Orphan Genes Part 1: Unexpected Results in DNA Sequencing

In his book, Why Evolution is True, biologist Jerry A. Coyne describes modern evolutionary theory with the following statement:

Life on earth evolved gradually beginning with one primitive species—perhaps a self-replicating molecule—that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species.”

Based on this foundational principle, various species are expected to share similar (or homologous) structures due to common ancestry. Berkeley’s Evolution 101 page notes, “Evolutionary theory predicts that related organisms will share similarities that are derived from common ancestors. Similar characteristics due to relatedness are known as homologies.”

Wikipedia’s homology entry lists the following example: “…the forelimbs of vertebrates, where the wings of bats, the arms of primates, the front flippers of whales and the forelegs of dogs and horses are all derived from the same ancestral tetrapod structure.”

Image via wikipedia: “The principle of homology: The biological relationships (shown by colours) of the bones in the forelimbs of vertebrates were used by Charles Darwin as an argument in favor of evolution.”

The Berkeley source provides the following example in the case of plants:

However, the relatively recent advent of DNA sequencing has produced some very unexpected results- surprisingly contrary to this evolutionary theory prediction.

DNA Sequencing- We’ve Come a Long Way Baby

DNA is the blueprint, or instruction manual, containing the instructions which make every species unique. DNA (pictured below) is defined as, “…a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.”

In the 1960’s scientists developed the ability to “read” this DNA instruction manual in a process called DNA sequencing. This was a monumental scientific breakthrough. Britannica defines DNA sequencing and reveals its significance with the following entry:

…technique used to determine the nucleotide sequence of DNA… The nucleotide sequence is the most fundamental level of knowledge of a gene or genome. It is the blueprint that contains the instructions for building an organism, and no understanding of genetic function or evolution could be complete without obtaining this information.” (emphasis mine)

The last sentence is imperative. While Darwin and his predecessors could hypothesize that common ancestry is the most reasonable explanation for similarities shared among various species based on visual comparison, common ancestry cannot be proven and the very concept of evolution cannot be understood without the ability to “read” an organism’s instruction manual (DNA).

For several decades DNA sequencing was a very slow and expensive process. However, the Human Genome Project, initiated in 1990 and completed in 2003, had a revolutionary effect. The goal of this international project, to map the entire human genome, spurred tremendous technological advances in gene sequencing which has continued far beyond the project’s completion. James Heather concludes his History of Sequencing DNA by stating, “Over the years, innovations in sequencing protocols, molecular biology and automation increased the technological capabilities of sequencing while decreasing the cost, allowing the reading of DNA hundreds of basepairs in length, massively parallelized to produce gigabases of data in one run.”

It is this burgeoning wealth of genetics information that has revealed the “mystery” of orphan genes.

What are Orphan Genes and Why are They Problematic for Evolutionary Theory?

Cornelius Hunter, writing for Evolution News, provides the following definition, “The term orphan refers to a DNA open reading frame, or ORF, without any known similar sequence in other species or lineages. Hence ORFan, or ‘orphan.’” The author of this article in Uncommon Descent explains orphan genes this way, “Orphan genes are presumed protein coding genes that exist in only one species and have such non-similarity to anything in any other species they are called orphans…”

Why is this troubling? If the theory of evolution and (by default) common ancestry are true, a coding gene that is species specific, with no recognizable counterpart in other species should be an extreme rarity. Ann Gauger writes in Orphan Genes: A Guide for the Perplexed, “The working assumption had been that, given common descent and the fact that most housekeeping genes are shared among living things, and the assumption hitherto that evolution occurs by incremental small changes, orphan genes…should be rare if not non-existent.”

So, just how common are they? This 2009 study published in Trends in Genetics found, “Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species.” According to Richard Buggs (writing for Ecology and Nature), researchers originally believed that the mystery of these orphan genes would be resolved over time as more genomes were sequenced, finding precursors for the sequences that are now categorized as orphans. However, the opposite has proven true.

For example, Dr. Jeffrey Tompkins discusses ants, “When comparing the ant genes to other insects, researchers discovered 28,581 genes that were unique only to ants and not found in other insects. While the various ant species shared many groups of genes, only 64 genes were common to all seven ant species…The researchers concluded that on average, each ant species contained 1,715 unique genes—orphan genes.”

