Orphan Genes Part 2: Evolutionists’ Response

In Part 1 of this series we discussed how the relatively recent technological advances in DNA sequencing led to some very unexpected findings. In particular, the discovery of the prolific existence of “orphan genes.” Given the evolutionary assumption of shared genes among all living things with changes occurring incrementally over vast eras of time, these mystery genes are a direct contradiction to any scenario predicted by evolutionary theory on a foundational level. Therefore, such evidence requires a very serious response. As we’ll see, the explanations evolutionists offer have certainly been revelatory, but not from a scientific standpoint. What has been revealed is a highly unscientific, faith-based commitment to the theory of evolution.

Nelson Velasco Debate

In the 2014 design vs evolution debate between Paul Nelson (Discovery Institute) and Joel Velasco (Texas Tech), the subject of orphan genes arose. Velasco’s 5 points are perfectly representative of the initial evolutionist response. Cornelius Hunter, writing for Evolution News, recounts Velasco’s arguments:

  1. “… there isn’t much to be concerned with here because ‘Every other puzzle we’ve ever encountered in the last 150 years has made us even more certain of a fact that we already knew, that we’re all related.’”
  2. …the whole orphan problem is contrived, as it is nothing more than a semantic misunderstanding — a confusion of terms…”
  3. … many of the orphans are so categorized merely because the search for similar sequence is done only in ‘very distantly related’ species.”
  4. …orphans are really nothing more than a gap in our knowledge… the more we know about a species, the more the orphan problem goes away. And which species do we know the most about? Ourselves of course…: ‘…How many orphan genes are in humans?… Zero.’”
  5. …while new orphans are discovered with each new genome that is decoded, the trend is slowing and is suggestive that in the long run relatives for these orphans will be found..”

As you can see, Velasco doesn’t offer a scientific explanation for the existence of orphan genes. Initially, evolutionists were very reluctant to even concede that they legitimately existed in numbers large enough to warrant discussion. Instead, he frames his case around faith that an explanation which fits evolutionary theory will arise. His answer is a catch all attempt to cover all the bases. Hunter sums up the inadequacy of Velasco’s view:

So to summarize Velasco’s position, the orphan problem will be solved so don’t worry about it, but actually orphans are not a problem at all but rather a semantic misunderstanding, but on the other hand the orphan problem is a consequence of incomplete genomic data, but actually on the other hand the problem is a consequence of insufficient knowledge about the species, and in any case even though the number of known orphans keeps on rising, they will eventually go away because the orphans as a percentage of the overall genomic data (which has been exploding exponentially) are going down.”

Velasco’s 4th Point

The one point listed that most resembles an actual argument is Velasco’s 4th. Is it true that the human genome, the one we know most about, doesn’t have any orphan genes?

The short answer is no.

A 2007 study by the Lander group did indeed reject thousands of proposed orphan genes that had been identified within the human genome, but not all. Authors of the study noted that not all proposed orphans were able to be rejected. In fact, this 2015 study “identified 634 human-specific genes” that appear to have arisen de novo in the human genome. Most telling, however, is why the Lander study rejected the majority of the orphans:

If the orphans represent valid human protein-coding genes, we would have to conclude that the vast majority of the orphans were born after the divergence from chimpanzee. Such a model would require a prodigious rate of gene birth in mammalian lineages and a ferocious rate of gene death erasing the huge number of genes born before the divergence from chimpanzee. We reject such a model as wholly implausible. We thus conclude that the vast majority of orphans are simply randomly occurring ORFs that do not represent protein-coding genes…” (emphasis mine)

On what grounds would such a model be considered “wholly implausible”? Apparently, because their existence cannot be plausibly explained within the constraints of evolutionary theory. Hunter notes the following:

This is what philosophers refer to as theory-ladenness…There was no scientific evidence that those human sequences, identified as orphans, were ‘spurious.’ The methods used in the Lander study were full of evolutionary assumptions. The results entirely hinged on evolution. Although the paper did not explicitly state this, without the assumption of evolution no such conclusions could have been made. Although the paper authoritatively concluded that the vast majority of the orphans in the human genome were spurious, this was not an empirical observation or inference…”

On Second Thought…

Over time evolutionists have been forced to accept that orphan genes do in fact exist in numbers great enough to require a revamping of long held beliefs regarding the formation of genes. In other words, the evolutionists’ explanation of the origin of genes had to… evolve.

