Evolutionary Evidence Since Darwin

Evolutionary Evidence Since Darwin

Significant challenges to large-scale evolution continue to multiply

Leonard R. Brand

In the 19th century, Charles Darwin and his contemporaries put together the core of the modern theory of evolution. In Darwin’s era, virtually nothing was known about molecular biology or about DNA and mutations. But as Darwin observed generation after generation of some animals, he noticed that slight variations began to show up. As he considered the implications of those variations, he realized that some of them would make the animals that were better suited to survive in their environment, while others would decrease their ability to survive.

This realization led to the logical conclusion that the better-adapted organisms would live longer and produce more offspring than would the more poorly adapted organisms. Thus, the more helpful variations would tend to survive and increase with the organisms they aided. Darwin called this process “natural selection,” and he concluded that it was this process, acting upon generation after generation of living organisms through long periods of time, that resulted in the evolution of all types of plants and animals.

Philosophical trends already at work in the 19th century, combined with Darwin’s careful maneuvering in the academic world of the sciences, prepared the way for acceptance of this theory. Most 19th-century scientists weren’t convinced that natural selection was powerful enough to explain all the forms of life that this world contains, but the mass of evidence Darwin presented in support of his theory—from fossils, observations of variation and selection in domestic animals, and biogeography—convinced many scientists that life could have arisen and developed without a creator.

Further, the laws of genetics that Gregor Mendel had discovered in the 1860s through extensive research were rediscovered in the early 20th century, leading to a great growth in the understanding of genetics. Developments in the field of genetics clarified the power of natural selection. Then, in the 1930s and 1940s, a group of biologists, paleontologists, and mathematicians combined what was then known about genetics, fossils, anatomy, natural selection, and the mathematical analysis of genetic changes in populations of organisms. The more advanced and sophisticated version of evolution that these scientists developed became known as the neo-Darwinian theory of evolution, or the Neo-Darwinian Synthesis. At this point, most biologists considered Darwin’s process of natural selection as the driving force in evolution, and neo-Darwinism was regarded as the theory that could explain all that was needed to know about the evolution of simple organisms into the extraordinarily widespread and diverse biological world we see around us.

In the 1950s, two developments added to the growing confidence in evolution. One was the description by James D. Watson and Francis Crick of the structure of DNA, which increased our understanding of how DNA functions as the source of genetic information in all organisms.1 This discovery was a significant addition to the neo-Darwinian theory. Stanley Miller and Harold Urey’s experiments also showed that natural processes could make amino acids (the components of proteins) in the conditions presumed to exist on the primitive Earth.2 In the eyes of many scientists, this made the naturalistic origin of life more plausible. God now seemed truly to be unnecessary.

Scientists then envisioned the chance formation of one-celled organisms in a primordial chemical soup to be a relatively simple matter. These primitive organisms, then, were the material on which evolution could work, enabling the neo-Darwinian processes of random mutation and natural selection to produce increasingly complex plants and animals. The mutations are random in the sense that the mutation process doesn’t know what the organism needs. But ultimately, the process isn’t really random because natural selection tips the scale in favor of the survival of beneficial mutations and against the survival of harmful mutations. This is the process that, it was said, added improvement to improvement and thus produced the most complex creature of all—humans. There was enthusiastic confidence that this fully naturalistic process could satisfactorily explain biological origins and the evolution of life forms with increasing variety and sophistication of form and function.

The word evolution has a variety of meanings, and confusing them should be avoided. Changes in life forms such as the development of resistance to antibiotics in bacteria and the adaptation of mice to different environments by changes in the color of their fur are also called evolution. These micro-evolutionary processes of adaptation and the development of new species are not contrary to biblical creation and are supported by a lot of evidence.

When microevolution results in small changes that keep two populations of plants or animals from interbreeding, these two populations are considered, by definition, to be two differing species. This process is easily within the types of change that have occurred within created groups. There are approximately one thousand species of rats and mice, and they illustrate this process of speciation since the creation.

