Feature Article - September 2015
by Do-While Jones

The Genetic Case Against Evolution

If the Theory of Evolution is true, then the species with the closest common ancestor should have the most similar DNA—but they don’t.

This month’s two Evolution in the News columns are devoted to the cover story of the August 13 issue of the respected journal Nature (which reported the recently completed analysis of the octopus genome) and an earlier article in Science about plants containing caffeine. Those articles are full of discoveries inconsistent with evolutionary theory. This month’s Email column contains correspondence from someone who willfully ignores all scientific evidence against evolution, including the genetic evidence.

To set the stage for the rest of this newsletter, let’s establish some background, and review how genetic discoveries have been undermining the theory of evolution for nearly two decades.


Here are some definitions from the National Human Genome Research Institute to assure everyone knows what we are talking about.

The genome is the entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the nucleus, as well as a small chromosome found in the cells' mitochondria. Each set of 23 chromosomes contains approximately 3.1 billion bases of DNA sequence. 1

A chromosome is an organized package of DNA found in the nucleus of the cell. 2

DNA (Deoxyribonucleic Acid) is the chemical name for the molecule that carries genetic instructions in all living things. 3

The gene is the basic physical unit of inheritance. Genes are passed from parents to offspring and contain the information needed to specify traits. Genes are arranged, one after another, on structures called chromosomes. A chromosome contains a single, long DNA molecule, only a portion of which corresponds to a single gene. Humans have approximately 20,000 genes arranged on their chromosomes. 4

An allele is one of two or more versions of a gene. An individual inherits two alleles for each gene, one from each parent. 5

The genome is all the genetic material in the cell. It is made up of chromosomes. Each chromosome is a single DNA molecule, which carries thousands of genes. Each gene has multiple variants, called alleles.

Now, there is one final important definition:

A genotype is an individual's collection of genes. The term also can refer to the two alleles inherited for a particular gene. The genotype is expressed when the information encoded in the genes' DNA is used to make protein and RNA molecules. The expression of the genotype contributes to the individual's observable traits, called the phenotype. 6

Geneticists say, “The genotype determines the phenotype.” Just as a blueprint tells how a structure will be built, and software tells a computer what to do, the genotype determines the characteristics of the living thing containing those genes. Blueprints, software, and genotypes are the plans which determine the results.


The Theory of Evolution is based on the concept of “descent with modification.” Perhaps the best way to look at this is to ponder what descent without modification would be from the perspective of both evolutionists and creationists.

Evolutionists start with the assumption that somehow one living cell came into existence. If reproduction occurred by descent without modification, then the world would be filled with innumerable identical copies of the first living cell, and nothing else.

Creationists start with the assumption that every basic kind of creature was created individually. If reproduction occurred by descent without modification, then all leopards would have exactly the same spot pattern, and every creature would be identical to every other creature of that same species.

Evolutionists and creationists agree that there are small differences between individuals of the same species. That’s because of descent with modification—that is, children inherit the characteristics of their parents with slight differences. The question is, “What causes these differences?”

Evolutionists and creationists agree that the differences in individuals of a species come from different combinations of alleles, and the differences in species come from different combinations of genes.

The fundamental point of disagreement is whether the similarities between species are the result of common descent or common design. Evolutionists believe that similar species are similar because they inherited traits from a common ancestor, with modifications. Creationists believe that similar species are similar because they were designed by a designer who tended to reuse the same techniques.

Is there any way to distinguish between similarity that comes from common ancestry and similarity that comes from common design? We believe there is.

Common Ancestry

The Theory of Evolution is based on the notion of common ancestry. That is, two very similar species are similar because they have descended from a close common ancestor. If that is true, both species should have DNA that is nearly identical to the common ancestor, with just a few unique aspects which distinguish the two closely related species from each other. (The prejudicial term “related” implies the assumption of close common ancestry.)

In the past, species were assumed to be closely related because of physical similarity. That is, humans look more like apes than butterflies, so one might naturally assume that humans are more closely related to apes than butterflies. But that is a subjective judgment call based upon similarity of the phenotype (physical characteristics).

Paleontologists quantify the phenotype by measuring such things as dimensions of teeth and bones (and ratios of those measurements) and try to come up with some algorithm that will produce a numerical value of how similar teeth and bones are in an attempt to make comparisons more objective. The problem with this approach is that the numerical results depend upon what one chooses to measure, and how individual characteristics are weighted. Consequently, the comparison is really a subjective judgment wearing a mask of objectivity.

Current technology makes it easier to calculate similarity of genotypes because you can compare genes and see how many match exactly, how many are different, how much they differ, and so on. Evolutionists expected that comparisons of genotypes would produce an unambiguous, perfectly accurate, evolutionary tree.

Inherited Similarities

Suppose there is a species called “A” who has offspring called “B1” and “B2.” If there were no descent with modification, B1 and B2 would have exactly the same genome as A. But suppose that a random mutation makes B1 slightly different from A. B2 has a different mutation which makes B2 slightly different from A. If you compared the whole genome of A to either B1 or B2, you would find one difference. But if you compare the genome of B1 to B2 you would find two differences (that is, the two mutations which caused B1 and B2).

Suppose B1 has descendents C1 and C2, and B2 has descendents D1, D2, and D3. As you go down the genealogical alphabet, the genomes have more and more differences from species A, and the similarly lettered species have fewer differences between themselves.

Evolutionists believe that they can eventually reconstruct the evolutionary genealogy by comparing differences in genomes because the species that evolved the most recently from a close common ancestor will be the most similar genetically.

Initial Genetic Tests

Until recently, scientists did not have the ability to decode entire genomes and compare them. So, they compared the only parts of the genome they could measure. At first, they thought this would work because if the whole genomes are nearly identical, most of the parts will be nearly identical. So, one might get minor differences depending upon which part they compare; but generally speaking, it should not matter which part of the genome is compared.