Since a designed genome is not an option for evolutionists, an alternative explanation for the existence of these orphan genes had to be considered. In late 2014, Tautz D. published the following conclusion in his The discovery of de novo gene evolution:

Genes can evolve via duplication and divergence mechanisms, but also de novo out of non-coding intergenic sequences. This latter mechanism has only recently become fully appreciated, while the former mechanism was an almost exclusive dogma for quite some time. This essay explores the history of this development: why a view developed, with the alternative hardly being explored. Because of the prevailing view, an important aspect of the nature of genes and their evolutionary origin escaped our attention. Evidence is now rapidly accumulating that de novo evolution isa very active mechanism for generating novelty in the genome, and this will require anew look at how genes arise and become functional.” (emphasis mine)

With evolution assumed, Tautz concludes that new genes must be able to arise “from scratch” (“de novo”) from non coding sequences. He also makes three admissions: (1) they have only recently become forced to abandon (due to the discovery of the existence of these orphan genes) the exclusive evolutionary dogma that dominated genetic understanding; (2) this dogma caused a blindness with regard to their understanding of the nature and origin of genes; (3) they will have to figure out how these genes could exist.

As the 20th century evolutionist Theodosius Dobzhansky famously said, “Nothing in biology makes sense except in the light of evolution.” This is the bias mainstream science operates under. The theory of evolution is never questioned- it is an assumed foundational truth. Since orphan genes are now acknowledged to exist, evolutionists assume that there must be a naturalistic mechanism to explain new genes appearing from scratch in the genome.

What Next?

Evolutionists are left with the task of explaining a naturalistic mechanism by which these “de novo” genes come to exist. In Part 3, we’ll take a look at the plausibility of these proposed mechanisms.

Should Christians Consult Mediums?

Most Christians know that there are many topics on which varying Christian denominations disagree. Whether or not Christians should consult mediums, however, doesn’t happen to be one of them. The answer to this question is a unanimous and resounding NO!

Despite this fact, some believers may be confused because modern culture has muddied the water in this area. For starters, some mediums actually claim to be Christian. Some are just great, all around people- very likable, sincere, and with genuinely good intentions. Not to mention extremely popular- having their own TV shows, appearing on various talk shows, and writing bestsellers. Sure, some are fakes. But others certainly appear to be “the real deal” (and I would argue that some probably are)- exhibiting knowledge of things that would be impossible to know without some type of communication with the spiritual realm. These may boast impressive testimonials from satisfied customers. Is consulting someone who fits this description really that bad?

Before we delve into the Scriptural answer to our question, which is truly the only one a Christian should seek, I believe it’s important to consider what might lead someone to turn to a medium. Generally speaking, a believer would not look to a medium for personal guidance. However, grief and loss are often powerful motivators. The loss of a loved one- maybe suddenly/unexpectedly, a child or a parent, or someone with whom one had unfinished business or a situation with a lack of closure may cause someone to consider options they normally wouldn’t. Under these circumstances, the desire to communicate with a loved one who has passed on would understandably be overwhelming. For this reason, it is imperative to approach this topic with love and empathy, yet without failing to be clear that Scripture leaves no ambiguity.

What Does the Bible Say?

Scripture roundly condemns consulting mediums, which is always categorized with occultic practices, throughout both the Old and New Testaments:

Old Testament:

Leviticus 19:31– “Do not turn to mediums or necromancers; do not seek them out, and so make yourselves unclean by them: I am the Lord your God.”

Leviticus 20:6– “If a person turns to mediums and necromancers, whoring after them, I will set my face against that person and will cut him off from among his people.”

– In this passage, turning to mediums is likened to spiritual adultery.

Leviticus 20:27– “A man or a woman who is a medium or a necromancer shall surely be put to death. They shall be stoned with stones; their blood shall be upon them.”

– In the Old Testament, people who practiced these things received capital punishment.

