William Paley argued that if we came across a watch on a beach, we would assume it had not arisen by chance because of its complexity. Therefore it must have been designed. But then Charles Darwin came along, and argued that the complexity found in nature could be explained by the accumulation of small variations selected by nature for fitness over long periods of time. Those who developed his arguments asserted that life might look designed, but this was merely an illusion.
Unfortunately, neither William Paley nor Charles Darwin were alive to see the blockbuster movie sequel to the original story, in which the device on the beach turned out not to have been a watch after all, but some kind of advanced nanotechnology disguised as a watch. It contained huge quantities of coded information tightly packed into microscopic fractal spaces, as well as advanced circuitry that could replicate itself, manipulate subatomic particles, and build complex molecular machines that could be assembled and disassembled easily.
If such a device had been found on the Moon, it would be heralded as irrefutable proof of extraterrestrial intelligence; and yet most of the cells in almost every living organism on Earth are precisely such devices.
Outside of biology, such a device would be seen as obvious evidence of design, so why is design dismissed so easily in the case of the cell? The reason is, modern science is committed to the dogma of naturalism. Since this has become an almost unquestioned and unquestionable assumption in the field of biology, only theories based on naturalism are allowed, meaning intelligent design is excluded.
Since Darwin’s day, scientists have gathered an incredible amount of knowledge about how the cell works, and it seems there is always more to discover. I would suggest that every person who believes, or has believed, that life arose by itself through natural processes, owes it to himself or herself to think deeply about the following important question:
Given that design was dismissed as an illusion by Darwin’s adherents, could it be that what looks on the surface like evolution is really the illusion? In other words, instead of the illusion of design, what if we are looking at the illusion of evolution?
After all, when it comes to our assumptions and beliefs, which are things we tend to take for granted, it makes sense to conduct a reality check once in a while, to make sure they are grounded in truth, and not merely wishful thinking. This applies just as much for the believer as it does for the atheist and skeptic.
Now, before we can examine the idea that evolution might be the illusion, we need to recognize that the word “evolution” can mean different things to different people. To be clear, the form of evolution I am challenging in this letter is the ability of natural phenomena such as mutations and natural selection to produce all the variety of life as we know it – what some call “molecules to man” evolution.
This form of evolution assumes all life is related by common descent, and that each species is a branch on a universal tree of life. This is treated as an unquestioned assumption starting from the school textbooks and continuing through scientific papers and the media.
Before biologists knew about what happened in the cell, many already believed that life had evolved. When they finally got to look inside the cell, they began to see a hazy outline of how life worked, including how proteins were encoded in the DNA molecule. But curiously, genes coding for proteins only make up a small fraction of the genome. They didn’t know what the rest was doing there, so it was labeled “junk DNA” and assumed to be useless vestiges of evolution. This term persisted for several decades, fueled not only by popular science writers and magazines, but often by scientists themselves.
In hindsight, this label seems incredibly arrogant, but it shows what happens when assumptions are treated as facts. This is one of many examples where evolutionary theorists hindered science. After all, why research something that is mere junk?
Fortunately, not all scientists were put off by the junk DNA label, and more and more uses for the other DNA were found. We now know that the majority or even most human DNA is transcribed into RNA or has some other purpose, even though only a small amount is converted into proteins. Some of it is involved in other roles such as gene regulation, controlling development, or to serve as structural or catalytic components in conjunction with proteins. As our knowledge increases, so the amount of junk keeps shrinking. In other words, junk DNA, which for a long time was argued as being absolutely necessary for evolution to happen, turned out to be an illusion.
Before we were able to peer into the cell, many biologists believed that humans and apes had evolved from a common ancestor perhaps around six million years ago, because they shared certain similarities, including a somewhat similar bone structure, hands with thumbs that can grip onto things, and the ability to walk on two legs.
When scientists figured out how to compare DNA fragments, human and chimpanzee genomes appeared to be about 99% similar. When the chimp genome was sequenced more fully, researchers came up with a more precise difference of 1.23%, based on an alignment of 2.4 billion out of 3 billion base pairs in the human genome. This figure, about a 1% difference between humans and chimps, gave the strong impression that we are closely related.
However, this widely popularized figure only included base substitutions, where one nucleotide base is replaced with another. It didn’t include insertions or deletions, or “indels” as they are called. These made up at least an additional 3% difference, bringing the similarity to around 95%, although the sample that had been compared still excluded hundreds of millions of base pairs. But it was idea of the 1% difference that somehow made it into the public consciousness, rather than the more accurate figures. No wonder one science writer dubbed it “The Myth of 1%.” 1
At the time, the DNA molecule could only be read in small chunks. These were assembled using the human genome as a template. However, later researchers acknowledged that this effectively humanized the ape genome, minimizing differences between the species. When they assembled ape genomes without using the human one as a template, only an estimated 83% of their genome could be aligned with the human one, excluding chromosome Y. 2
It turns out, there are also dramatic differences in certain regions of the human and chimp genomes. Humans have 23 chromosome pairs, while chimpanzees have 24. However, the most striking difference is in the Y chromosome, found only in males, and which earlier sequencing analysis had excluded, perhaps conveniently, so it wouldn’t disrupt the 1% myth.
