Orphan Genes Part 3: De Novo Gene Origination- What are the Odds?

In Part 1 of this series we discussed the discovery of orphan genes and in Part 2 we tracked evolutionist response: initial rejection of their possible existence transitioning into reluctant acceptance due to repeated undeniable confirmation. Since evolutionists operate under the assumption that evolution is true, this acceptance necessitated a response regarding proposed naturalistic methods for the origination of these genes which evolution requires to emerge “de novo” (or “from scratch”) into the genome. The plausibility of these propositions will be the focus of the final installment of this topic.

A Trip Down Memory Lane

It’s not as if the methods by which genetic diversity manifest in the genome had never been considered. The reluctance of evolutionary science to embrace the existence of orphan genes is completely understandable given the historical conclusions drawn regarding de novo gene origination. A giant in his field (Head of the Dept. of Cell Genetics at Institut Pasteur in 1960 and 1965 Nobel Prize in Physiology or Medicine winner), Francois Jacob, emphatically denounced de novo gene origination in his 1977 work Evolution and Tinkering:

Evolution does not produce novelties from scratch. It works on what already exists, either transforming a system to give it new functions or combining several systems to produce a more elaborate one.” He continued, “The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information.” (emphasis mine)

Francois Jacob (via Wikipedia)

A Second Look at the Junk Pile

Confronted with new facts, evolutionists turned to re-examine what they had previously considered a DNA garbage heap. The majority of DNA (99%) is non-coding, meaning that it doesn’t provide instructions for making proteins. As this NIH article explains:

Scientists once thought noncoding DNA was ‘junk,’ with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription).”

According to the same source, types of regulatory elements found in junk DNA include promoters, enhancers, silencers, and insulators. Since the revelation that this junk DNA is not actually useless is fairly recent, it’s not surprising that “the identity of regulatory elements and other functional regions of noncoding DNA is not completely understood.”

Proposed Models

How could this “junk” DNA give rise to de novo origination of genes? This McLysaght/Guerzoni study concludes:

We may thus imagine two scenarios: one where an arbitrary ORF appears in a locus of significant transcription (‘RNA first’) and one where a cryptic, arbitrary ORF experiences some low, perhaps sporadic, transcription (‘ORF first’).”

The authors go on to state, “Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.”

Of course, these conceptual models derive from what Dr. Kevin Anderson (writing for AIG) terms “historical reconstructions” which by their very nature “are only as good as the assumptions of the reconstruction.” In this case the assumption is evolution via mutation. No other possibility is considered.

Emily Singer writes in her article for Quanta, “The junk DNA must accumulate mutations that allow it to be read by the cell or converted into RNA, as well as regulatory components that signify when and where the gene should be active. And like a sentence, the gene must have a beginning and an end…In addition, the RNA or protein produced by the gene must be useful.”

What are the Odds?

Possibility is one thing. Plausibility is entirely another. On the likelihood of such a scenario occurring Singer notes, “…creating a gene from a random DNA sequence appears as likely as dumping a jar of Scrabble tiles onto the floor and expecting the letters to spell out a coherent sentence.”

If these are the odds of even one gene emerging de novo from junk DNA, what then must be the odds of such an event taking place over and over in every living species? Furthermore, trends indicate that scientists may merely have uncovered the tip of the iceberg when it comes to the number of de novo genes. Singer writes, “As scientists…are implementing new gene discovery technologies…the number of de novo genes might explode.”

More Problems…

Statistical improbability isn’t the only issue with de novo gene origination via mutation. Dr. Anderson writes, “If it takes at least seven mutations to transform a functional gene into a different gene, then it would require far more mutations to truly evolve a de novo gene…the more mutations required, the greater the potential that some will be harmful. Evolutionists recognize this issue as well. Joanna Masel, a University of Arizona biologist studying how evolution might avoid this pitfall, explains: “Proteins have a strong tendency to misfold and cause havoc. It’s hard to see how to get a new protein out of random sequence when you expect random sequences to cause so much trouble.”

Closely related to the issue of mutations is the amount of time it would take these mutations to result in the de novo emergence of a gene. Dr. Anderson writes, “…the time needed to transform a functional gene into a different gene bursts the evolutionary timescale. The de novo formation of new genes takes this problem to even greater magnitudes. Humans, for example, are supposed to have evolved from a primate ancestor in just 4–6 million years. Even by the most generous calculations, this is insufficient time for the de novo construction of the hundreds of human orphan genes.”

De novo gene origination is just one piece of the puzzle. Singer poses the next, equally confounding question: “how de novo genes get incorporated into the complex network of reactions that drive the cell.” And that’s not the only concern, “Evidence suggests that a portion of de novo genes quickly become essential. About 20 percent of new genes in fruit flies appear to be required for survival.” She continues, “It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it.”


Evolutionists routinely disparage creation science by labeling it pseudoscience and calling foul based on Biblical bias. However, the case of orphan genes is an excellent example of the hypocrisy of such a claim. Secular science operates under its own bias- faith in evolution. Dr. Anderson aptly describes the evolutionist view of de novo gene origination, “This conclusion is not based on observational data, but rather on evolutionary necessity. The presumption of evolution is so prevalent in biology that it trumps everything else, even if it means depending upon events with a ‘practically zero’ chance of occurring.”

While orphan genes are definitely a wrench in evolutionary theory, Dr. Anderson notes that orphan genes fit “within a biblical creation model, where humans, animals, plants were created with a fully functional genome. Since this initial creation, subsequent changes in the genome have introduced many mutations and other alterations to the DNA. Some of these have even provided a specific (and likely limited) adaptive benefit. Yet these benefits result from degenerative mutations, not the formation of new 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.