Feature Article - July 1999
by Do-While Jones

The DNA Dilemma

Evolutionists thought that when the DNA code was unraveled, it would clearly show the path of evolution. By comparing differences in DNA, they thought they would be able to see the sequence of modifications in the DNA code that produced each species in turn. Unfortunately for the evolutionists, it hasn’t worked out that way. Studies of DNA are raising some questions that evolutionists are finding hard to answer.

Instructions and the Result

In order to understand the DNA dilemma, you must understand the relationship between a blueprint and the thing built--between the instructions and the result. Let’s do this using a simple analogy.

Suppose I give you instructions how to get to a shopping center. I might tell you to start from the intersection of Ridgecrest and China Lake boulevards. Go north on China Lake until you get to Drummond. Turn east on Drummond and go about 500 feet, then turn right. If you do this, you will find yourself at the Rite Aide shopping center.

Now, suppose I give you just slightly different instructions. Suppose I tell you to start from the intersection of Ridgecrest and China Lake boulevards. Go north on China Lake until you get to Drummond. Turn east on Drummond and go about 500 feet, then turn left. If you do this, you will find yourself at the K-Mart shopping center.

K-Mart is on the northeast corner of Drummond and China Lake. Rite Aide is on the southeast corner. Since the instructions are nearly identical, you wind up at nearly the same place.

This is true of DNA as well. DNA contains the instructions for building a critter. If the DNA is nearly identical, it will build nearly the same critter.

Suppose I tell you to start from the intersection of Ridgecrest and China Lake boulevards. Go west on Ridgecrest until you get to Norma. Turn north on Norma and go to Ward. Turn east on Ward and go to China Lake. Turn south on China Lake and go about 500 feet past Drummond and turn right. These instructions are nothing like the instructions in the previous paragraphs. But, if you follow these instructions you will wind up at the Midway shopping center, right across the street from Rite Aide. It is possible to arrive at nearly the same place by entirely different routes.

This is true of DNA as well. If two critters are nearly identical they might not necessarily have nearly identical DNA. It is possible that two very different sets of instructions might build two very similar critters.

Let’s concoct a truly ridiculous theory of how business evolved in Ridgecrest to see how an analysis of instructions can shed light on a theory.

Suppose we’ve been taught that from the founding of Crumville1, people used to travel north along China Lake boulevard until they got to Drummond where they turned east, went about 500 feet, and turned right, where the Rite Aide drug store (the oldest business in Ridgecrest) was.

We find this hard to believe, because Rite Aide is obviously a very new store. But they say that Rite Aide has evolved and remodeled many times since it was founded, so the modern Rite Aide drug store doesn’t look much like the original Rite Aide drug store that was there 50 years ago. Everybody else believes it, so it must be true.

Then, as the story goes, one day some people accidentally turned left instead of right. When the K-Mart corporation saw all these people milling around in the vacant building that just happened to be there, they decided to fill it with K-mart merchandise. Since there were so many people going there by mistake, the K-Mart flourished.

We wonder why there was an empty building there, but we are told that empty buildings happen. After all, we are told that mutations create genes with no immediate purpose, but generations later turn out to be useful. Everybody believes that story. It is no sillier than the idea that empty buildings sit around waiting for business.

Finally, as the story goes, the instruction to turn east on Drummond was mistakenly written as “make a U-turn at Drummond”, so people started going to the southwest corner of Drummond and China Lake, and someone built the Midway shopping center there to accommodate them.

Granted this is a silly, absurd analogy--but it has to be. It has to be analogous to the silly, absurd theory of evolution.

Even though everyone believes this story, we decide to investigate it. Did business really develop in Ridgecrest that way? How can we tell? If it is true that business really developed as the result of mistakes in directions, the way to confirm or deny it would be to find the original directions. Did a right turn become a left turn to send traffic to K-Mart? Did a right turn become a U-turn to send traffic to the Midway shopping center?

Suppose we find the actual instructions of how to get to Rite Aide and Midway shopping centers as presented at the beginning of this essay. The directions are entirely different. Clearly traffic to Midway didn’t result from mistakes in the directions to Rite Aide.

The Dilemma

This is the problem that the evolutionists have. Some critters that they think evolved from the same ancestor have very different DNA sequences. Their DNA is more like other critters that traditionally have been thought to have evolved from a much different ancestor. Given these large differences in DNA, it is difficult to support the idea that some similar critters were really built from slightly different corruptions of a single original set of instructions.

