For the previous installments: part 1, 2, 3, 4, 5.

Chapter 14

Darwin_DoubtIn principle, a neo-Darwinian explanation of the origin of new body plans can only work if body plans are wholly determined at the genetic level.  If sources of information other than DNA are substantially responsible for the formation of body plans, then at best neo-Darwinism is inadequate as a holistic explanation for the diversification of life, and at worst it is simply the wrong explanation altogether.

Once again, modern discoveries in embryological development have discovered that there are many factors other than DNA that play a critical role in embryological development.  For example, it’s been shown that in many organisms, you can completely remove the DNA from the developing cells and the embryo will continue to develop up to a certain point.  If DNA alone was responsible for embryological development, this should be just as impossible as driving a car without gas.  If the car is driving, and there is no gas in the tank, then clearly something other than gas must be powering the car.  The same is true of embryological development.  While DNA is necessary to embryological development, it is not sufficient in itself.  There are sources of power other than DNA that are critical to the development of the organism.  Scientists call such sources “epigenetic information,” meaning it is information beyond the genetic information coded in DNA.

DNA can only direct protein synthesis.  It cannot arrange the proteins into higher-level structures: proteins into systems of proteins, systems of proteins into cell types, cell types into tissues, tissues into organs, and organs into body plans.  The process is comparable to building a home.  Just having the raw materials such as wood and nails (comparable to DNA) is not enough to build the house.  One also needs a blueprint that specifies how these raw materials are to be assembled (where and when) to construct a higher-order system.

Scientists have discovered that the form and structure of embryonic cells is critical for building the organism.  These serve as the blueprint, guiding the DNA.  Here are some of the epigenetic elements responsible for organizing embryological development:

  • The structure and location of microtubules in the cytoskeleton
  • The structure of the centrosome
  • The two-dimensional pattern of proteins in cell membranes
  • The arrangement of sugar molecules on the surface of the cell membrane
  • The arrangement of ion channels

The fact that embryological development depends on multiple sources of epigenetic information means that no matter how much you mutate the DNA, and no matter how much natural selection an organism undergoes, it can’t explain the rise of a new body plan.  If neo-Darwinism cannot explain the origin of new proteins, cannot explain how changes in DNA can affect embryological development, and cannot explain the epigenetic information required for embryological development, then neo-Darwinism is a vacuous explanation for the origin of biological diversity.  Biologists Scott Gilbert, John Opitz, and Rudolf Raff make it clear that neo-Darwinism is a dead-end for explaining the origin of phyla.  They write:

Starting in the 1970s, many biologists began questioning its [neo-Darwinism’s] adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or convert a fish into an amphibian.  Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest.  As Goodwin (1995) points out, “the origin of species – Darwin’s problem – remains unsolved.”[1]

Chapter 15

Evolutionary biologists have begun formulating a variety of hypotheses to explain the origin of new biological form (phyla).  In 2008, 16 influential evolutionary biologists met in Altenberg, Austria to discuss post-Darwinian models.  In 2009, renowned paleontologist, Simon Conway Morris, wrote an article in Current Biology declaring the bankruptcy of neo-Darwinism to address the Cambrian explosion, and predicted a post-Darwinian world to explain it.  What are some of these post-Darwinian models?


Self-organization theorists such as Stuart Kauffman propose that instead of biological form arising primarily due to random mutations and natural selection, “biological form often arises…spontaneously as a consequence of the laws of nature (or ‘laws of form’).”[2]  Natural selection does not create form, but merely preserves the form created by the laws of form.

There are several problems with this theory:

  1. It only explains order, not information. Ordered patterns usually convey very little information (repetitive patterns).  Life, however, requires large amounts of information.  We know there are no chemicals or forces that determine the order of nucleotides in DNA, and thus DNA cannot be explained by self-organization.
  2. No biological specifics are given. No chemicals or proteins are cited that behave in the manner theorized.  It is a theory derived from hypothesis alone, not biological evidence.
  3. It does not describe the origin of genetic information and genetic regulatory networks, but merely presupposes their existence.
  4. For the big jumps in body plan evolution, they must appeal to mutations in early development. And yet, we know that such mutations are always fatal to an organism.
  5. There is nothing about the shape or chemical properties of small groups of cells that requires they form higher levels of organization into tissues, organs, and whole body designs.
  6. No explanation is given for the epigenetic information

Chapter 16

Evolutionary theorists such as Sean B. Carrol and Rudolf Raff have proposed a theory known as “evo-devo” (evolutionary developmental biology).  Rather than mutations producing minor changes as Darwin envisioned, defenders of evo-devo hold that some mutations can produce major structural changes to an organism in a single generation.  The problem with evo-devo has been discussed already: the early-acting mutational changes necessary to produce large-scale development changes are always lethal to an organism.  One hundred years of mutagenesis experiments falsify an evo-devo view of evolutionary advancement.  “Major changes are not viable; viable changes are not major.  In neither case do the kinds of mutations that actually occur produce viable major changes of the kind necessary to build new body plans.”[3]