In Buggs’ 2017 ash tree genome paper published in Nature, he and his colleagues report that of the over 38,000 protein-coding genes found, “…one quarter (9,604) were unique to ash. On the basis of our research so far, I cannot suggest shared evolutionary ancestry for these genes with those in ten other plants we compared ash to: coffee, grape, loblolly pine, monkey flower, poplar, tomato, Amborella, Arabidopsis, barrel medic, and bladderwort. This is despite the fact that monkey flower and bladderwort are in the same taxonomic order (Lamiales) as ash.”

Not only are orphan genes common, they also appear to be functional. Dr.Tompkins writes, “These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature’s interaction with its environment. The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms).”


Orphan genes are certainly a fly in the ointment for evolutionary theory, but no surprise to either creation science or intelligent design. As Gauger points out, “ Then there is the elephant in the room that evolutionary biologists don’t want to acknowledge. Perhaps we see so many species- and clade-specific orphan genes because they are uniquely designed for species- and clade-specific functions. Certainly, this runs contrary to the expectation of common descent.”

In Part 2 of this series, we’ll take a look at how evolutionary biology responds to orphan genes.

Did the Human Genome Project Confirm Evolution?

Have you been told that evolution is an undeniable fact? That our very own DNA is the confirmation? That human DNA is 98% identical to chimpanzee DNA which proves that chimpanzees are the “missing link?” That, in light of these “facts” a literal interpretation of the Genesis creation account is naive? Secular science would have you believe that evolution is not just a theory, but fact- that studies on genetics and DNA (based on the human genome project) have “debunked” the Biblical narrative. Making Bible believers feel like backwards, uneducated, dummies for taking the word of God literally is in fact, the favorite age old tactic that secular science employs to make us question our faith and plant little seeds of doubt that undermine the reliability of the Bible. This is the favorite tactic because it works so fabulously.  So, we tend to accept all scientific “proof” as fact and work furiously to compromise the Bible to “make it fit” current scientific claims.

Carefully selected and isolated findings of the human genome project such as the similarities between human and chimpanzee DNA are often touted as the nail in the coffin of literal Biblical creation as well as the “undeniable” evidence of evolution. This is huge for evolutionists because of the disconcerting lack of transitional fossils in the fossil record- as in not even one that hasn’t been outed as a hoax. In actuality the human genome project raised more questions than it answered. But did the project really provide monumental evidence for evolution or just bring to light how little is actually known about our origins? Before we as Christians rush to compromise the very foundational account of creation in the Bible so as not to appear “foolish” in the eyes of the secular scientific community, maybe we should actually take a look at the evidence.

Ever since Watson and Crick won the Nobel Prize in physiology in 1962 for their discovery of the molecular structure of DNA, scientists have been comparing the DNA of animals and humans in an effort to “prove” the theory of evolution. When it was discovered that human and chimpanzee DNA are 98.5% identical, indeed the entire secular community did a victory dance. In 2000, scientists announced that they had deciphered the genetic code contained in the entire human genome! No doubt, the assumption was that this new information would strengthen the link between humans and chimps. Instead, in the years since all the results of the Human Genome Project were published, scientists have discovered that comparing the genetics of primates and humans is a lot more complicated than just “homologies” or similarities in DNA.

As it turns out, only about 1.5% of the human genome consists of genes. The rest consists of non-coding information sometimes referred to as “junk DNA”. Scientists are just now trying to figure out the function of this “junk DNA”. More on that in a moment. Bert Thompson and Brad Harrub note in their article for Apologetics Press, “These finding indicate that even if all of the human genes were different from those of a chimpanzee, the DNA still could be 98.5 percent similar if the ‘junk’ DNA of humans and chimpanzees were identical.”

For a little more perspective Thompson and Harrub quote Jonathan Marks (dept. of anthropology, UC Berkely) as he points out the problem with the line of thinking that revolves around DNA similarities, “Because DNA is a linear array of those four bases- A,G,C, and T- only four possibilities exist at any specific point in a DNA sequence. The laws of chance tell us that two random sequences from species that have no ancestry in common will match at about one in every four sites. Thus even two unrelated DNA sequences will be 25 percent identical, not 0 percent identical.” As Thompson and Harub put it, “Would it be correct, then, to state that daffodils are ‘one quarter human’?”