Recent Headlines

Let’s look at some of the headlines (and subheadings) in mainstream scientific journals in the last 12 months. This will give you an overall indication of the turmoil in the scientific community. Then we will look at what some of these articles say in detail. Here are the headlines, in chronological order:

7 August 1998 (Science page 774) “New Views of the Origins of Mammals--Paleontologists and molecular biologists take different approaches to questions of evolution and often come to different conclusions”

27 November 1998 (Science page 1653) “The Abominable Mystery”. The caption under two alleged evolutionary trees says, “In this analysis, Gnetales are more closely related to other gymnosperms than to the angiosperms.”

5 December 1998 (Science News page 358) “Turtle Genes Upset Reptilian Family Tree”. The caption under the photo of a turtle says, “Turtles: An evolutionary enigma”.

6 February 1999 (Science News page 88) “DNA’s Evolutionary Dilemma--Genetic studies collide with the mystery of human evolution”.

26 February 1999 (Science page 1310) “Evolutionary and Preservational Constraints on Origins of Biologic Groups: Divergence Times of Eutherian Mammals--Some molecular clock estimates of divergence times of taxonomic groups undergoing evolutionary radiation are much older than the groups’ first observed fossil record”.

5 March 1999 (Science page 1435) “Can Mitochondrial Clocks Keep Time?”.

6 March 1999 (Science News page 159) “Turtles and Crocs: Strange Relations”.

21 May 1999 (Science page 1305) “Is It Time to Uproot the Tree of Life?--More genomes have only further blurred the branching pattern of life. Some blame shanghaied genes; others say the tree is wrong”.

Two “Related” Problems

Evolutionists believe that a common ancestor had descendants that evolved into two different species. In each of those two groups of descendants, certain ancestors had descendants that evolved into two other different species. This happened countless times, producing all the species we see today. Evolutionists have been telling school children for decades which species came from a common ancestor, and when the bloodlines diverged. They expected the DNA analysis to confirm which species are “brother and sister” and how long ago the species diverged from each other.

The headlines above deal with two related problems. The first is that the DNA evidence is contradicting the presumed relationships. The second is that the DNA evidence is contradicting the presumed time when those relationships split apart. Evolutionists are trying hard to reconcile their interpretation of the DNA evidence with their interpretation of the ages of the fossils and their supposed family tree. They aren’t being very successful.

The Genealogical Problem

A year ago, biologists looking over newly sequenced genomes [DNA] from more than a dozen microorganisms thought these data might support the accepted plot lines of life’s early history. But what they saw confounded them. Comparisons of the genomes then available not only didn’t clarify the picture of how life’s major groupings evolved, they confused it (Science, 1 May 1998, p. 672). And now, with an additional eight microbial sequences in hand, the situation has gotten even more confusing--so confusing that some biologists are ready to replace what has become the standard history with something new. 2

In other words, the more DNA analysis they do, the less it agrees with what one would expect if life evolved the way evolutionists think it did.

Advances in molecular systematics have provided new data that, in theory, have the potential to unravel relationships that are opaque because of apparently intractable morphological variation, or convergence. And breakthroughs in software make it possible to analyze large data sets quickly and accurately. The torrent of analyses, instead of providing clarity, has often yielded conflicting hypotheses of phylogeny. 3

There are some relationships that evolutionists have a difficult time explaining because they are “opaque” (hard to see through). The problem is that the “morphology” (the way they appear) is difficult to explain. Take the duck-billed platypus, for example. Did it evolve from a beaver, or a kangaroo, or a duck? It is hard for evolutionists to tell because it is so like many different species, but very different from them, too. The usual explanation is “convergence” (the evolution of the same feature, such as the duck’s bill, in un-related species).

Phylogeny is a big word that means “evolutionary relationship”. Evolutionists thought that DNA analysis would have to show the evolutionary path in these difficult cases. But it didn’t. It just produced even more contradictions.

For example, there is a problem with turtles.

Paleontologists have long viewed turtles as evolutionary slowpokes, the sole survivors of an ancient group that later gave rise to other reptiles, birds, and mammals. A new genetic analysis, however, dramatically redraws the evolutionary tree of vertebrates and challenges the conventional wisdom on turtle origins.

According to the standard evolutionary story, turtles retain some characteristics of the ancient anapsids. As such, biologists have regarded them as an example of the stock from which reptiles, birds, and mammals later evolved.