Deuteronomy 18:9-14– “9 When you come into the land that the Lord your God is giving you, you shall not learn to follow the abominable practices of those nations. 10 There shall not be found among you anyone who burns his son or his daughter as an offering, anyone who practices divination or tells fortunes or interprets omens, or a sorcerer 11 or a charmer or a medium or a necromancer or one who inquires of the dead, 12 for whoever does these things is an abomination to the Lord. And because of these abominations the Lord your God is driving them out before you. 13 You shall be blameless before the Lord your God, 14 for these nations, which you are about to dispossess, listen to fortune-tellers and to diviners. But as for you, the Lord your God has not allowed you to do this.”

    • This passage explicitly condemns these practices, they are considered an abomination. In fact, God says that it is one of the reasons He is giving the Israelites the land that these people had been living in.

1 Chronicles 10:13-14– “13 So Saul died for his breach of faith. He broke faith with the Lord in that he did not keep the command of the Lord, and also consulted a medium, seeking guidance. 14 He did not seek guidance from the Lord. Therefore the Lord put him to death and turned the kingdom over to David the son of Jesse.”

    • This passage is referring to the incident with Saul and the Witch of Endor recorded in 1 Samuel 28:3-19. Whether or not this medium was truly able to summon Samuel is debated, but with respect to our topic, whether or not she did doesn’t really matter. It should be noted, that Scripture indicates that the Witch of Endor seemed surprised that she had succeeded in raising Samuel. What we do know, is that whether the medium raised Samuel or a demon, he (or it) spoke the truth in predicting Saul’s future. Neither the witch’s ability to raise Samuel, nor the accuracy of the report made it any less of an abominable act that God has forbidden us to engage in. In other words: even if you can, it doesn’t mean you should.

New Testament:

Acts 16:16-18– “16 As we were going to the place of prayer, we were met by a slave girl who had a spirit of divination and brought her owners much gain by fortune-telling. 17 She followed Paul and us, crying out, ‘These men are servants of the Most High God, who proclaim to you the way of salvation.’ 18 And this she kept doing for many days. Paul, having become greatly annoyed, turned and said to the spirit, ‘I command you in the name of Jesus Christ to come out of her.’ And it came out that very hour.”

    • In this passage, Luke is recounting Paul’s response to a young slave girl who is a medium. Apparently a very successful one since she is very profitable to her owners. However, Paul recognizes the source of her abilities as demonic possession. After casting the demon out, the slave girl is no longer able to perform. Note that even this demon recognized that Paul and the disciples were God’s servants and that they were proclaiming the the true path of salvation. Paul was subsequently jailed for casting this demon out due to fact that the owners of the slave girl lost a source of income when she lost her abilities.

Paul casting the demon out of the slave girl- from a 14th century miniature

Acts 19:18-20– “18 Also many of those who were now believers came, confessing and divulging their practices. 19 And a number of those who had practiced magic arts brought their books together and burned them in the sight of all. And they counted the value of them and found it came to fifty thousand pieces of silver. 20 So the word of the Lord continued to increase and prevail mightily.”

    • This passage records the response of some mediums/sorcerers who turned to Christ as a result of Paul’s evangelism in Ephesus. After their conversion, they did not continue their activities. John Piper writes, “If we turn to the New Testament we find nothing to change this divine rejection of the occult. On the contrary the rejection is confirmed… When the word of Christ captures a person’s mind and heart, all involvement with magical arts goes. It is Jesus versus the occult; you cannot have both.”

Galatians 5:19-21– “19 Now the works of the flesh are evident: sexual immorality, impurity, sensuality, 20 idolatry, sorcery, enmity, strife, jealousy, fits of anger, rivalries, dissensions, divisions, 21 envy, drunkenness, orgies, and things like these. I warn you, as I warned you before, that those who do such things will not inherit the kingdom of God.”

    • In the latter part of this chapter Paul is teaching believers how we can recognize each other. In verses 19-21 he gives a list of practices that people will not engage in when they are being led by the Holy Spirit. Sorcery is included in this list. Verses 22-24 go on to list actions that constitute the “fruit of the Spirit,” or behaviors that do characterize believers who are being led by the Holy Spirit.