According to the researcher who led the work into comparing the Y chromosomes of chimps and humans, they are “horrendously different from each other,” like there had been “a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” 3
His research team found that the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome, and only 47% as many protein-coding elements. Furthermore, more than 30% of the chimp Y chromosome couldn’t be aligned with a human counterpart, and the parts that could be lined up had been relocated. Given that the human Y chromosome consists of about 60 million base pairs, or about 2% of the genome, and earlier studies had excluded this, clearly the figure of 98% or 99% similarity can’t be true.
There are many other significant differences. At the end of each chromosome are repeating DNA sequences called “telomeres” that protect the ends from deterioration, like the plastic or metal at the end of a shoelace. The telomeres of primates such as monkeys, chimps and orangutans are about 23,000 bases long, but human ones are only 10,000 bases long.4
“Alu elements” are short sequences, about 300 nucleotides in length, that repeat themselves throughout the genomes of primates, which evolutionary classification includes humans. There are more than a million copies of Alu elements in the human genome, accounting for over 10% of it. They were originally assumed to be junk DNA, or selfish genes with the sole purpose of replicating themselves, like genetic parasites. But they are now known to have important functions. They help to regulate tissue-specific genes, and affect the way genes are turned on. There are at least 7,000 Alu elements unique to humans. One study identified about 15,000 mobile genetic elements that are specific to humans.5
In other words, taking into account all the differences, and the fact that the human genome was originally used by researchers as a template for the chimp genome, it’s highly unlikely that our genomes are even 95% similar. The high degree of similarity was another illusion, propped up by cherry-picking areas for comparison. Certainly the Y chromosome smashes this illusion to pieces.
But why does it matter whether we are 85%, 95% or 99% similar to chimps? According to evolutionary theorists, humans and apes descended from a common apelike ancestor around six million years ago. If we assume a 99% similarity, this is a difference of about 30 million base pairs.
In evolutionary theory, mutations can occur regularly, but a mutation is only significant over the long haul if it gets fixed in the wider population of a species. It takes time for a single mutation to be fixed, so it can be passed on to succeeding generations.
During most of the supposed six million or so years of human evolution, the population size of humans was fairly small. Assuming a new generation every 20 years, there have been about 300,000 generations from the supposed divergence of humans and chimps from a common ancestor, and 30 million mutations were fixed during this time, which means about 100 mutations needed to be fixed for each new generation born.
However, if the similarity between humans and chimps is closer to, say, 90%, this would take the number of mutations in each generation to around 1,000. This means evolution has to work ten times harder than at 99% similarity. In the end, this isn’t a major problem for evolutionary theorists, because they can just tweak their figures to make it work in support of evolution.
I suppose they could argue for a higher mutation rate in the past, but this would throw doubt on the idea of mutations being regular and clock-like; and if they changed the length of time from which we supposedly diverged from a common ancestor, this would cause problems with their dates for existing fossils.
In any event, the reality seems to be that we are nowhere close to a 99% similarity, and some parts of the human and chimp genomes are drastically different, which is why researchers have talked about dramatic renovation and a rapid rate of change in those areas. This language reflects the built-in assumption that chimps and humans share a common ancestor. But maybe what researchers are seeing is an illusion created by their own assumption. Maybe humans and chimps share many similarities, but aren’t actually related by common descent. Instead, perhaps they both have a common designer.
Many or even most of the proteins needed to make a human being would be similar to those needed to build a chimp, which would account for the similarity in the parts of the DNA that code for proteins. But a lot of major and minor tweaks would also be needed to make us distinct, which would also be consistent with what researchers have found.
Now, once scientists were able to sequence individual genes, they discovered an interesting pattern. The protein “cytochrome c” is an essential part of the electron transport chain, and is made up of about 100 amino acids. The gene is identical in humans and chimps. By comparing the cytochrome c gene in different organisms, scientists found there is greater similarity between species assumed to be more closely related in the evolutionary tree of life, and larger differences in species that are more distantly related.
For example, the gene is identical in pigs, cows and sheep, and there are only two differences between ducks and chickens. There are 11 differences between the human and dog versions of the gene, and 44 differences between the human and yeast versions. This pattern would seem to be consistent with the idea of universal common descent, and that the bigger the evolutionary distance between organisms, the further apart the gene sequence gets.
However, another explanation is that the differences are related primarily to the needs or physiology of the creature. Humans and chimps aren’t vastly different in shape and size, and neither are pigs, cows and sheep. However, humans tend to differ from yeast, so the needs of the two organisms are probably very different. Maybe the differences relate to the size, shape and makeup of the organism.