Need even more perspective? Thompson and Harrub write, “The entire genome of the tiny nematode (Caenorhabditis elegans) has also been sequenced as a tangential study to the human genome project. Of the 5,000 best-known human genes, 75% have matches in the worm. Does this mean that we are 75% identical to a nematode worm? Just because living creatures share some genes with humans does not mean there is a linear ancestry.”

Pictured above is a nematode- see any family resemblance? If you’re beginning to think it’s a little premature to toss out a literal interpretation of Genesis’ creation of man, I’m right there with you.

In light of the human genome project, it would seem that the key components to what make a human a human, and what make a chimp a chimp are far more different than what we have been led to believe. Thompson and Harrub explain just how large the seemingly minuscule 1-2% divergence between man and chimp actually is, “The truth is, if we consider the absolute amount of genetic material when comparing primates and humans, the 1-2% difference in DNA represents approximately 80 million different nucleotides (compared to the 3-4 billion nucleotides that make up the entire human genome).”

The human genome project has demonstrated that similar organs between species, are not all created from identical genetic code as one might assume. Instead, completely different genetic coding can and does produce similar organs. This fact is nothing short of devastating for evolutionists who are attempting to connect linear evolutionary dots based on similar characteristics between species. Biologist John Randall admits, “The older textbooks on evolution make much of the idea of homology, pointing out the obvious resemblances between the skeletons of the limbs of different animals…Now if these various structures were transmitted by the same gene couples, varied from time to time by mutations and acted upon by environmental selection, the theory would make good sense. Unfortunately, this is not the case. Homologous organs are now known to be produced by totally different gene complexes in the different species. The concept of homology in terms of similar genes handed on from a common ancestor has broken down.”

Now, imagine for a moment, the audacity of a group of people who declare the results of the human genome project to be undeniable evidence that the Biblical account of creation has been “debunked” when the very same project brought to light the fact that scientists DO NOT understand the function of a whopping majority (over 98%) of the human genome. These scientists actually referred to it as “junk DNA”. Now that scientists have had several years to look into the matter they are realizing that this “junk DNA” actually does have a purpose and that the body’s “building plans” are a lot more complicated than they originally thought. (Shocking, I know…)

Ewan Birney of European Bioinformatics Institute in Cambridge wrote an article for Scientific American entitled “Hidden Treasures in Junk DNA”. Birney writes, “I get this strong feeling that previously I was ignorant of my own ignorance, and now I understand my ignorance. It’s slightly depressing as you realize how ignorant you are. But this is progress. The first step in understanding these things is having a list of things that one has to understand, and that’s what we’ve got here.” Now that’s certainly a refreshing admission! And much closer to the reality than the idea that science “has it all figured out”.

According to the same article in Scientific American, Birney and his team of researchers (called the ENCODE project) have “produced a stunning inventory of previously hidden switches, signals, and sign posts embedded like runes throughout the entire length of human DNA.” It has been observed that anywhere from 9% all the way up to as much as 80% (well that’s quite the range- again confirmation that they’re still in the “who really knows” phase of research) of this “junk DNA” appears to serve a regulatory function in the gene.

Even more disturbing (for evolutionists) is that this regulatory DNA seems to follow completely different “evolutionary rules” than coding DNA. Apparently it “turns over much faster” than coding DNA- in other words, more rapid evolution. This should be interesting for them to work through since a hallmark of  evolution  is the billions of years required to effect change. When refuting evidence that man is merely 6,000-7,000 old instead of the accepted “requirement” of 200,000 years- one of evolution’s “go to” rebuttals is that the rate of mutation that would be required to achieve our current state of variation (varying racial characteristics, etc) in such a short period of time would “mutate us out of existence”. So yes, this explanation should be interesting to hear.

Is it just me, or did the revelations of the human genome project actually make the theory of evolution look even more ridiculous considering the exposed layers of unfathomable complexity revealed in DNA- the “Book of Life”? The human genome project is more like a neon flashing sign that reads “Creator Required”. Unless, that is,  you are an individual who refuses to even consider that possibility.