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Primer: Summary of Problems with Biological and Chemical Evolution

There are a number of scientific problems with neo-Darwinian (biological) and chemical evolution. They include:
  • The failure of evolutionary biology to provide detailed explanations for the origin of complex biochemical features. (For details and documentation, please see: “The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information,” “Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones's Straw Tests of Irreducible Complexity for the Bacterial Flagellum,” or “Opening Darwin's Black Box”.)

  • The failure of molecular and anatomical homology to provide evidence for universal common descent. (For details and documentation, please see: “A Primer on the Tree of Life".)

  • The failure of the fossil record to provide evidence for gradual neo-Darwinian change. (For details and documentation, please see “Intelligent Design Has Scientific Merit in Paleontology” or “Punctuated Equilibrium and Patterns from the Fossil Record”.)

  • The failure of developmental biology to bolster common descent. (For details and documentation, please see: “Evolving views of embryology,” “A Reply to Carl Zimmer on Embryology,” or “Textbooks misuse embryology” or "Challenging the Precious Pharyngula" or "Three Flawed Evolutionary Models of Embryological Development and One Correct One.")

  • The failure of genetics and chemistry to explain the origin of the genetic code. (For details and documentation, please see “The origin of life remains a mystery” or “Problems with the Natural Chemical ‘Origin of Life’”.)

  • The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species. (For details and documentation, please see “Biogeographical Challenges to Neo-Darwinian Evolution”.)

  • A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called “junk” DNA. (For details and documentation, please see: “Intelligent Design and the Death of the ‘Junk-DNA’ Neo-Darwinian Paradigm,” “The Myth of Junk DNA,” “The Latest Proof of Evolution: The Appendix has No Important Function,” or “Does Darrel Falk's Junk DNA Argument for Common Descent Commit ‘One of the Biggest Mistakes in the History of Molecular Biology’?” or “Junk No More: ENCODE Project Nature Paper Finds 'Biochemical Functions for 80% of the Genome'”.)
  • Other good resources on problems with evolution include:
  • Jonathan Wells’ article “Survival of the Fakest," which is a good critique of standard lines of evidence used to support Darwinian evolution.

  • Primer: Evolutionary Theory

  • Biophysicist Cornelius G. Hunter's website Darwin’s Predictions discusses many failed predictions of neo-Darwinian evolution.

  • A good summary of problems with claims of common ancestry can be found at But Isn't There a Consilience of Data That Corroborates Common Descent?

  • The website also has a list of Articles Critical of Darwinian Evolution and Chemical Evolution
  • Finally, the section below is an excerpt from The College Student's Back to School Guide to Intelligent Design in response to the claim "Intelligent Design Has Been Refuted by the Overwhelming Evidence for Neo-Darwinian Evolution": Objection #9: Intelligent Design Has Been Refuted by the Overwhelming Evidence for Neo-Darwinian Evolution

    The Short Rebuttal: The evidence for neo-Darwinian evolution is not “overwhelming.” While it remains the dominant view within biology, a growing minority of scientists dissent from Darwin. Over 800 doctoral scientists have signed a public statement proclaiming, “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life.”49 Signers of the list include members of the national academies of science in the United States, Russia, Poland, the Czech Republic, and India (Hindustan), as well as faculty and researchers from a wide range of universities and colleges, including Princeton, MIT, Dartmouth, Ohio State, Tulane, and the University of Michigan. Biological and chemical evolution lack supporting evidence in fields such as genetics, biochemistry, taxonomy and systematics, paleontology, and the chemical origins of life.

    The Long Rebuttal: Biological and chemical evolution lack supporting evidence in many scientific fields:

    Genetics: Mutations Tend to Cause Harm and Do Not Build Complexity. Darwinian evolution relies on random mutations which are selected by natural selection, a blind and unguided process that has no goals. Such a random and undirected process tends to harm organisms. It does not seem capable of improving organisms or building new, complex systems. Many scientists have questioned whether natural selection acting upon random mutation is sufficient to generate new species or new complex biological features. Leading biologist Lynn Margulis criticizes the standard Darwinian mechanism by stating that the “Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric.”50 She further observes that “new mutations don’t create new species; they create offspring that are impaired.”51

    Stanley Salthe, author of an evolutionary biology textbook, proclaims, “I have become an apostate from Darwinian theory and have described it as part of modernism’s origination myth.”52 Philosopher Jerry Fodor recently wrote that “at a time when the theory of natural selection has become an article of pop culture, it is faced with what may be the most serious challenge it has had so far.”53 National Academy of Sciences member Phil Skell also questions the explanatory utility of natural selection, observing that, “Darwinian evolution—whatever its other virtues—does not provide a fruitful heuristic in experimental biology.”54

    Biochemistry: Unguided and Random Processes Cannot Produce Cellular Complexity. Cells contain incredible complexity, similar to machine technology but dwarfing anything produced by humans. Cells use circuits, miniature motors, feedback loops, encoded language, and even error-checking machinery which decodes and repairs our DNA. Past U.S. National Academy of Sciences President Bruce Alberts (who opposes ID) has described this complexity in the journal Cell as an elaborate factory: “The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”55 But could such integrated complexity evolve in a stepwise, Darwinian fashion? Michael Behe recalls that in Origin of Species, Darwin admitted that if “any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”56 According to Behe, “by opening the ultimate black box, the cell,” modern science “has pushed Darwin’s theory to the limit.”57