Revelation 21:8– “But as for the cowardly, the faithless, the detestable, as for murderers, the sexually immoral, sorcerers, idolaters, and all liars, their portion will be in the lake that burns with fire and sulfur, which is the second death.”

    • Yet again, sorcery (which is used synonymously with psychics/mediums, etc) is categorized with evil.

Scripture is abundantly clear that any connection with the occult is forbidden. As we noted above, Moses provides the definition of occultic practice as any of the following: child sacrifice; individuals (sorcerers/charmers/mediums/necromancers) who practice divination, fortune-telling, interpreting of omens, or communication with the dead (Deuteronomy 18:9-14 above). 

It’s obvious to see why some of these practices are forbidden, but what about the ones that seem innocent? Some people who have been able to communicate or receive messages (or at least believe that they have) from the deceased feel great comfort and relief to hear that their loved one is at peace. Why would God be opposed to this?

It’s Clear God is Opposed to Any Involvement with the Occult, No Matter How Small- But Why?

In John Piper’s article Jesus Vs. the Occult, he lists two major reasons:

The first, is that it “belittles God and exalts man.” Piper writes, “All forms of the occult present us with a similar temptation: will we act like humble children of the heavenly Father and submit to God’s wisdom in limiting our knowledge and power, or will we, like Adam and Eve, hanker for the fruit that can make us ‘wise’ and for the power that belongs to God? Will we belittle God and exalt ourselves, or will we humble ourselves and exalt God by being content with his revelation and his use of power on our behalf?” He continues “Consulting mediums, tea leaves, fortune cookies, horoscopes, crystal balls, palmists, or any other oracles beyond God’s Word is wrong because it belittles God as an inadequate revealer of mysteries. It says that God is either unable or unwilling to tell me all that is good for me to know. Therefore, he lacks the power or the goodness to help me, and so I will take matters into my own hands. Therefore, people who really love God and trust his goodness and depend on his sovereign power shun all practices of the occult.”

Second, turning to the occult in any way is considered “spiritual harlotry.” Drawing off of the Leviticus 20:6 description, Piper further develops his point using the New Testament illustration of Jesus’ relationship to the Church, “Consulting mediums is like committing adultery against God. Jesus Christ is the husband of the church. He is God’s fullest revelation. All that we need to know and all the power which it is good for us to have comes through him and his Word. When we go after other secret oracles and psychic powers, we say in effect that our husband is unsatisfactory and we must seek for lovers elsewhere.”

Believers who desire to communicate with a loved one who has passed on are struggling with intense grief. A medium claiming that he/she can facilitate a connection between the living and the dead can be a very difficult opportunity to reject. However, hearing that God views such endeavors as a rejection of His sufficiency and sovereignty is necessary.

We know that God rejects these practices and why, but who are these people who have these abilities? Not all mediums/psychics believe that their powers come from evil sources. As a matter of fact, many claim to embrace Jesus.

The Vast Majority of Mediums are Part of the New Age Movement

Many Christians may have no idea what the New Age Movement is and therefore may be intrigued to hear an individual who associates themselves with occultic activity (whether they recognize it as occultic or not) speak positively of Jesus. However, a New Ager’s understanding of Jesus and a Christian’s understanding of Jesus are not compatible. Former New Ager Steven Bancarz, explains:

For most people in the New Age movement, the view of Jesus is watered down. Bible verses are cherry-picked from to fashion a politically correct Christ who embraces all faiths. Jesus is not the exclusive Son of God and only means of salvation, but just another ‘prophet’ and ‘teacher’ here to show us a universal path to enlightenment. Sin means nothing, the cross means nothing, and the death and resurrection of Jesus ultimately means nothing.”

Abby Wynne, a self-titled “Shamanic Psychotherapist” and “Energy Healer,” describes Jesus’ relationship to her “source energy”:

Christ Consciousness is a vibration of Source Energy that lives within us all, no matter what our creed or culture or ancestry. (Source Energy can also be called Chi, Prana, Reiki, or Divine Consciousness, it’s a Soul Energy.) Jesus Christ was the epitome of Christ Consciousness. I believe he was a man who lived on Earth at a specific time, and did some amazing things, and had many stories written about him. His Soul Essence vibrated at the frequency of Christ Consciousness, and it’s the first time anyone really wrote about it, so that’s where the name came from. However, many others also lived on Earth at other times, both before Jesus and after him, also embodying the same vibration. Humanity presently is waking up to the realisation that we all can vibrate at the frequency of Christ. To me, this is a resurrection of Christ Consciousness…This energy, however, has nothing to do with religion, and it can be very difficult for people to separate Jesus from Christianity.”

