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Signature in the Pseudogenes, Part 2

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May 17, 2010 Tags: Genetics
Signature in the Pseudogenes, Part 2


As we indicated in Part 1 of this series, pseudogenes are remnants of once-functional genes. Since they are segments of a DNA molecule, they are faithfully copied and passed along generation after generation through the millennia of time. For this reason, they serve as excellent markers. They allow us to trace ancestry.

Consider, for example, the lineage shown in the diagram at right. In this example, Species A and B diverged from a single ancestor (red) fairly recently. Since there has been little time for them to evolve, the species are similar to each other.

Species A, B, C are also derived from a common ancestor (blue). That ancestor lived much longer ago, so the three species have had more time to diverge. Thus they may look quite different from each other. Finally, a very long time ago, there lived an even more ancient ancestor (yellow). This one gave rise to all four of these species. Having had lots of time to evolve, this ancestor’s descendents have become increasingly different from one another.

With regard to pseudogenes, the theory of common descent makes a prediction. Let’s say that in sequencing a genome, one finds a specific pseudogene (we’ll call it ‘y’) in Species A, but it is not found in Species B (see below).

If the theory of common descent is true:

  1. The event which gave rise to pseudogene ‘y’ occurred recently. It could not have been present in the common ancestor highlighted in red in the diagram to the left; otherwise both Species A and B would have had it.
  2. Since the Species A/Species B common ancestor didn’t have the pseudogene, earlier ancestors could not have had it either.
  3. Species C and D, because they are derived from those earlier ancestors, would not have pseudogene ‘y’ either.

With the sequencing of many genomes, it is now a straightforward matter to test this hypothesis. This can be done not by examining one or two genes, but by examining hundreds, even thousands. Do all pseudogenes fit into this sort of pattern? We will examine this question by considering one particular subset.

Our sense of smell is made possible through a set of proteins, the olfactory receptors, found on the surface of cells lining the nasal cavity. Airborne compounds bind to these receptors, thereby sending signals to the brain, which then interprets the pattern of binding as a particular odor.

Recently it has become apparent that many mammals have lost some of their olfactory receptor proteins through mutation of the genes which produce them: the mutated genes have been converted into non-functional pseudogenes. It is possible to compare the distribution of numerous olfactory receptor pseudogenes in several primate species.

Let’s first consider 15 pseudogenes1 present in humans but not in chimpanzees. According to the theory of common descent, these 15 pseudogenes have arisen since humans and chimps last had a common ancestor about six million years ago. If this is so, we would predict that none of the 15 pseudogenes will be present in primates believed to have diverged even earlier. As illustrated at right, this is exactly what we find when examining gorilla and orangutan genomes.

What about other olfactory pseudogenes? Do they follow the same sort of pattern? Are they in the “correct” places? Indeed they are – every one:

Six pseudogenes with identical inactivating mutations are found in all four species. Humans and chimpanzees share twelve identical pseudogenes (6 plus 3 plus 3) in common, but humans and gorillas share only nine (6 plus 3). These nine, as predicted, are a subset of the twelve shared by humans and chimpanzees.

Using pseudogene evidence alone, in the absence of any other line of evidence (gene homology, shared synteny, anatomy, etc), it would assemble these species into the same pattern of relatedness as any of the others. Indeed for the 47 pseudogenes studied, not one is out of place. We can tell when in the ancestry each arose relative to the others, and no cases exist where the same pseudogene appears in a manner inconsistent with the proposed lineage. Also recall that this is only 47 pseudogenes within a single family of genes: many, many more have been analyzed and they give parallel results.

