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​New Evidence Leaves Macroevolution Dangling

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As scientists who accept the literal intent of the Genesis account of origins, we have faced many challenges to our faith during our undergraduate and graduate education, and later on as professional scientists. Sometimes these challenges left us shaken, puzzled, or otherwise uncertain about what to do with some particular piece of information. Often we were driven back to our knees and to God’s Word for reassurance that we were moving in the right direction. Always we were directed to analyze more carefully the data from which the challenge had been derived.

One of the major challenges has been the question of macroevolution. The theory of macroevolution asserts that the first living cells, and all types of life, are the result of nondirected, naturalistic processes without the intervention of an outside agency (God). This theory became dominant in the nineteenth century, when scientists knew nothing about the complexity of living cells. It might have been easy to believe a cell could have arisen spontaneously when it was viewed as little more than a fluid-filled sac.

Enter DNA

As we learned more of cellular complexity, including DNA, in the twentieth century, naturalistic scientists had no choice but to believe that this amazing system of molecules that undergirds all life originated by accident. What other theory was there? Certainly they could not accept the idea of a Creator, since their naturalistic assumptions prohibited this possibility. Now in the twenty-first century, three crucial discoveries have undermined the foundation on which the evolutionary origin of life forms seemed to be resting.

Discovery 1: The Human Genome Project

The Two Percent. In 1990 the Human Genome Project began as a massively funded effort by a large contingent of scientists to determine the entire information sequence of human DNA. Scientists discovered, much to their perplexity, that only a tiny fraction (about 2 percent, about 20,000 genes) of human DNA coded for proteins (contained instructions for making a specific protein), yet it was known that nearly 100,000 different proteins were made in human cells. That discrepancy demanded an explanation, and the explanation was stunning. It turned out that those portions of DNA that coded for an amino acid sequence in a protein (exons) could be combined in various ways to make different proteins. This explained how only 2 percent of our DNA could make so many proteins.

It became evident that there would have to be another level of control to determine which exons to stitch together, in which order to make the appropriate protein. Then there would have to be an additional level of control to regulate that, and so on. This multilevel DNA management system was completely beyond anything that had previously been visualized for the complexity of the genetic system.

The Ninety-eight Percent. What was the other 98 percent of the DNA doing? Evolutionary biologists had long ago decided the DNA that was not coding directly for proteins must be “Junk DNA.” This nonfunctional DNA, they declared, was being modified by random mutations to produce new genes that, when functional, would become part of the organism’s genome. By this process, over time, an amphibian could become a reptile, a reptile could become a mammal, and a mammal could become a human. In fact, “Junk DNA” quickly became a strong argument for evolution among biologists.

But trouble was on the way. A new massive, federally funded initiative, called the ENCODE project, was launched to find out what the 98 percent of the DNA that was not coding for proteins was doing. In September 2012 the project simultaneously published a series of papers on the results of their work.1 The consortium announced that at least 80 percent, and probably a lot more of the human DNA that had been thought of as “junk,” was functional DNA. It is not only functional, but also critically important.

Much of this 98 percent of the DNA that did not code directly for proteins was regulating the protein production system; it was part of the multifunctional control of the genetic system. Evolutionists were quick to condemn the report, in spite of the fact that more than 400 of the top molecular biologists in the world had been working on the project. But the results have held up scientifically and are now widely accepted.

The protein-coding genes, 2 percent of the DNA,2 are very similar in all animals. We share 70 percent of our protein coding genes (70 percent of 2 percent) with an acorn worm, 92 percent with a mouse, and up to 96 percent with a chimpanzee. The rest of the DNA (98 percent), clearly, is what makes a human different from an acorn worm, a mouse, or a chimpanzee. This was a huge blow to the theory of evolution, but was long ago predicted by creationists, who recognized that a designer was not likely to burden the cell with junk.

Imagine you go into a well-organized machine shop and observe how it functions. It has hundreds or thousands of drawers along the walls. In each drawer are tools or parts necessary for construction of anything that a machine shop can make. One drawer might have a particular size of drill bit; other drawers may contain specific sizes of machine bolts or washers or nuts. Each drawer has something unique but essential for the construction of a product. Not all products will require the use of all drawers.

These drawers represent the protein coding genes. They are important, even essential, but they cannot produce a thing without the machinist and the blueprint. When the machinist is given a blueprint, he gathers the necessary parts, turns on the needed machines, and, with the skill borne of experience and years, creates the required product. Without the machinist and the blueprint, the machine shop could not produce anything, ever. The machinist and the blueprint represent the regulatory DNA that makes up the majority of the genome. Evolution has no evidence to explain how that genetic system originated. But that’s just the beginning of problems for naturalistic explanations; there is more.

Discovery 2: Epigenetics

Until a few years ago, biology dogma was that genes controlled everything, and that it was genes that determine who one is and what one could become. Now that has changed. For generations students of science have been indoctrinated to believe inheritance from outside of DNA (also known as Lamarckism) would be an absurdity: an example would be a giraffe acquiring a long neck because its ancestors kept reaching for higher leaves in the trees. However, beginning about two decades ago, scientists began to recognize another level of control that turned portions of DNA on or off, without changing the information in the DNA.