On God she writes:

“I am saying this now – I pray to God and I feel God in me. And that has made me feel more fulfilled than anything else that I have experienced in my life. Once you start the path of Energy Healing, you open to Source Energy, and as the energy flows through you you become more clear, and the energy raises it’s vibration and so do you. And when your vibration is high, you feel that connection to pure Source, to the Universe, to Great Spirit, or to God – it’s all the same thing. Let’s call it like it is. And then you remember who you are, that you are God and God is you, that we are all one at the energetic level. And it’s blissful.”

These two quotes should provide ample reason for believers to reject any inclination to allow these individuals to provide us with special revelation or communication with the dead no matter how tempting the prospect may be. As Christians, we know that anyone who rejects Jesus as fully God and fully man- the only path to salvation- does not have the indwelling of the Holy Spirit. Whatever she is describing that she feels, no matter how wholesome and good she believes it is, is not the Holy Spirit. If she feels an indwelling of a spirit (and I don’t doubt for a second that she does), and that spirit is certainly not the Holy Spirit, then there is only one option left.

Some may scoff at the idea that someone who seems to be a genuinely good person, does good things, and helps people could possibly be indwelt by a demonic spirit. Demons can’t do good things, right? However, this logic is flawed. Satan’s primary goal is to turn people away from God- to lead as many people as possible to reject Him. He is a deceiver and a tempter. Scripture tells us that when we rely on a medium instead of on God, we are indeed rejecting Him. The error is in assuming that Satan doesn’t use methods that appear good and enticing to ensnare us. 2 Corinthians 11:14 warns us, “And no wonder, for Satan himself masquerades as an angel of light.”

With this verse in mind, consider the following description of how mediums describe what they experience when communicating with the dead:

…through the practice of Eastern meditation. This mildly altered state of consciousness enables the channeler to psychically perceive spirit messages. These manifest themselves as a ‘thought voice,’ which is perceived in the stillness of the medium’s mind. Experienced mediums can enter into a trance state whereby the spirit entity takes direct control over the medium’s voice, speaking through it in an accent quite distinct from the medium’s normal mode of speech. It is claimed that the telepathic communications come from highly evolved spirit beings existing in the normally invisible realms of the spirit dimension. Sometimes the medium will have a vision in which he or she sees the spirit in a visible form, manifested in the imagination faculties of the medium’s consciousness. The spirit guides are said to sometimes wear white robes and often radiate brilliant, golden-white light.”

Good feelings, “spirit guides,” “white robes,” and radiating “brilliant, golden-white light” are no assurance that one is not in contact with, or being taken control over by, a demonic spirit. This fact should be terrifying to a believer.

What About Mediums Who Claim to be Christian?

Most (not all) mediums who claim to be “Christian” are using the term quite loosely and most indicate that they are Catholic. One well known example due to her reality show on TLC is Theresa Caputo, also known as “The Long Island Medium.”

The Official Catholic Position

To be perfectly clear, the Catholic Church categorically renounces mediums and psychics according to their Catechism 2116 and 2117:

2116: “All forms of divination are to be rejected: recourse to Satan or demons, conjuring up the dead or other practices falsely supposed to “unveil” the future.48 Consulting horoscopes, astrology, palm reading, interpretation of omens and lots, the phenomena of clairvoyance, and recourse to mediums all conceal a desire for power over time, history, and, in the last analysis, other human beings, as well as a wish to conciliate hidden powers. They contradict the honor, respect, and loving fear that we owe to God alone.

2117: All practices of magic or sorcery, by which one attempts to tame occult powers, so as to place them at one’s service and have a supernatural power over others – even if this were for the sake of restoring their health – are gravely contrary to the virtue of religion. These practices are even more to be condemned when accompanied by the intention of harming someone, or when they have recourse to the intervention of demons. Wearing charms is also reprehensible. Spiritism often implies divination or magical practices; the Church for her part warns the faithful against it. Recourse to so-called traditional cures does not justify either the invocation of evil powers or the exploitation of another’s credulity.”