Creationists’ objections to the theory of evolution, however, have to do primarily with large-scale evolution—the evolution, for instance, of worms, reptiles, and humans from a common ancestor.


Evolution and the Fossil Record

The theory of large-scale evolution uses the fossil record as a history book that documents the story of the evolution of increasingly more complex organisms through deep time (many millions of years). This history book begins with marine invertebrates, which are preserved in Cambrian rocks. From that beginning, the passage of time is recorded in the rock layers stacked on top of the Cambrian layer, each successive layer containing fossils of new, more complex life forms. Fish are found quite early in the record, then amphibians, and later, reptiles, which are followed by birds and mammals, with humans being one of the last types to appear as fossils. The order in which these animal groups appear in the fossil record fits the theory of evolution quite well.

There is a problem, however, in the fossil record that Darwin agonized over because he realized it could compromise his theory. In most cases each group of organisms appears as fossils without a series of intermediate forms showing how they evolved from their supposed ancestors.3 This is still a serious problem for evolution, although some vertebrate fossils have been found that can be interpreted as filling evolutionary gaps between living vertebrate groups.

Creationists have alternative explanations for most of these presumed evolutionary links, but a few are quite puzzling. We don’t have the answers for all of the questions, but that’s OK. No one has the answers to all his or her questions about unobservable ancient history.


Cracks in the Theory

Confidence that evolution will triumph over creationist ideas has increased, and this theory is universally proclaimed in textbooks, popular media, public schools, and now often in Christian pulpits, too. And those who disagree are commonly portrayed as ignorant and poorly educated. This confidence results as much or more from a deepening commitment to the philosophy of naturalism than from the accumulation of more solid evidence, although many scientists proclaim that the evidence is overwhelming.

In reality, there are cracks in the naturalistic edifice, and they are growing. Those holding the naturalistic worldview are attempting to fill the cracks with many eloquent words, but those looking on from the outside of naturalism can see that the plaster isn’t sticking, and the cracks are becoming more obvious.

One of the deepest cracks runs through the attempts to explain the origin of life. After publication of Miller and Urey’s experiments, it was enthusiastically proclaimed that it would soon be known how life arose independent of any intelligent creator. Since then, more careful thinking and experiments have shown that the Miller and Urey scenario wasn’t realistic.

However, the origin of life by natural processes, with complex biological molecules forming and gradually accumulating to become the first living cells, is still textbook orthodoxy. Those holding to naturalism must believe it happened that way. However, a few scientists, even some bona fide naturalists, admit that how life arose is still unknown.4


Intelligent Design

As a result of some scientists’ awareness of the cracks in naturalistic theory, a movement began during the 1980s that called attention to the need for better explanations. This Intelligent Design movement (ID) was begun by a highly qualified group of scientists and philosophers led by Phillip Johnson, a law professor at UC Berkeley. The ID movement emphasizes that the origin of life can be explained only as the work of an intelligent agent.

Some conservative Christians are critical of ID because ID proponents don’t mention the Christian God as the creative agent and don’t address questions of the fossil record or of the evolution of life through time. These criticisms are missing something significant about ID. The ID movement has limited itself to one issue of critical importance—the essentiality of a designer/creator to the origin of life. This is a matter of science as well as of philosophy and theology. That is, current scientific evidence for the beginning of life is best explained by design, and there are valid reasons for believing the origin of life cannot be explained without that designer/creator. But science can’t determine who the designer is, and so ID leaves that determination to others (although some ID leaders are young-life-on-Earth creationists).

By limiting itself to the one central issue that science can address, ID is working toward filtering the unnecessary and damaging philosophical assumptions of naturalism out of science. Increasing people’s awareness of the difference between objective science and naturalistic assumptions is a necessary first step toward opening minds to the realization that an unbiased study of the origin leads to the conclusion that there must have been a designer. Those who have made the study of ID their concern have a full plate. They have to leave the next step—demonstration that God is that designer and that His Word is a reliable record of the history of life—up to others.