These epigenetic modifications, from outside of DNA, affected an animal’s anatomy, function, and even behavior.3 In 2014, scientists studying behavior in mice were able to show convincingly that when a mouse learned an aversion to a specific pleasant odor (animals were shocked when the odor was presented), this aversion could be passed on through three or four generations of offspring. The title of the editorial comments in the scientific journal Nature voices the thought that will occur to any Bible reader: “Epigenetics: The Sins of the Fathers.”4

In the example of the mice and in other epigenetic effects the hereditary outcome is not the result of any mutations or other change in the DNA. The epigenetic chemical changes are passed to future offspring as long as they are needed, and the changes may be reversed in future generations. For example, a parent’s diet, behavior, or stress level during pregnancy can affect their offspring without any DNA mutations, and these changes can be passed on to subsequent generations.

Epigenetics presents a dramatic challenge to evolution. Evolution requires all new genetic information to arise by random changes. Without a Creator, the genetic process cannot know in advance what the animal will need. But epigenetics allows the environment to induce changes that will be beneficial, without the help of natural selection. What kinds of control mechanisms and design are involved in developing a system so sophisticated that it can pass on behavioral information that persists, without a change in genes? This is a serious difficulty for evolutionary theory as it has been taught for 100 years. But there were more challenges to come for evolution.

Discovery 3: Orphan Genes

Orphan gene” was coined to designate protein-coding regions (that is, genes) in an animal that were not found in any related animal type, or maybe not in any other species. In other words, there were no similar “ancestral genes” the orphan gene could have evolved from. It is just there, doing a task unique to that animal, like allowing a honeybee to make honey.5 It looks like the animal was designed with that gene because that specific animal needs it. Orphan genes are pervasive in all life forms and pose a critical, perhaps even fatal, obstacle to those seeking to explain the origin of life forms by the evolutionary process.

With continued research the total number of orphan genes identified and recognized has continued to increase, and at present may be as high as 10 to 30 percent of all known genes. More than 1,000 orphan genes are recognized in humans. At least some of these orphan genes are very important; one of them is responsible for the large brain in humans.6

An explanation consistent with the evidence is that the genes were part of the original creation, and their existence in the individual taxa is because of original design. Perhaps some of these orphan genes could be genes that became activated because of altered environmental conditions on the earth after the entrance of sin (epigenetics). In any case, they represent a sobering challenge to the theory of naturalistic evolution.

A Better Explanation

Evolutionary theory claims that new and different types of organisms, such as fish, reptiles, and mammals, originated without a Creator. This theory is now facing serious challenges because of the sophisticated mechanisms of molecular biology that have been unveiled during the past half century. Evolution theory remains alive because it is on artificial “life support,” in the form of philosophical commitment to naturalism, with its assumption that life did not have a Creator. Three recent discoveries, epigenetics, the ENCODE project results, and orphan genes, have further undercut the intellectual feasibility of “life support” for macroevolutionary theory. For many individuals, naturalism and macroevolution are still the only acceptable explanation for life, but this commitment is based increasingly on philosophy, not on adequate evidence. We hope to convince the adherents of evolution that there is a better and viable alternative that not only has explanatory value in science, but holds the promise of eternal life to those who accept it.


  1. ENCODE. Thirty papers published at the same time in scientific journals, including eight articles and reports in Nature 489 (Sept. 6, 2013): 45-113. See also N. Carey, Junk DNA: A Journey Through the Dark Matter of the Genome (New York: Columbia University Press, 2015).
  2. J. Cohen, “Relative Differences: The Myth of 1%,” Science 316 (June 29, 2007): 1836.
  3. B. G. Dias and K. J. Ressler, “Parental Olfactory Experience Influences Behavior and Neural Structure in Subsequent Generations,” Nature Neuroscience 17 (2014): 89-96. Cf. D. Noble, “Physiology Is Rocking the Foundations of Evolutionary Biology,” Experimental Physiology 98 (2014): 1235-1243. Doi: 10.1113/expphysiol.2012.071134.
  4. V. Hughes, “Epigenetics: The Sins of the Fathers,” Nature 507 (Mar. 6, 2014):22-24.
  5. B. R. Herb, F. Wolschin, K. D. Hansen, M. J. Aryee, B. Langmead, R. Irizarry, G. V. Amdam, and A. P. Feinberg, “Reversible Switching Between Epigenetic States in Honeybee Behavioral Subcastes,” Nature Neuroscience 15, no. 10 (2012): 1371-1373. Cf. W. C. Jasper, T. A. Linksvayer, J. Atallah, D. Friedman, J. C. Chin, and B. R. Johnson, “Large-scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honeybees,” Molecular Biology and Evolution 32, no. 2 (2015): 334-346.
  6. M. Florio, M. Albert, E. Taverna, T. Namba, H. Brandl, E. Lewitus, and W. B. Huttner, “Human-specific Gene ARHGAP11B Promotes Basal Progenitor Amplification and Neocortex Expansion,” Science 347, no. 6229 (2015): 1465-1470.

Arthur Chadwick, Ph.D., is research professor in the Biology and Geology Department at Southwestern Adventist University, Texas. Leonard Brand, Ph.D., is professor of biology and paleontology at Loma Linda University, California.

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