The fact that many of the amino acids in cytochrome c are the same across vastly different creatures suggests those amino acids serve an essential purpose. They can’t change without breaking the gene.
Many biologists assume the ones that have changed are more neutral. In other words, those amino acids can change without significantly changing the function of the protein. In a sense, this would perhaps make them more like placeholders, which may be true in some cases, but others could have been put there deliberately.
Researchers create what are called “phylogenetic trees” based on similarities in the physical or genetic characteristics of species, and also of genes. They assume the tree represents an evolutionary history, in the same way a family tree diagram represents a family history. The assumed evolutionary lineage of a species or gene is called its “phylogeny.” However, what these phylogenetic trees could be showing is mainly the physiological similarity or differences between creatures, rather than an evolutionary history.
For example, pigs, cows and sheep are all roughly the same size and have identical cytochrome c genes, even though each creature is presumed to have evolved separately. Ducks and chickens are also of similar size to each other, and they have just two differences in the gene. Humans and dogs are pretty different from a physical point of view, and the 11 differences in their cytochrome c gene could reflect their different physical makeup. Humans and yeast have 44 differences in the gene, maybe because they are very different organisms with vastly different needs. Drosophila fruit fly, wheat and yeast cytochrome c genes have several amino acids at the beginning that don’t appear in the human or chicken version. Presumably these amino acids are useful for those particular creatures, but not for others.
Many genes have their own distinct pattern of differences across species. The protein “lysozyme” is a small antibacterial enzyme that forms part of our natural immune system, and is able to attack the cell walls of bacteria. It was discovered by Alexander Fleming while he had a cold. He added a drop of mucus to bacterial culture and discovered, to his surprise, that it killed the bacteria. The enzyme is found in places where nature doesn’t want bacteria to grow, such as human milk, egg whites, mucus, tears and blood.
There are three distinct types of this gene, the c-type (chicken or conventional type), the g-type (goose type) and the i-type (invertebrate type). The lysozyme g version from goose eggs is larger than lysozyme c, and there isn’t much sequence similarity between them. In fact, the different forms aren’t very similar in terms of amino acid sequences, but they do share similar overall structures, which is why biologists view them as three types of the same enzyme. This suggests the protein has been adapted to serve the needs of its different hosts.
For example, lysozyme found in the white of a hen’s egg can reach a higher temperature than lysozyme in human milk, before it loses its antibacterial abilities. This means a mother hen can safely sit on her eggs and keep them warm, without having to worry about bacteria munching away at her offspring’s only food source while they are still inside the egg. The gene sequence for this enzyme must be different between humans and hens, so the hen version can incorporate this feature.
For proteins, what matters most is the shape it folds into once it has been made by a ribosome. This usually determines its function. For example, the protein “myosin II” is responsible for producing muscle contraction in most animal cell types. It consists of two heavy chains about 2,000 amino acids in length, forming two “heads” and a “tail” domain. The tail folds into three segments. Despite turkeys and scallops supposedly being separated by 600 million years of evolution, their myosin II proteins are structurally identical.6
Phylogenetic trees of proteins are constructed in an attempt to trace their evolutionary origins across the tree of life. But if proteins didn’t evolve that way, but instead were built into the first creature in a family, and were then somehow adapted to serve the needs of each creature, then phylogenetic trees are really just similarity trees, and don’t necessarily reveal ancestry, except in closely related species.
In other words, gene comparisons and phylogenetic trees across widely different families may be giving the illusion of evolution. It could simply be that the bigger the difference in the physiology and needs of two creatures, the bigger the difference in the gene sequences.
Some genes such as cytochrome c are fairly similar across the so-called tree of life, while others such as lysozyme are very different. As evidence for evolution, the public are generally shown the ones that seem to differ in a regular clock-like manner, to imply a clock-like regularity of evolution from common ancestors.
But this is contradicted by the fossil record, in which large groups of creatures appear very quickly, as well as by genes that have completely different supposed rates of change, or that essentially stay the same, or that appear completely unexpectedly in whole branches of the evolutionary tree, and are therefore explained by magic wands such as “translocation” in the guise of horizontal gene transfer.
I think the evidence from genes as a whole suggests that genetic differences across the spectrum of life are related much more to function, physiology and the specific needs of the organism, rather than simply by how related organisms are on an assumed universal tree of life.
In other words, phylogenetic trees may be contributing to the illusion of evolution. They are drawn up based on similarities, and these are then assumed to be the result of evolution. But maybe they are just similarities, in the same way that a Ford and a Chevy share many similarities. If we were to look at their design blueprints, we would find many almost identical features; but this doesn’t mean they evolved from a common ancestor. They were both designed, and both manufacturers had similar intentions for their vehicles, which explains why many features overlap. But creating a phylogenetic tree involving a Ford and a Chevy would be misleading.