Two Components

Science has helped us to recognize the amazing laws of chemistry and physics that God uses to operate His universe. If a boulder is pushed off a cliff, gravity will determine the outcome. No intelligent thought is required to make the consequences of this action consistent with those of other, similar actions.

What then is so unique about life? Don’t we operate within the same laws as the rest of the universe?

Yes—but only up to a point. Books are made of two very different components, one being the physical paper and ink, or, more recently, the screen and electrons, that bear the letters that books contain; and the other being information—the meaning carried by the sequences of letters that form words and sentences. There is no law that specifies the order in which the letters are placed on the paper. The order of the letters is determined by ideas, by information; and ideas and information are the province of an intelligent mind. Information originates only in intelligence.

Like books, life is comprised of two components: physical molecules and the information contained in the sequences of those molecules. Simple biological molecules, like amino acids, will form by the unaided action of chemical laws. But amino acids by themselves don’t make anything alive. These simple molecules, and many others, must be arranged in the proper sequence to function properly. The sequence of amino acids in a protein is controlled by the sequence of another kind of simple molecules—nucleotides—also found in DNA. These amino acids and nucleotides are like bricks. Bricks alone won’t make a palace; there must also be an engineer and a blueprint. And just as no natural law sets the sequences of letters and words on this page, no natural law sets the sequences of amino acids and nucleotides in the living cells that make up our bodies. All of these sequences of molecules contain and communicate information that is directly comparable to the information contained and communicated in the sequences of letters in a book or in the letters and lines on a blueprint.

Crystals can be very beautiful, but they are simple, non-living structures composed of a very repetitive sequence of a few elements. Their law-governed chemical composition can be represented by a sequence of letters, such as AFR AFR AFR AFR. In contrast, biological molecules are extremely complex. There are, for example, thousands of types of proteins in every cell, and each type of protein is composed of thousands of subunits that must be in the right sequence for the protein to do its job. Just as the sequence of letters in the phrase “God loves you” conveys information, so do the sequences of molecules that make up the proteins that enable the living cell to perform its function. This is why crystals and living cells are radically different from one another.

Life exists because every life form contains a massive amount of information recorded in an incredibly complex and wonderful instruction book inside its cells—DNA. It has been demonstrated repeatedly that there is no adequate explanation for such information other than that an intelligent “inventor”—in this case, God—put it there. The only alternative is pure chance, and the probability of all that information appearing in a cell spontaneously is so remote as to render this alternative a dead end. Mainline science denies that such complexity demands a Creator, but if the mind is open to think about it carefully, that denial doesn’t ring true.

The ID movement is drawing attention to the distinction between information, on one hand, and law-governed phenomena on the other. This movement is having an influence, opening the minds of those who are willing to see beyond modern, dogmatic naturalism, which they see that science doesn’t need.


Molecular Biology

Next, there is the crucial issue of the presumed large-scale evolution of life forms—the progression from bacteria to worms and other invertebrates, and then from those creatures to fish, amphibians, reptiles, and mammals—and, finally, to humans. The structures, physiology, and brain functions of each life form are governed by information in DNA. Each step in the proposed evolutionary sequence requires a large amount of new DNA information. The origin of the first simple life forms and the unguided evolution of more complex life forms like starfish, reptiles, and humans, all require the origination of volumes of new biological information. Are random mutations and natural selection up to the task? Mainline science insists Yes, but that answer depends upon assumptions. Here also the cracks are becoming wider—largely because of advances in molecular biology.

Darwin and his contemporaries had no idea how complex a living cell is. The scientists who put together the neo-Darwinian synthesis in the 1940s also knew relatively little about the nature of life. In their day, almost all the modern discoveries in molecular biology still lay in the future. Unfortunately, their view of life’s origins, based on naturalistic theories, became entrenched in the scientific mindset before scientists knew enough to make an objective evaluation of those theories. And since that approach has become deeply imbedded in the thinking of an entire community, changing it is difficult.

