.  Gene products provide necessary, but not sufficient conditions for the development of three-dimensional structure within cells, organs, and body plans.  But, if this is so, then natural selection acting on genetic variation alone cannot produce the new forms that arise in the history of life” (Meyer, under “Novel Body Plans”). 

20. Biochemist Roland Hirsch, in an essay published in 2004,4 while noting that the Darwinian theory of evolution, in the Darwin Centennial Year of 1959, was confidently proclaimed to be the foundation of the science of biology, maintains that “such confidence is not warranted today,” because “new technologies have revealed that life is more complicated than was imagined in 1959” (Hirsch, p. 1).  By 2004, base sequences for more than a hundred genomes had been determined, and “these complete genome sequences have revealed several complexities that Darwinian evolutionary theory did not anticipate.”  Four of these unanticipated complexities are the following: a)transfer genes; b)bacterial species evolving also by deletion of genetic material; c)the finding that some portions of the genome that do not code for proteins are not, nevertheless, “junk DNA;”  d)the finding that “the expression of genes is controlled by regulatory circuits that are as complicated and as precisely arranged as the most sophisticated engineering diagrams” (Hirsch, pp. 2-3). 

21. Regarding transfer genes, comparison of the genome sequences “revealed that for at least two microbial domains (bacteria and archaea), much of the inheritance is in a horizontal direction,” and that significant portions of respective genomes did not come from their ancestors but rather at various times “from the species that were its neighbors through what is termed ‘horizontal gene transfer.’”  These new discoveries have made it clear that “there is no single ‘tree of life,’ but rather a ‘web’ or ‘net’ of interconnections that are both vertical and horizontal.  . . .  There was no ‘common ancestor cell,’ but rather it is now thought more likely that there was a pool of cells that changed communally over a long period of time” (Hirsch, pp. 3-4).  By way of example, Hirsch points out that photosynthetic bacteria are found in five different phyla, and “the genome comparisons show that significant numbers of genes relevant to photosynthetic function must have been transferred horizontally among the species studied” (Hirsch, p. 4). 

22. Regarding deletion of genetic material, Hirsch reports that “the standard Darwinian mechanism of random mutation and natural selection is inconsistent with the observed fact of a non-random bias toward deletion of DNA” (Hirsch, pp. 5-6).

23. Regarding the so-called ‘junk DNA,’ Hirsch refers to more recent data:  “Today the experimental evidence suggests that much, though probably not all, of the non-coding regions of the genome have critical roles in the development and function of an individual.  . . .  The small number of genes (in the human genome) suggests that the non-coding regions must have key roles to play, including even repetitive portions of the DNA” (Hirsch, p. 6).

24. Regarding the recently discovered regulatory circuits, Hirsch avers:  “The mechanism by which expression of many of these genes is controlled is much more complicated than was previously believed.  It is not a simple matter of the code carried by a gene being decoded to make a messenger RNA (mRNA) to enable the synthesis of a protein.  Instead, a group of genes encodes a set of regulatory factors that controls the transcription of the gene that is to be decoded for synthesis of a protein by the cell (translation of the genome code into a polypeptide).”  Hence, “variation in gene sequence does not explain all variation in function among members of a species.” Thus, it is the conclusion of this empirical scientist that Darwinian evolutionary theory “failed to anticipate several key discoveries about genetics, inheritance, and gene expression and development” (Hirsch, pp. 7-8).