However, researchers looking at genetic sequences claimed they found clear evidence that proved we were directly related to chimps. Many creatures are able to make their own vitamin C and can produce it in large quantities. The manufacture of vitamin C in an organism involves several processes, the last of which requires an enzyme known as GLO or GULO. However, it seems the gene is broken in humans, chimps, guinea pigs and some other creatures. It has become a pseudogene. As a result, these creatures can’t make their own vitamin C and need to get it from fruit and vegetables.
The deletion of a single nucleotide in the same position in this gene is shared by both chimps and humans, and this is claimed to be proof of common descent. Humans and chimps, it is assumed, inherited the same deletion from a common ancestor.
In the evolutionary paradigm, chimps and guinea pigs evolved along different paths, and their GULO pseudogenes are quite different. Despite this, a comparison of human and guinea pig sequences found dozens of matching substitutions, even though they had supposedly evolved along very different lines.7 In other words, if we assume “common mistakes” provide evidence of common ancestry, then based on this, we are much more related to guinea pigs than chimps.
What is the cause of such shared mistakes, even in species that are only distantly related according to the evolutionary paradigm, and therefore can’t be the result of inheriting the mistakes from a common ancestor?
It seems mutations often occur in what are referred to by biologists as “mutation hotspots,” areas in the genome that are much more prone to mutation.
For example, close to half of all insertions and deletions are concentrated in about 4% of the genome, most of which are caused by DNA polymerase, the machinery that copies the genome, pausing, backtracking and then repeating the sequence it had already copied. Furthermore, areas of the genome containing sequences of repetitive nucleotides are more prone to this type of mutation.
Single nucleotide variants are the most common in humans, where one nucleotide base has been changed to another base, and they comprise about 80% of the genetic differences between two people. On the other hand, in the gene coding regions of the genome, there are about seven times more of these type of mutations than short insertions and deletions.8
In a study of hundreds of Arabidopsis thaliana plants conducted in a lab, researchers found patches in the plant’s genome with lower than normal mutation rates. These patches contained many essential genes such as those involved in cell growth and gene expression. Natural selection wasn’t responsible for this, because of the way the experiment was set up, so these areas of the genome were being protected from mutations in some other way, such as epigenetics. As one of the researchers concluded: “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.” 9
Mutational hot spots could explain the dozens of apparent “common mistakes” between the GULO pseudogene in humans and guinea pigs, and is also a reasonable explanation for why primates and humans share the same mutation at one particular point. It could simply be a location in the genome that is more prone to mutation.
While the offending nucleotide has been deleted in both the chimp and human genomes, the same nucleotide varies in other animals. The letter at this position is a G in pigs and guinea pigs, an A in mice, rats and chickens, and a C in cows and dogs. In all of these creatures, the nucleotide is surrounded on either side by the letter G, suggesting they are much more stable positions than the one in the middle, and implying the mistake shared by chimps and humans is indeed a mutational hot spot within the GULO gene or pseudogene.10
Incidentally, why is this gene broken in some creatures and not in others? Humans and chimps are able to obtain vitamin C easily enough from their diet, so when the gene broke it wasn’t fatal. We could still survive without it. At the same time, while the GULO pseudogene was originally the last step for producing vitamin C, it may still have a secondary function, which would explain why it hasn’t just mutated away but remains somewhat intact and recognizable. Alternatively, maybe the mutation happened fairly recently.
Skeptics and atheists ask, why would a creator put a pathway for making vitamin C in all these species, and then inactivate it? 11 The question assumes the creator inactivated it, but that doesn’t need to be the case at all. However, this shows why some kind of revelation or communication from the creator would be useful, otherwise we would be left to guess what was going on.
I have argued throughout this letter that such a communication exists, which explains quite clearly that humans fell away from God, and thus subjected themselves to breakdown, of which the GULO gene could be one example.
To give a human analogy: if a manufacturer offered a lifetime repair warranty for a product, but the customer rejected the warranty, they can’t later expect the manufacturer to repair the product for them if it breaks down. Pseudogenes are consistent with this idea. They are evidence that we are devolving and losing genetic information.
There are also other reasons why pseudogenes exist, assuming they really aren’t functional any more. Some sequences that have been called pseudogenes at one time have turned out not to be, or have other important functions.
Either way, pseudogenes would still exist in many creation models. For example, God could have created distinct “kinds” of creatures with the potential for variations, and those variations would eventually become all the species within a family of creatures. As each species adapted to its environment, some genes might get turned off or broken, becoming pseudogenes. A good example of this would be the antifreeze gene discussed in an earlier chapter, which seems to have become a pseudogene in one species of codfish that no longer lives in freezing waters.
In other words, most creationists accept a limited form of common descent, where a species could be descended from a common ancestor in a family tree, but they usually reject the idea of universal common descent, where all species are connected in one tree of life.
Curiously, the vitamin C pathway isn’t consistent across different forms of life. Yeast, plants and animals use different pathways to make it or a variation of it. Vitamin C is produced in the kidneys of some fish, amphibians and reptiles, but in the liver of mammals. In birds, it is a mixture.