A Catholic website devoted to “Mystics of the Church” which otherwise embraces communication with the dead also renounces Caputo. Not on the grounds that her communication with the dead is not authentic, but instead focusing on two other elements:

It all boils down to the action of invoking or calling upon the dead (or ‘spirit’ as she often calls it). When a person, referred to by Theresa as a ‘client’ comes to her for a session, and Theresa then actively seeks a message for them from their loved one(s)–then this may very well be crossing the line into the grave sin of necromancy because for her part Theresa is then actively seeking to channel the spirits of the dead, and this is what is specifically condemned by God in the Old Testament and in the Catechism of the Catholic Church, as stated above. And what causes even further concern is that Theresa charges money from the person(s) involved for these hour long channeling sessions. If a person receives a gift or charism from God, the gift should be given to others freely, without charge…

Another popular medium, Susanne Wilson, says that she goes to a “traditional mainstream church” and describes herself as “spiritual AND religious.” In her article, Is it okay for religious people or people who go to church to use a Medium or Psychic, she attempts to frame a Scriptural case supporting fortune telling and speaking with the dead. Her arguments amount to these three points:

First, she appeals to 1 Corinthians 12:4-11 claiming that her abilities (communicating with the dead, etc) are gifts of the Spirit. The passage reads as follows:

4 Now there are varieties of gifts, but the same Spirit; 5 and there are varieties of service, but the same Lord; 6 and there are varieties of activities, but it is the same God who empowers them all in everyone. 7 To each is given the manifestation of the Spirit for the common good. 8 For to one is given through the Spirit the utterance of wisdom, and to another the utterance of knowledge according to the same Spirit, 9 to another faith by the same Spirit, to another gifts of healing by the one Spirit, 10 to another the working of miracles, to another prophecy, to another the ability to distinguish between spirits, to another various kinds of tongues, to another the interpretation of tongues. 11 All these are empowered by one and the same Spirit, who apportions to each one individually as he wills.”

Given the abundance of passages in direct opposition to her interpretation of the passage above there is absolutely no logical basis on which to identify any of the gifts listed above as including fortune telling or communication with the dead. In order for this argument to be true, one would have to toss all Scripture which asserts the opposite out as invalid.

Second, she asserts that Jesus’ teachings do not advocate the belief that the dead cannot communicate with us. This is essentially a moot point. What happens directly after death a highly debated topic, but even if one could prove that communication is possible, it would not prove that the Jesus condones it.

Finally, she appeals to the old “Jesus didn’t specifically say we couldn’t” schtik. This is always a poor argument. Jesus didn’t explicitly mention several things that Christianity unanimously recognizes as sin: homosexuality, bestiality, pedophilia, etc. The rest of Scripture, all of which is Divinely inspired, unequivocally condemns those who practice these activities as well as those who seek them out.


Desperate times may leave some Christians vulnerable to the influence of those who say they have access to hidden knowledge and offer comfort in contact with those we miss dearly. Especially if the believer in question isn’t very familiar with what Scripture teaches on the subject. Likely, the idea that the act of consulting a medium is tantamount to telling God that you will not accept the fact that He doesn’t allow you to communicate with a loved one after death- even if it is possible and even if it would be comforting- hasn’t even crossed your mind. Less still the fact that what you are doing is the equivalent of having an affair. This is why believers should always be ready to help our brothers and sisters in Christ by speaking the truth in love.

Piper writes, “This is the victory that overcomes the world, our faith. Over against all the allurements of the occult stands Jesus Christ, the embodiment of all God’s revelation. Faith takes its stand on the sufficiency of this revelation and seeks no other secret knowledge. Faith lays itself open to the power of God through Jesus Christ alone and seeks no other psychic or spiritual power. Faith cleaves to Jesus, loves Jesus, adores Jesus, trusts Jesus, extols the all-sufficiency of Jesus, and shuns, in all her many garments, the temptress of the occult.”

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.