More than a decade ago, at an annual meeting of the Society of Vertebrate Paleontologists, a prominent evolutionary scientist said that the neo-Darwinian synthesis needs to be redone, and “this time we aren’t going to blow it.” Only now is his meaning finally becoming evident. Over the past several decades, molecular biology research has revealed increasing levels of sophistication in the operation of every cell in the human body. King David marveled that we are so “fearfully and wonderfully made” (Ps. 139:14, NKJV), and he knew only the most basic functions of this marvelous machine, the living body. How he would marvel now!

Research has revealed that the cell’s mechanisms for correcting mistakes in the duplication of DNA are vastly more precise than previously thought. And it is also now known that cells have many sensors that monitor their environment, gathering information that enables them to make needed alterations in their function. So the DNA’s control of the cells is not an automatic, one-way operation. Those environmental sensors provide feedback that can alter how the information in DNA is interpreted in the making and the operation of an organism.

In fact, the environment that we grow up in even makes what are called epigenetic changes in how the DNA is interpreted. These epigenetic changes don’t alter the DNA, but they do influence how that DNA blueprint is interpreted, changing the offspring of those organisms. Those changes may be passed down several generations. And if the environment returns to what it was originally, the organisms can go back to interpreting the information in the DNA in the original way.

In other words, because of epigenetics, the conditions in which a baby is born and raised can affect it and its offspring negatively or positively for several generations. This makes one think of the biblical statement, “The Lord . . . punishes the children for the sin of the fathers to the third and fourth generation’” (Num. 14:18, NIV). It seems that He who inspired the Bible writers knew something about epigenetics.

One eminent evolutionary biologist involved in these discoveries describes the genetic system as doing what he calls “natural genetic engineering.”5 He points out that cells and organisms don’t passively carry out fixed genetic instructions. Instead, they assertively use environmental information from their sensors to determine the most effective way to use the information in DNA. The genetic system “decides” what modifications will best serve the organism of which it is a part.

This same author states that these new discoveries about the genetic system leave no room for the random mutations proposed by Darwinian theory. This author is not a creationist; he is clearly committed to the evolution of life through deep time. The evidence has convinced him, however, that this must happen through some mechanism other than the random mutations of conventional Darwinian theory. When more traditional evolutionists, believers in Darwinian random mutation and natural selection, criticize him—and they do—he responds that “their position is philosophical, not scientific, nor is it based on empirical observations.”6 He also admits that he has no idea how this genetic system evolved. Even scientists who don’t believe in creation, if they’re open to the evidence, can see that the sophistication of a living cell is mind-boggling.

There is much more that could be said about the difficulties faced by evolution theory because of advances in molecular biology, molecular genetics, the human genome project and its spin-offs, and careful analysis of population genetics. These difficult challenges to large-scale evolution will likely multiply. 

The cracks in this part of the naturalistic worldview are growing wider and more menacing in the field of biology. Perhaps this is why the more vocal opponents of creationism are becoming increasingly aggressive. The increasingly difficult challenges facing evolutionary theory don’t mean that creationists have answers for all of the questions that still remain for creation.  Many things in nature are so evil that they are hard to explain, even though it is accepted that the work of the enemy, Satan, lies behind them. Geology poses questions, however, that are even more challenging than those posed by biology.


Leonard R. Brand, Ph.D., is Professor of Biology and Paleontology and Chair of the Department of Earth and Biological Sciences at Loma Linda University in Loma Linda, California.



1. J. D. Watson and F. H. C. Crick, “Molecular Structure of Nucleic Acids,” Nature (April 25, 1953):737, 738.


2. S. L. Miller, “Production of Amino Acids Under Possible Primitive Earth Conditions,” Science, (May 1953), p. 528.


3. S. J. Gould and N. Eldredge, “Punctuated Equilibria: the Tempo and Mode of Evolution Reconsidered,” Paleobiology (April 1977):115–151.


4. J. Shapiro, Evolution: A View From the 21st Century (Upper Saddle River, N.J.: FT Press, 2011), p. 125; F. H. Crick and L. E. Orgel, “Directed Panspermia,” Icarus (1973):341–346.


5. J. Shapiro, ibid., p. 55.


6. Ibid., pp. 55, 56.