This poses a challenge to the idea of a universal tree of life, but could be useful for determining whether there really are smaller phylogenetic trees of life based on genetically identifiable “kinds.” At a minimum, it suggests a modularity to at least some of life’s functions, where whole systems like vitamin C manufacture can be moved into different organs, even in the same type of creature!
Whatever the case, the idea that we must have a common ancestor with chimps could simply be another illusion of evolution.
Another part of evolutionary theory is the concept of convergence. When the same function or feature appears in creatures on different branches of the supposed tree of life, but not in their common ancestor, evolutionary theorists call this “convergent evolution,” or “homoplasy” in more technical circles. It means nature invented the same thing more than once.
Echolocation is often cited as a good example of this. Some bats and dolphins are able to emit high-pitched sounds which they use to catch food, yet these creatures are only distantly related on the supposed tree of life. In the evolutionary paradigm, nature came up with echolocation at least twice.
Curiously, when researchers looked at the genomes of different creatures including bats and dolphins, they found that echolocating bats and the bottlenose dolphin, which also uses echolocation, had nearly 200 genes altered in a similar way, genes that seemed to be linked to hearing or vision, and that presumably contributed to the echolocation ability.12
The concept of convergence is used to explain features that keep cropping up and that don’t fit neatly into a tree of common descent, but more and more examples are being found even at the genetic level.
In one study, researchers wanted to learn more about how the brains of birds develop. They compared the genomes of parrots with 30 other birds, and found that regions of the parrot genome regulating brain development are the same as humans. These elements supposedly evolved in both species at very different times, but with similar results.13
In another study, researchers found that short interspersed elements in humans and mice regulated the same genes the same way in both species, yet they are said to have evolved independently in the two lineages.14
How do evolutionary theorists explain this? They argue that creatures with a common feature were likely under similar selective pressures, and so natural selection gradually led them down the same path.
Since natural selection can only select from what already exists, I suppose it makes sense that a complex feature like echolocation would have to evolve from something already existing in a common ancestor of bats and dolphins; and that from a similar starting point, there may be only one way to build such a feature.
But evolutionary theory can’t tell us in detail how echolocation evolved even once, let alone twice. If about 200 hearing and vision-related genes need to be altered for a creature to acquire this ability, how does nature arrive at this once, let alone twice? The theorist would answer, “cumulatively, in small steps,” but this assumes there is a cumulative pathway available, with each step having a significant survival advantage. Theorists can perhaps describe these steps in broad storytelling strokes, but they rarely if ever test out all of the nucleotide changes that would be required along the path to echolocation; and even if such a path could be constructed on paper, this doesn’t mean echolocation was built this way.
Incidentally, some species of bats don’t have echolocation. Could they have lost the ability? Research suggests this may be the case. In early development, the inner ears of bats grow in a way that can facilitate the sonar ability, but this isn’t sustained into adulthood in some species such as fruit bats, implying they may have lost the echolocation ability at some point. In other words, they could have devolved.15
Whatever the case, given that similar features and functions occur so frequently, could it be that “convergent evolution” is an illusion made up by evolutionary theorists, and that similar features exist in different creatures because they share a common designer? A car manufacturer doesn’t need to reinvent the wheel every time it wishes to design a new vehicle. It can draw from existing blueprints and design principles, and re-use features from previous models. This is an intelligent process, and not done by gradually shuffling letters in the car manual.
What about the fossil record? The claim is often made that it supports the story of evolution. The record is usually broken up into periods or epochs within the evolutionary timetable. But if we remove our evolutionary glasses for a few moments and just look at the record without any assumptions, we simply see lots of dead creatures that fossilized within different layers of sedimentary material.
Fossilization is not the normal state of affairs for dead creatures, since a dead body usually decays quite quickly, although bones tend to take somewhat longer, and then scavengers and other organisms eat up the remains. Furthermore, the fossilization process is often assumed to take thousands or even millions of years, but experiments have shown that organic matter encased in sediment, and subjected to high pressure and temperature, can be fossilized in as little as a day.16 If only we could conceive of a catastrophe that could cause animals to be covered in sediment so quickly!
One of the most interesting parts of the fossil record is the so-called Cambrian Period, in which a vast range of multi-cellular life seems to have appeared rapidly. This phenomena is often described as the “Cambrian Explosion.”
At the bottom are trilobites that moved over the sea bed, and are considered to have been one of the earliest creatures to have evolved. They appear suddenly in the fossil record around the world, with a complex body plan and multiple organs.17
Curiously enough, if we lose the naturalistic and evolutionary lenses and assume instead that a worldwide Flood happened, we would see exactly the same thing. Huge volumes of sediment would have been shifted around and deposited in layers, burying millions of animals and causing them to fossilize, with the poor trilobites at the bottom, because everything would have been dumped on top of them. Of course, this raises the question of dating and timescales, which I will discuss in a later chapter.