    The simplest cell requires hundreds of genes, numerous complex biological machines and biochemical pathways, and a fully functional genetic code in order to survive. Darwinian evolution—blind natural selection acting on random mutations—has failed to provide Darwinian explanations for how basic cellular biochemistry might have evolved. Five years after Behe published Darwin’s Black Box, biochemist Franklin Harold stated in an Oxford University Press monograph that “there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”58

    Paleontology: The Fossil Record Lacks Intermediate Fossils. The fossil record’s overall pattern is one of abrupt explosions of new biological forms, where possible candidates for evolutionary transitions are the exception, not the rule. For example, in the Cambrian Explosion (530 million years ago), nearly all the major body plans of animals appear in a geological instant without any apparent evolutionary precursors.

    In 1979, paleontologist David Raup wrote that “we are now about 120 years after Darwin, and knowledge of the fossil record has been greatly expanded ... ironically, we have even fewer examples of evolutionary transition than we had in Darwin’s time.”59 Evolutionists may claim that there are a multitude of transitional forms known from the fossil record, yet a textbook published over 20 years later acknowledges that the fossil record has not given clues to help explain the origin of animal phyla in the Cambrian explosion: “Most of the animal phyla that are represented in the fossil record first appear, ‘fully formed,’ in the Cambrian some 550 million years ago...The fossil record is therefore of no help with respect to the origin and early diversification of the various animal phyla.”60

    This is not the only such explosion in the fossil record. Paleontologists have observed a fish explosion, a plant explosion, a bird explosion, and even a mammal explosion. Abrupt explosions of mass biological diversity seem to be the rule, not the exception, for the fossil record. Transitions plausibly documented by fossils seem to be the rare exception. As evolutionary biologist, the late Ernst Mayr, wrote in 2001, “When we look at the living biota, whether at the level of the higher taxa or even at that of the species, discontinuities are overwhelmingly frequent. . . . The discontinuities are even more striking in the fossil record. New species usually appear in the fossil record suddenly, not connected with their ancestors by a series of intermediates.”61 This phenomenon exists not only at the species level but also among higher taxa, as one zoology textbook admits: “Many species remain virtually unchanged for millions of years, then suddenly disappear to be replaced by a quite different, but related, form. Moreover, most major groups of animals appear abruptly in the fossil record, fully formed, and with no fossils yet discovered that form a transition from their parent group.”62

    Taxonomy and Systematics: Biologists Have Failed to Construct Darwin’s Tree of Life. Biologists hoped that DNA evidence would reveal a grand tree of life where all organisms are clearly related. Yet trees describing the alleged ancestral relationships between organisms based upon one gene or biological characteristic commonly conflict with trees based upon a different gene or characteristic. This implies a challenge to universal common descent, the hypothesis that all organisms share a single common ancestor.

    Evolutionists commonly assert that shared amino acids in genes common to many types of organisms indicate that all life shares a common ancestor. This circular argument rests upon the assumption that shared genetic similarities must be the result of common descent. Intelligent design is not necessarily incompatible with common ancestry, but it must be noted that intelligent agents commonly re-use parts that work in different designs. Thus, similarities in genetic sequences may also be generated as a result of functional requirements and common design rather than by common descent.

    Darwin’s tree of life—the notion that all living organisms share a universal common ancestor—has faced increasing difficulties in the past few decades. Phylogenetic trees based upon one fundamental gene or protein often conflict with trees based upon another gene or protein. In fact, this problem is particularly acute when one studies the “ancient” genes at the base of the tree of life, which many evolutionists wrongly claim demonstrate universal common ancestry. As W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”63 Doolittle attributes his observations to gene-swapping among microorganisms at the base of the tree. But Carl Woese, the father of evolutionary molecular systematics, finds that such problems exist beyond the base of the tree: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”64

    Evolutionists will commonly cite the congruence of the Cytochrome C tree with standard evolutionary trees as confirming theories of common descent. They rarely discuss the Cytochrome B tree, which has severe conflicts with the standard phylogeny of animal groups.65 Cherry-picking data does not inspire confidence in the methods used to construct phylogenetic trees and advocate for common descent.

    Looking higher up the tree, a recent study conducted by Darwinian scientists tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”66 The basic problem is that phylogenetic trees based upon one gene or other characteristic will commonly conflict with trees based upon another gene or macro-characteristic. As a review article in New Scientist recounted, even among higher organisms “[t]he problem was that different genes told contradictory evolutionary stories,” leading one scientist to say that “We’ve just annihilated the tree of life.”67 Indeed, the Cambrian explosion, where nearly all of the major living animal phyla (or basic body plans) appeared over 500 million years ago in a geological instant, also raise a serious challenge to Darwinian explanations of common descent.