Evo-devo supporters will often appeal to mutations in the cis-regulatory regions of the genome as capable of producing large structural changes in organisms.  The problem is that cases cited are actually minor changes (such as changes in the coloration of wing spots), not body-plan changes.  Hopi Hoekstra and Jerry Coyne argued that most cis-regulatory gene mutations  result in a loss of genetic information, not new information.  While these mutations can explain the loss of traits and function, they do not explain the origin of new traits and function.   Hoekstra and Coyne concluded that “there is no evidence at present that cis-regulatory changes play a major role – much less a pre-eminent one – in adaptive evolution.”[4]

Others, such as Jeffrey Schwartz, appeal to Hox genes.  These genes build proteins that regulate the expression of protein-coding genes during embryological development by switching them on and off at key junctures of the developmental process.  It’s argued that mutations to the Hox genes could have profound effects on animal development.  The problem with this theory is that they do have a profound effect on animal development.  Experimentally, however, the effect is always negative, and almost always fatal precisely because Hox genes act like conductors, conducting the symphony of genes to develop the embryo.  Also, Hox genes are always expressed after the body plan has already begun to form, so they can’t be responsible for major modifications to the body plan.  At best they could affect regional changes to the body plan, not the global body plan itself.  Modifications to the whole body plan would require modifications to the developmental gene regulatory networks, which we have already noted are extremely resistant to mutational changes.  Also, Hox genes do not have within themselves all of the genetic information necessary to generate new tissues, organs, or body plans, nor do they affect epigenetic information.  Indeed, epigenetic information “determines the function of many Hox genes, not the reverse.”[5]

Non-adaptive evolution

Michael Lynch, a geneticist at Indiana University, proposes a non-adaptive theory of evolution in which natural selection plays only a minor role.  He observes that natural selection is weakest in smaller groups of animals, and more effective in larger groups (microbial life).  That means that mutations, gene duplications, genetic recombinations, and genetic drift are more likely to occur in smaller populations without being weeded out of the gene pool.  This means the genomes will grow larger as well, with more non-protein-coding sections of DNA being added that natural selection is not able to weed out.  This is important to explaining the origin of the Cambrian explosion since the populations of these animals would have been relatively small.

Lynch maintains that random environmental factors play a larger role in evolution than does natural selection, but does he explain how these environmental factors can generate new information (genes, proteins) or build complex systems (tissues, organs, body plans)?  No.  He never even addresses the problems of combinatorial inflation and the rarity of functional genes.  While he shows that natural selection cannot be responsible for creating new biological complexity for most organisms, he doesn’t show how environmental factors can do so either.   Also, neutral theories of adaptation do not show how genetic variation becomes fixed in a population.  Genetic drift can just as easily fix a beneficial mutation in a population as it can eliminate it, increasing the wait times for such beneficial mutations to accumulate to produce something biologically novel.


Scientists such as Massimo Pigliucci and Eva Jablonka recognize the role epigenetic information plays in embryological development, and argue that there can be changes in the epigenetic information experienced during one’s life that are passed on to the offspring wholly independent of any genetic changes.  But can this help explain the Cambrian explosion?  No.  Such changes are not stable, and usually only last a few generations.

Natural Genetic Engineering

James Shapiro theorizes that organisms modify themselves in response to environmental changes, which he calls “natural genetic engineering.”  When an organism is stressed by the environment, signals in the body will produce specific and directed (not random) mutations that help the organism survive.  Variation within organisms is not random as Darwin assumed.  Instead, organisms come with a preprogrammed adaptive capacity to help them survive.

While there is empirical evidence to support his claim, can it explain the Cambrian explosion?  No.  It does not explain the origin of new information.  It can explain the survival of a species, but not the origin of a new species.  Also, it begs the question as to how an organism is able to mutate its own DNA to help it survive.  How did such a system originate in the first place?  Surely it wasn’t there from the beginning.  So what was the process that created such a system?  A system that is able to mutate itself in a directed way to help it survive adverse circumstances sounds like an intelligibly designed system, not a haphazard result of undirected forces.


[1]Scott Gilbert, John Opitz, and Rudolf Raff, “Resynthesizing Evolutionary and Developmental Biology,” Developmental Biology, 173 (1996), 361, quoted in Meyer, 287.
[2]Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (Harper One: , New York, 2013), 293.
[3]Ibid., 315.
[4]Hopi E. Hoekstra and Jerry Coyne, “The Locus of Evolution: Evo Devo and the Genetics of Adaptation,” Evolution 61 (2007), 996, quoted in Meyer, 317.
[5]Stephen Meyer, Darwin’s Doubt, 320.