Another line of evidence used to support evolution are so-called transitional forms. Given that evolution is supposed to be a gradual process of change over time, we would expect to see the fossil record full of transitions, as nature tinkers constantly with forms. Yet it is surprisingly stable. True, there is plenty of variation, but we can usually recognize what family a dead species may have belonged to.
Nevertheless, a handful of creatures are held up as evidence of a major transition from one major form of life to another. Archaeopteryx is a well-known example, claimed to represent an evolutionary transition between dinosaurs and birds. Its feathers were identical to modern bird feathers, and it could probably fly for short bursts, like quails and pheasants.18
The fossil species Tiktaalik has also been assumed to be a transition from fish to land dwelling creatures. One writer called it “a fish with a wrist,” 19 although a wrist has many more bones. However, it is similar to a modern fish that can move on land, so maybe it was just an ancient fossil of a related type of fish.
Perhaps the most famous of all so-called transitions is the Neanderthal, once portrayed as a primitive human, implying they were the “missing link” between humans and chimps. Later research showed that they were fairly similar to modern humans, who even interbred with them. However, to keep the human evolution story going, researchers keep digging up new bits and pieces of fossils, which they then give names to and declare to be our missing ancestors.
Now, I could spend many pages arguing about whether these creatures really are transitional forms on some kind of evolutionary scale, but instead I will make my point with a simple analogy.
Imagine that human society in the future has been wiped out by the artificial intelligence we created to solve all our problems and make our life easier. I suppose wiping us out did solve all our problems. Millions of years later, these AI entities have entirely forgotten about their human creators, and believe that the forces of the Earth must have put their ancestors together, in some kind of evolutionary process.
As they examine the “fossil record,” they see evidence that reinforces their beliefs. They find creatures they label as belonging to the class they call vehicles. The AI scientists debate over the exact ordering, or phylogeny, in the evolution of the vehicles, but most agree that the unicyclium order came first, followed by bicylium. This was followed in rapid succession by the evolution of creatures in the orders of carium, busium, truckium, coachium and motorbikium. These all seemed to evolve relatively quickly, in a period they call the Wheelian Explosion.
Now, this analogy might be slightly amusing, or perhaps a little depressing, but it highlights the consequences of their flawed logic. Since their initial assumption that these things evolved was faulty, the entire process of identifying a tree of life would also be flawed.
They could come up with stories for how each group evolved. Obviously the bicylium came about as a result of tandem duplications of the unicyclium genes. Some busium and truckium parts seem similar, but with no clear common ancestor this was probably a case of horizontal gene transfer; although a faction of AI scientists argued that truckium evolved by the endosymbiosis or swallowing up of an ancient motorcyclium by a busium.
Of course, couching an idea in scientific terminology that sounds vaguely plausible doesn’t make it true, because the entire reasoning is based on incorrect assumptions. This is what I am suggesting is also the case in reality.
If life was actually created in a top-down manner, with the initial creations capable of rapid speciation, and then large amounts of these variations were destroyed in a global catastrophe, the fossil record would be no different to what we see today. In this case, creatures such as Archaeopteryx and Tiktaalik wouldn’t be transitional but simply variations, just as a bicycle isn’t a transitional species between a unicycle and motorbike, but is simply another form of vehicle. Similarly, Neanderthals would just be an extinct branch of the human family, and not an evolutionary transition. In older textbooks they were made to look more primitive than they may have been, to support the illusion that we evolved from an apelike ancestor.
In Darwin’s day, many creationists apparently believed each species was directly created by God; or at least, this is what Darwin argued against, with his idea that all species evolved from a universal common ancestor.
The famous finches studied by Charles Darwin on the Galapagos Islands are held up as icons of evolution for their beaks that vary in size. Three species of finch were known to occur together in the highlands of Floreana – the small, medium and large tree finch – each differing in body size and in the shape of the beak.
Later studies showed that the large tree finch had disappeared from the island. The evidence indicated it may have disappeared due to hybridization, where two species fuse into a single population. Similarly, on the island of Daphne Major, two species of ground finch have been morphing into one, because of a change in the food supply. These things happened in the space of a few decades.20
On the island of New Guinea in the Pacific Ocean, eleven species of estrildid finch proved to be even more interesting. The plumage of each species has its own distinctive patterns of black, brown, gray and white, along with differences in beak size. Yet when researchers studied their genomes, they were strikingly similar, suggesting all of the species arose quickly and recently, assuming the evolutionary timetable.21
The researchers identified about 20 genes that differed among the eleven finch species, including a handful which seemed to control coloration. Different versions of the genes, alleles, had been mixed and matched in the species, perhaps as a result of occasional interbreeding, providing wonderful variety. Millions of years of slow accumulating mutations weren’t needed to produce these different species. It just needed a little sex between them.
The process of speciation is often assumed to be slow, happening by natural selection gradually fixing tiny mutations in a population over a long period of time. But research increasingly indicates this assumption may be wrong, and that species can arise quickly as a result of the reshuffling of genetic information, almost as if nature was designed to produce interesting and colorful variations quickly.