25. Hirsch brings in another defect of Darwinian theory regarding the observed folding of protein molecules where he says that “the folding process is possible only because it was guided,” inasmuch as “a process of folding in which the protein chain bends entirely in random ways could not achieve the functional fold of that protein in any useful period of time.”  Only recently has it been realized that most cellular functions are carried out by highly organized protein machines, and part of the reason for the delay in understanding this is that the Darwinian concept of evolution by random mutation and natural selection practically forced biologists to treat each protein, or gene product, “as a distinct unit in the functioning of an organism.”  But, says Hirsch, “how could a function requiring multiple proteins in a cellular machine ever arise through the required random mutations that developed one protein molecule at a time and in a stepwise manner, and gave no intermediate product with any function that would allow Darwinian natural selection to work?” (Hirsch, p. 11).  To Roland Hirsch it is clear that the accepted idea of organisms evolving from simple to complex does not apply to the protein synthesis machinery that works “with a precision exceeding that of the most complicated devices designed and engineered by humans” (Hirsch, p. 13).  It is Hirsch’s general conclusion that much of what was taught forty years ago in keeping with Darwinian theory “has had to be unlearned or has become irrelevant,” because it cannot explain much of what today’s experiments and field research reveal about biological life (Hirsch, p. 19).

26. How then to address Francis Collins’ observation (p. 141) that it is nearly impossible to see how  to correlate the immense data being generated from the studies of genomes without the use of Darwin’s theory of evolution?  Well, Microbiologist Michael Denton has observed that even most evolutionary biologists use traditional taxonomy and not Darwinian theory to organize their data.  And Roland Hirsch quotes Adam Wilkins, editor of the review journal BioEssays, in introducing the issue of December 2000, dedicated to the subject of evolution, as remarking:  “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that ‘nothing in biology makes sense except in the light of evolution,” most can conduct their work quite happily without reference to evolutionary ideas.  ‘Evolution’ would appear to be the indispensable unifying idea and, at the same time, a highly superfluous one” (quoted in Hirsch, p. 19).  Collins admits that “on the surface” the arguments advanced by the intelligent design movement seem to be compelling, but “if logic truly has merit on scientific grounds,” he counters, why do no rank-and-file biologists show interest in pursuing these arguments, not even the many who are also believers in God (pp. 186-187)?  As noted above, many biologists are in fact pursuing the theory of intelligent design.  But most others are not, and there are several reasons for this. One reason is fear.  Collins himself points out that most scientists who adhere to theistic evolution, as he does, are reluctant to speak out “for fear of negative reaction from their scientific peers” (p. 202).  This is the factor of peer pressure.  It is common knowledge that any scientist who brings design into the picture of evolution is in great danger of being marginalized by his colleagues and even of losing his job.  But it is not only fear of their peers.  Evolution is a highly emotional issue, and there are powerful secular humanist groups and interests that have been pushing the Darwinian and neo-Darwinian theories of evolution for more than a century in order to transform the Judeo-Christian worldview into an evolutionary one in the minds of all people.  Another reason is the pull of the flesh.  It is easier and more convenient to just “go with the flow” and not stand out as being different. But there is also a third reason, and that has to do with the very nature of the theory of evolution. It appears to me that the Darwinian theory of evolution is being used partly as a theory of empirical science, but mainly as an overview, as an historical-philosophical explanation that exceeds and stands outside of the purview of empirical science.  Rank-and-file biologists and other empirical scientists are usually not versed in historical and philosophical science, and, therefore, they do not presume to oppose the “official wisdom” handed out to them by their teachers and their peers.  In view of these three reasons, it is easy to see why empirical scientists are not disposed to welcome opportunities to overturn the theory of evolution.

27. Many biologists seem to have confused evolution as a working hypothesis with evolution as an historical theory.  The basic concept of the Darwinian theory of evolution is that the species living today emerged from prior living species by a process of random mutation and natural selection.  This is an historical theory aimed at explaining how the concrete forms of biological life on Earth today actually arose.  As an historical theory it is not called upon to be predictive of how new species will arise; it is only required to verify that this historical succession of events took place.  Now, intelligent design theory is aimed to refute the Darwinian claim that the species arose by a process of random mutation and natural selection, and it does so by showing that the chances of the production of a new species by random mutation and natural selection are virtually zero.  And intelligent design goes on to show that, not only is the random evolution of a new species virtually impossible, but the random evolution of a new bodily organ, or even the random evolution of one new kind of protein is statistically almost zero.  Francis Collins, in proposing the by chance providing of later intermediate steps in the formation of the blood-clotting cascade, did not study the mathematical probability of this happening, but Behe and others have done so.  In the words of microbiologist Michael Denton:  “It is surely a little premature to claim that random processes could have assembled mosquitoes and elephants when we still have to determine the actual probability of the discovery by chance of one single functional protein molecule.”5  