Zardoya and Meyer explored this hypothesis by comparing the sequences of two mitochondrial genes from turtles to those of iguanas, tuataras, alligators, chickens, and mammals. Turtles fell squarely within the modern diapsids rather than in their expected position on a branch outside the group. 4

Turtles aren’t the only misfits in the evolutionary view of reptiles.

Paleontologists will find other aspects of the genetic results perhaps even more disturbing than the news regarding turtles. Hedges and Poling provide some of the first DNA analysis of tuataras, a group of four-legged reptiles that look superficially like lizards and are regarded as their closest living relatives. The analysis by Hedges and Poling, however, places tuataras nearer to crocodiles than to lizards. “From a paleontological point of view, I cannot even begin to imagine how a tuatara could not be [closely] related to lizards and snakes,” says Rieppel. 5

The problem isn’t confined to reptiles. There is trouble in the plant world, too. A technical (and not very quotable) article3 in Science describes the problem of classifying flowering plants. Outward appearance and common sense would indicate that angiosperms and gnetales are more closely related to each other then they are to cycads, ginkgo, and conifers. But DNA analysis places angiosperms and gnetales at opposite ends of the flower family tree, with cycads, ginkgo, and conifers between them.

The Time Problem

DNA analysis is not only supposed to tell what different kinds of critters are related to each other, it is also supposed to tell when they split apart. Those analyses aren’t helping evolutionists, either.

Fossils and molecules are also at odds over when most modern orders of birds and mammals appeared. Paleontologists haven't generally found them before about 65 million years ago, after the great Cretaceous-Tertiary extinction wiped out the dinosaurs. But molecular studies using both mitochondrial and nuclear DNA conclude that many living species diverged much earlier, up to 130 million years ago. …

The long-standing view from the fossil record is that mammals first appeared 225 million years ago as small, shrewlike creatures and that only after a mass extinction 65 million years ago at the end of the Cretaceous period killed off the dinosaurs were mammals able to evolve into everything from primates to rodents to carnivores. But in this week’s issue of Nature, a pair of researchers compared genes from hundreds of vertebrate species and used the differences as a molecular clock to date when animal lineages originated. The molecules show, they say, that the modern orders of mammals go back well into the Cretaceous period, in some cases to more than 100 million years ago. 6

Evolutionists believe that there are so many mutation opportunities that one can use statistics to predict how many mutations will occur over a given time interval. Therefore, they can use the number of mutations as way to determine how much time has elapsed. They think that certain similar critters must have shared a common ancestor, and therefore had common DNA. They think that the number of differences in their DNA is the result of mutations at a particular rate, which can be used to tell how long ago the two species diverged.

When they compare the DNA from species (various mammals, for example) that they are sure diverged at a particular time, they don’t get the expected results. Since there are more differences than they expect, they either have to believe that the split occurred longer ago, or that mutations happened faster in the past than they do now.

Since they believe “the present is the key to the past”, many evolutionists are reluctant to assume that the past rates were appreciably faster than present rates. There is no evidence to support the faster rate, other than the large differences in the DNA of “closely related species.” This forces them to believe that the species diverged sooner than they used to believe. That’s why some evolutionists now believe that mammals evolved before dinosaurs became extinct.

Another Possibility

Of course, there is another possibility. The DNA of “closely related species” might be very different because the species are not really related at all. They were all created separately and distinctly. They just happen to bear a superficial resemblance which mislead people into thinking that they evolved from a common ancestor. The DNA analysis might not show the expected evolutionary development because evolution didn’t happen.

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1 Ridgecrest originally was called Crumville because the only business there was the Crum brothers’ dairy. Later, when people didn’t like the name (we can’t imagine why), they tried to change the name to Sierra View. The Post Office objected because there were too many Sierra Something-or-others. So, the name was changed to Ridgecrest, instead.
2 Science, 21 May 1999, “Is It Time to Uproot the Tree of Life?” p.1305 (Ev)
3 Science, 27 November 1998, “The Abominable Mystery” p. 1653 (Ev)
4 Science News, 5 December, 1998 “Turtle Genes Upset Reptilian Family Tree” p. 358 (Ev)
5 Science News, 6 March 1999, “Turtles and Crocs: Strange Relations” p. 159 (Ev)
6 Science, 1 May 1998, “Genes Put Mammals in Age of Dinosaurs” pp. 675-676 (Ev)