The finches we have just discussed are still finches. The genetic variation built into their gene pool allows for beak variations and a variety of colors and patterns, but I suspect they will always be finches. People are entitled to call this evolution, but it’s really just variations on a theme, which is what many creation models predicted.
Genetic variation can also be seen in the peppered moth, often cited as an example of natural selection in action. During the Industrial Revolution, when soot from coal-burning factories blanketed the English countryside, light-colored moths began to stand out on trees. During this time, dark-colored peppered moths may have arisen, and they enjoyed better camouflage from predators. As a result, their population increased rapidly. Later, when pollution was reduced, the light-colored moth took over again.
Apparently, peppered moths weren’t the only species affected by pollution. Dark forms increased in over 100 moth species during the Industrial Revolution, leading a group of researchers to wonder whether the moths were all relying on similar genetic mechanisms.
The researchers examined the genomes of the British peppered moth along with the “pale brindled beauty” and “scalloped hazel” moth species. The mutation for a dark trait seemed to occur in the same genetic region as a gene called cortex in all three species, but the origins of the trait in the other two species appeared to be much older than the one in the British peppered moth, which may have happened as recently as the 1800s, giving rise to dark-colored ones.22 According to the researchers, this implied there was a “master switch” for the dark trait in these moths.23
Later research suggested that the ability to “go dark” is likely a feature of what are known as “micro RNAs.” These are short pieces of RNA about 20 base pairs long that act as genetic switches, playing a role in regulating gene activity and cell development.24
The dark peppered moth is a good example of natural selection at work, but the evidence at the genetic level indicates it was likely switching on a trait already built into the species, but lying dormant – namely, the ability to “go dark.” The genes may have been designed in such a way that, if dark forms were needed for the species to survive, the trait could be switched on.
Once again, people are entitled to call this evolution, but it’s also evidence that traits have been designed to be flexible, allowing species to adapt to their environment rapidly. They certainly don’t need millions of years. The dark mode was switched on in the peppered moth within just a few decades. This would harmonize nicely with many creation models, where speciation and adaptation are predicted to happen very fast. It also suggests design ingenuity, where one or more switches related to a gene can effectively turn on the dark mode of a moth when needed.
Let’s examine one more evolutionary idea: the concept of “vestigial” organs. These are organs or features that have apparently lost all or most of their original function. They are often held up as evidence for large scale evolution.
The appendix is perhaps the most famous example, once considered a vestige of a redundant organ with digestive functions. However, the appendix turns out to be a safe house for useful bacteria that might otherwise get flushed out of the rest of the intestines, and may also play a part in the immune system.
Whales and dolphins have pelvic bones that are often assumed to be remnants from when their ancestors supposedly walked on land. But it turns out, the pelvic bones of these creatures help with reproduction. They’re actually doing something useful.25
The coccyx, or tailbone, is supposedly the remnant of a lost tail. According to evolutionary theorists, it hasn’t disappeared because it serves as an attachment site for tendons, ligaments and muscles.
Now, if we remove our Darwinian lenses for a moment, and just look at the evidence for what it is, we see that the appendix, the coccyx and the whale’s pelvic bone all have useful functions, and the idea that they are vestiges of some lost function is just an assumption based on evolutionary thinking.
Incidentally, on occasion, human babies have been born with what appears to be a tail. One type was associated with birth defects, while another was assumed to be the remnant of an evolutionary ancestor. However, the evidence suggests that both are due to an incomplete fusion of the spinal column.26
Wisdom teeth are often viewed as vestigial. It is assumed that our ancestors had larger jaws with more teeth, but modern humans have smaller jaws and therefore need less teeth. The fact that wisdom teeth still grow in many humans shows there is quite a lot of potential variability in the makeup of humans, but this isn’t really evolution as such. It’s just variation. However, if modern humans really are smaller, this suggests we might be devolving, which fits creation models.
Whatever the case, the concept of vestigial organs is used to prop up the idea that large scale evolutionary changes have occurred, when in reality, those organs perform a useful function, and everything else is yet another illusion, gifted to us out of the imagination of evolutionary theorists.
The point of this chapter hasn’t been to go into detail about every issue related to evolution versus design. That would need a whole book, although I will tackle a few more important issues a little later.
Instead, I have selected a range of issues from junk DNA to vestigial organs, to show that when we remove the evolutionary lenses through which we have been conditioned to look at life, starting from the school textbooks and continuing right through to academia, science and the media, in many cases the idea that we evolved from fatty RNA protocells looks more like the illusion.
A stage magician relies on a number of psychological tricks to convince the audience of his illusion. He may misdirect them with a hand gesture, hide something important with sleight of hand, and rely on his authority to reinforce the illusion.
Could it be that those with a vested interest in the naturalistic dogma are using the same tricks to convince you that life came about all by itself? Evolutionary theorists say that life has the appearance of design, but this is simply an illusion. I’d suggest that evolution is the illusion.