Chromosomes were among the first things that biologists discovered. They have long known how many chromosomes each species has. A reasonable assumption would be that the more complex a creature is, the more chromosomes it should have. A person must surely have more chromosomes than a worm or a fly; and it does. If you look at the table of chromosome counts on Wikipedia, 7 you will see that fruit flies have 8 chromosomes, an earthworm has 36, and a human has 46. That makes sense!

But that same table also says that Rhesus monkey has 42 and a gorilla has 48. Does that mean a Rhesus is less highly evolved than a human, but a gorilla is more evolved? A carp (goldfish) has 104 chromosomes. Is it really more than twice as highly evolved as a human? A butterfly has 268 chromosomes. So, simply looking at the number of chromosomes doesn’t tell evolutionists the story they want to hear.

The First Sign of Trouble

In 1998, since they did not have the capability to decode the entire genome, and since simply counting chromosomes didn’t work, scientists tried decoding 18S rRNA sequences. We reported in March of that year that this analysis showed that a scallop and a sea urchin and a brine shrimp all had an 82% correlation of their 18S rRNA sequence—but the scallop and a tarantula had a 92% correlation, which foolishly implies a scallop is more closely related to a spider than a sea urchin! 8 Evolutionists tried to brush this off by saying that the technology is still in its infancy and has some bugs to be worked out.

A year later, we reported eight articles in the professional scientific literature which found major discrepancies between DNA analysis and conventional evolutionary thinking (which was previously based on fossil evidence). 9 So, near the end of the 20th century, this resulted in a heated debate between the paleontologists and the geneticists.

To make a long story short, over the past 17 years we have published 45 articles about “shocking” or “surprising” genetic results which confound evolutionists. We encourage you to go to the DNA tab 10 on our Topics page to read them in reverse chronological order (from the bottom up). You will see that as the evidence against common descent mounts, increasingly the evolutionists’ response is “convergent evolution.” That is, they believe the exact same genes evolve in completely unrelated species by chance.

Characteristics of Design

DNA analysis isn’t consistent with descent with modification—but, in my opinion, it is consistent with design. I freely admit that my opinion is based on my personal experience.

I spent more than three decades working in the defense industry. Some of that time was spent engineering American missiles and radars. The rest of that time was spent reverse engineering Russian missiles and radars. The latter employment, referred to as “Foreign Material Exploitation (FME)” in polite circles, has taught me how to recognize design through style.

The primary purpose of FME is to determine how the enemy weapon works in order to discover weaknesses which can be exploited to render the weapon ineffective. The process begins by obtaining (through some nefarious process) the foreign weapon and/or documentation of the foreign weapon. Then it can be tested, taken apart, replicated, and analyzed.

That process will reveal certain things about the weapon that don’t make sense initially. Why would the Soviets do it that way? The most natural human reaction is to think, “That’s dumb!” because we Americans are much smarter than Russians, and know the best way to design weapons. It doesn’t take too long working on foreign material for that arrogant attitude to be replaced by humility. I quickly learned that if I didn’t understand why the Russians did it that way, it is because I wasn’t smart enough to see the wisdom in it.

When biologists started analyzing DNA, there were large portions of the molecule they didn’t understand, which they termed “junk DNA” because they thought it served no purpose. Over the years, they gradually discovered that it really did serve a purpose. They did not recognize the wisdom inherent in the junk DNA.

The second thing I learned from my experience doing FME is the distinctiveness of style. If you show me the electrical and mechanical drawings for a 1980’s era weapon I have not worked on, I bet I could tell you whether it is an American or Russian weapon just from certain stylistic aspects. Russian engineers just design things differently than American engineers do.

If you are even remotely familiar with art, you can tell a painting by Monet from a painting by Picasso. Picasso just didn’t use the short, dot-like brush strokes that Monet used. Monet didn’t use the crisp, straight lines Picasso used. Style is recognizable in art, and engineering, and biology.

The more we learn about the genomes of very different creatures, the more commonality we find. This commonality can’t be the result of inheritance from a close common ancestor because these different animals don’t have a close common ancestor (presuming they even have a common ancestor). These similarities in different creatures just cry out, “STYLE!”

After a few years of reverse engineering Russian weapons, I gradually came to imagine the Russian engineer who designed the weapon. I called this imaginary engineer, “Ivan.” I would look at a circuit I didn’t understand and ask myself, “Why would Ivan do that?” Remembering what Ivan typically did on other weapons, it would usually make sense to me. It is hard to explain, but I really felt a kinship with my Russian opponent. I felt like I knew him through his work.

When reading the scientific analysis of genomes of different creatures in Science and Nature, I ask myself, “Does this seem to be the result of random mutations filtered by natural selection? or is there a consistent style that recurs over and over again that seems to be the result of design? The answer is that it looks like someone reused the same genes in many different living things. Genetic analysis is absolutely consistent with the presumption of design.

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1 http://www.genome.gov/Glossary/index.cfm?id=90
2 http://www.genome.gov/Glossary/index.cfm?id=33
3 http://www.genome.gov/Glossary/index.cfm?id=48
4 http://www.genome.gov/Glossary/index.cfm?id=70
5 http://www.genome.gov/Glossary/index.cfm?id=4
6 http://www.genome.gov/Glossary/index.cfm?id=93
7 https://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count
8 Disclosure, March 1998, “The Failure of Genetics”, http://www.scienceagainstevolution.info/v2i6n.htm
9 Disclosure, July 1999, “The DNA Dilemma”, http://www.scienceagainstevolution.info/v3i10f.htm
10 http://www.scienceagainstevolution.info/topics-dna.htm