28. Evolution as a theory of empirical science.  It is a fantastic jump from the recorded observance of gene duplication and shuffling to the prediction that, “given enough time,” higher biological species, such as fleas or horses, could emerge from it.  Predictions can be made from the functioning of the laws of chemistry and physics, but there are no laws of evolution as such.  Darwin proposed random mutation and natural selection as laws of evolution, but random mutation is no law, it is the absence of all law, and natural selection can work only on existing populations, it cannot help to produce a population.  So there is no law of the emergence of new species.  This means that working evolutionary biologists are not using any actual “laws of evolution” in their work; they are simply reading an evolutionary worldview into the results of their work.

29. Evolution a theory of historical science The Darwinian theory of evolution has to do with the emergence by chance of new species from individuals of prior species, and, as such, it can have no predictive ability.  No evolutionist can predict or even imagine what new species a bacterium, a flea, or a mouse might turn into, because every living species is an artistic creation that goes beyond human imagination.  Evolutionists can talk about new strains of bacteria, but new strains of bacteria are still just bacteria.  Biologists have classified thousands of morphologically different living species, apart from the immense number of minor species that are so similar to one another that they are irrelevant to the present discussion. Collins points out that Darwin did not postulate the origin of living species from non-living matter, but rather assumed the existence of a few original forms with the potential to develop into other forms without the need of divine interventions (Collins, p. 98).  What we are mainly discussing here is the origin of new body forms, such as those of the different phyla and not the emergence of less distinct forms, such as those of families of species, and whether they have or have not, in fact, emerged from one original form or a small number of forms.  This is an historical question concerning a series of events that did or did not really take place.  Darwin said that his theory would have to be verified in the fossil record, or it would fail. The fact that it has not been verified in the fossil record has been a very embarrassing thing for Darwinian and neo-Darwinian evolutionists.  According to Darwinian theory, which states that new species arose as a result of many successive small changes over a long period of time, there should be in the fossil record an enormous number of specimens with partially formed organs, such as part of a wing, or of an arm, or of an eye, or of a heart, etc., but they have not appeared.  Darwinian theoreticians such as Eldridge and Gould, or Huxley and Dawkins, have suggested desperate explanations like “punctuated equilibrium,” by which the organ or species being transformed would hold the accumulating new morphological form dormant in its DNA for up to millions of years until it was fully formed and functional, while natural selection systematically was eliminating all of the other deleterious or non-functional mutations.  But why would not natural selection eliminate this only in-the-future functionable organ or species, unless it was designed to grow undisturbed?  Yet, rank-and-file biologists and other empirical scientists do not systematically question these insufficient attempts at explanation to the extent that the fragile ideas are in keeping with the official wisdom and they themselves are not historical theoreticians.


1. Quoted in Francis S. Collins, The Language of God, p. 141.

2. Stephen C. Meyer, “Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories,” in Proceedings of the Biological Society of Washington, Nov. 30, 2005. Available on the Internet here

3.  Darrel R. Falk, Coming to Peace with Science: Bridging the Worlds Between Faith and Biology (Downers Grove, Illinois: Intervarsity Press, 2004).

4. Roland F. Hirsch, “Darwinian Evolutionary Theory and the Life Sciences in the 21st Century,” in Uncommon Dissent (Willliam Dembski, ed.: ISI Books, 2004). Available on the Internet at

5.  Michael Denton, Evolution: A Theory in Crisis (Bethesda, Maryland: Adler and Adler, 1985), p. 324.

Francis S. Collins, The Language of God: A Scientist Presents Evidence for Belief
Click here to buy it from Amazon

Go to: Roman Theological Forum | Living Tradition Index | Previous Issue | Next Issue