    Chemical Evolution: The Chemical Origin of Life Remains an Unsolved Mystery. The mystery of the origin of life is unsolved, and all existing theories of chemical evolution face major problems. Basic deficiencies in chemical evolution include a lack of explanation for how a primordial soup could arise on the early earth’s hostile environment, or how the information required for life could be generated by blind chemical reactions. Leading evolutionary biologist Massimo Pigliucci has admitted that “we really don’t have a clue how life originated on Earth by natural means,”68 and leading origin of life researcher David Deamer asserts that “genetic information more or less came out of nowhere by chance assemblages of short polymers.”69

    Origin of life theorists have struggled simply to account for the origin of pre-biological organic chemicals on the early earth, with little success. For example, it is now known that the gasses used in the famous Miller-Urey experiments were not present on the early earth. But this is only the beginning of the problem. When trying to “make” the first life-form, scientists cannot rely upon Darwinian processes. Darwinian evolution requires replication, and prior to the origin of life there was no replication. Origin of life theorist Robert Shapiro explains that an explanation for the first self-replicating molecule “has not yet been described in detail or demonstrated” but “is taken for granted in the philosophy of dialectical materialism.”70 Accounting for the origin of a self-replicating molecule would still not explain how modern cells arose. Our DNA code requires an irreducibly complex system requiring the information in DNA, the enzymes that assist DNA’s replication and protection, a protective cell membrane, and a complex system of machinery used to transcribe and translate language of DNA into protein. Faced with the complexity of this system, biologist Frank Salisbury lamented in 1971 that “the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don’t see them at the moment.”71 In 1995, leading biologists John Maynard Smith and Eors Szathmary explained that accounting for the origin of this system remains “perhaps the most perplexing problem in evolutionary biology” because “the existing translational machinery is at the same time so complex, so universal and so essential that it is hard to see how it could have come into existence or how life could have existed without it.”72

    Scientists may one day create life in the lab, but they will have done so using intelligent design. The theory that life could have originated via blind natural chemical processes and sheer dumb luck remains unexplained.

    References Cited:

    [49.] See "A Scientific Dissent from Darwinism," at

    [50.] Lynn Margulis & Dorion Sagan, Acquiring Genomes: A Theory of the Origins of the Species, pg. 29 (Basic Books, 2003).

    [51.] Lynn Margulis quoted in Darry Madden, "UMass Scientist to Lead Debate on Evolutionary Theory," Brattleboro (Vt.) Reformer (Feb 3, 2006).

    [52.] Stanley Salthe quoted in Discovery Institute, "40 Texas scientists join growing national list of scientists skeptical of Darwin" (September 5, 2003), at

    [53.] Jerry Fodor, "Why Pigs Don't Have Wings," London Review of Books (October 18, 2007), at

    [54.] Philip S. Skell, "Why Do We Invoke Darwin? Evolutionary theory contributes little to experimental biology," The Scientist (August 29, 2005), at

    [55.] Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, Vol. 92:291 (February 8, 1998).

    [56.] Charles Darwin, Origin of Species (1859), Chapter 6, available at

    [57.] Michael J. Behe, Darwin's Black Box: The Biochemical Challenge to Evolution, pg. 15 (Free Press, 1996).

    [58.] Franklin M. Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, pg. 205 (Oxford University Press, 2001).

    [59.] David Raup, "Conflicts Between Darwin and Paleontology", Field Museum of Natural History Bulletin, Vol. 50 (1) (1979).

    [60.] R.S.K. Barnes, P. Calow & P.J.W. Olive, The Invertebrates: A New Synthesis, pgs. 9-10 (3rd ed., Blackwell Sci. Publications, 2001).

    [61.] Ernst Mayr, What Evolution Is, pg. 189 (Basic Books, 2001).

    [62.] C.P. Hickman, L.S. Roberts, and F.M. Hickman, Integrated Principles of Zoology, pg. 866 (Times Mirror/Moseby College Publishing, 1988, 8th ed).

    [63.] W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science, Vol. 284:2124-2128 (June 25, 1999).

    [64.] Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998).

    [65.] See Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14: 177-178 (1999).

    [66.] Antonis Rokas, Dirk Krueger, Sean B. Carroll, "Animal Evolution and the Molecular Signature of Radiations Compressed in Time," Science, Vol. 310:1933-1938 (Dec. 23, 2005).

    [67.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

    [68.] Massimo Pigliucci, "Where Do We Come From?," in Darwin, Design and Public Education, pg. 196 (Stephen C. Meyer and John Angus Campbell, eds., Michigan State University Press, 2003).

    [69.] David Deamer quoted in Susan Mazur, “David Deamer: Line Arbitrary Twixt Life & Non-Life” (September 10, 2008), at

    [70.] Robert Shapiro, Origins: A Skeptics Guide to the Creation of Life on Earth, pg. 207 (Summit Books, 1986).

    [71.] Frank B. Salisbury, "Doubts about the Modern Synthetic Theory of Evolution," pg. 338, American Biology Teacher (September, 1971).

    [72.] John Maynard Smith and Eors Szathmary, The Major Transitions in Evolution, pg. 81 (W.H. Freeman, 1995).