I think the evidence indicates that life has the appearance of design because it is actually designed, by someone with a high degree of intelligence and ingenuity. But in the modern world in which we live, the stage magician’s toolkit of authority, misdirection and sleight of hand has been employed by the magicians of naturalism, so the public only gets to see what those magicians want them to see.
1 See the article “Relative Differences: The Myth of 1%” by Jon Cohen, published in Science, June 29, 2007. 2 Kronenberg et al, “High-Resolution Comparative Analysis Of Great Ape Genomes”, Science, 2018. 3 See the article “The fickle Y chromosome” by Lizzie Buchen, Nature, January 13, 2010. 4 Kakuo et al, “Human is a unique species among primates in terms of telomere length”, Biochemical and Biophysical Research Communications, 1999. 5 Tang et al, “Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase”, DNA Research, 2018. 6 Jung et al, “Conservation of the regulated structure of folded myosin 2 in species separated by at least 600 million years of independent evolution”, PNAS, 2008. 7 Inai et al, “The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene–the gene responsible for scurvy–and the evolution of repetitive sequences thereon”, Journal Of Nutritional Science And Vitaminology, 2003. 8 Nesta et al, “Hotspots of Human Mutation”, Trends in Genetics, 2020. 9 Monroe et al, “Mutation bias reflects natural selection in Arabidopsis thaliana”, Nature, 2022. For the quote, see the article “Genetic mutations may not be random” by Sophie Ormiston, published at frontlinegenomics.com on January 14, 2022. 10 See Figure 3 in the article “An illusion of common descent” by Peer Terborg, published in Journal Of Creation and at creation.com in 2010. 11 For example, Jerry Coyne asks this exact question on page 73 of his book Why Evolution Is True, Oxford University Press, 2009. 12 Parker et al, “Genome-wide signatures of convergent evolution in echolocating mammals”, Nature, 2013. 13 Wirthlin et al, “Parrot Genomes and the Evolution of Heightened Longevity and Cognition”, Current Biology, 2018. See also the article “Parrots are clever because their brains evolved the same way as ours” by Chelsea Whyte, published in New Scientist, December 15, 2018. 14 Lucas et al, “Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay”, PNAS, 2018. See also the article “Study finds convergent evolution of gene regulation in humans and mice” by Tim Stephens, published by UC Santa Cruz Newscenter at news.ucsc.edu on January 18, 2018. 15 Wang et al, “Prenatal development supports a single origin of laryngeal echolocation in bats”, Nature Ecology & Evolution, 2017. See also the article “Some bat species lost sophisticated sonar ability as they evolved” by Jamie Deasy on ucd.ie on January 9, 2017. 16 Saitta et al, “Sediment‐encased maturation: a novel method for simulating diagenesis in organic fossil preservation”, Palaeontology, 2018. See also the article “Researchers Have Discovered How to Make Proper Fossils – In a Day” by Michelle Starr, published at sciencealert.com on July 27, 2018. 17 Paterson et al, “Trilobite Evolutionary Rates Constrain The Duration Of The Cambrian Explosion”, PNAS, 2019. For an interesting commentary on this article from an intelligent design perspective, see “New Paper Confirms the Trilobite Explosion” published at evolutionnews.org on March 15, 2019. 18 See the article “This Famous Dinosaur Could Fly—But Unlike Anything Alive Today” by Michael Greshko, published at nationalgeographic.com on March 13, 2018. 19 See Your Inner Fish by Neil Shubin, page 38. First edition, 2008. Published by Pantheon Books. 20 Peter R. Grant, B. Rosemary Grant, “Speciation undone”, Nature, 2014. Also “Hybridization increases population variation during adaptive radiation”, PNAS, 2019. 21 Katherine Faust Stryjewski, Michael D. Sorenson, “Mosaic genome evolution in a recent and rapid avian radiation”, Nature Ecology & Evolution, 2017. See also the article “Birds of a Feather: Finches from remote corners of New Guinea help solve an evolutionary puzzle” by Catherine Caruso, published in The Brink at bu.edu on February 12, 2018. 22 E. van’t Hof et al, “The industrial melanism mutation in British peppered moths is a transposable element”, Nature, 2016. 23 E. van’t Hof et al, “Genetic convergence of industrial melanism in three geometrid moths”, Biology Letters, 2019. See also the article “‘Industrial melanism’ linked to same gene in three moth species” published by the University of Liverpool at liverpool.ac.uk on October 16, 2019. 24 Richard H. ffrench-Constant, Alex Hayward, “Melanism: Cryptic control by non-coding RNAs”, Current Biology, 2024. 25 See the article “Whale reproduction: It’s all in the hips” by Robert Perkins, published by USC News on September 8, 2014. 26 See the article “Some Babies Are Born With ‘Tails’, But Not For The Reason You Might Think” by Carly Cassella, published at ScienceAlert.com on June 25, 2023.