As compelling as this pattern is, pseudogene data can also be extended to much more distantly-related species. All mammals, for instance, are predicted to be the evolutionary descendents of egg-laying ancestors. Indeed, the fossil record contains species classified as “mammal-like reptiles” as well as “reptile-like mammals” that blur the distinction between these groups. The evolutionary prediction that mammals are descended from egg-laying ancestors was tested recently using the hypothesis of shared synteny to look for the inactivated remains of a gene devoted to egg-yolk production in the human genome. This gene, called the vitellogenin gene, is used as a component of egg yolk in a wide array of egg-laying species. This research group wondered if it would be possible to find the remains of the vitellogenin gene in the human genome. To help in their search, they employed the prediction of shared synteny.

You may recall from our previous post on synteny that over time, blocks of genes in diverging species are increasingly “broken up” into smaller and smaller blocks. Very closely linked genes, however, can stay together for a very, very long time. Using this knowledge, the researchers:

  1. Located the (functional) vitellogenin gene in the chicken genome,
  2. Took note of the gene “next door” to the vitellogenin gene in the chicken,
  3. Looked to see if this neighboring gene was present in the human genome (it was – a functional version of this gene is found in humans),
  4. Looked in the same relative spot next door to this gene in the human genome, and
  5. Discovered the mutated remains of the vitellogenin gene in the human genome in precisely this location.

While it might be possible to present a (strained) argument for the presence of olfactory receptor pseudogenes in humans, the mere presence of the mutated remains of a gene required for making egg yolk in the human genome should give even the most ardent anti-evolutionist pause. That this gene was found using the prediction of shared synteny between humans and chicken only adds to the impact.

Common ancestry is an elegant, parsimonious explanation for the pattern of pseudogenes that we observe, yet many Christians reject common ancestry for theological reasons. The challenges for a non-evolutionary explanation of this data, however, are many:

  1. Why do humans (or any species for that matter) have so many inactivated genes?
  2. Why does the distribution of these inactivated genes match precisely the pattern of relatedness (phylogenies) predicted by other, independent criteria? Why are there no “out-of-place” pseudogenes?
  3. Why are pseudogenes found in the precise locations predicted by shared synteny?
  4. Why are some of these inactivated genes dedicated to functions that make no sense for the species that harbors them (e.g. defective genes for egg-yolk production in placental mammals like humans)?

To be blunt, if this pattern is not to be accepted, why did God put it in place for us to discover? And if this pattern is not to be trusted, how can anything in genetics be certain? As a colleague once commented, this pattern “would deceive all honest investigators” if in fact it is not accurate.

Many believers are troubled by the idea of humans sharing ancestry with other forms of life (and its attendant theological issues). Consider the opposite, however: suppose that common ancestry is in fact incorrect. The trouble is this: the data doesn’t go away. In this case, one still has to explain why the data looks the way it does: why did God choose to create independent species with this pattern? Even among anti-evolutionists there is no satisfying answer to this question. Time and again, what we see from Christian anti-evolutionary organizations is not an attempt to wrestle with the data, but rather to obfuscate it.

These lines of evidence are becoming more and more widely known among believers and non-believers. If Christians continue to insist on denying the implications of this (very solid) science, we greatly risk setting a stumbling block before our brothers and sisters in Christ, or bringing the faith into disrepute with those whom we seek to reach with the Good News.


1. Of course, there is always a possibility that the same gene may acquire a mutation and become a pseudogene independently in other species. In this case, the inactivating mutations in the two species will be different, and they will be classified as “species-specific” events. It is also possible that species-specific mutations can obscure previously shared mutations (for example, the complete deletion of a previously-mutated pseudogene).


Brawand, D., Wali, W. and Kaessmann H. 2006. Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation. PLoS Biology 6: 0507-0517. Available free here

Gilad, YG., Man, O., Paabo, S., and Lancet, D. 2003. Human specific loss of olfactory receptor genes. Proc. Natl. Acad. Sci. 100: 3324-3327. Available free here

Zhang, ZD, Cayting, P., Weinstock, G. and Gerstein, M. 2008. Analysis of of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Mol. Biol. Evol. 25: 131-143. Available free here


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Joe - #14151

May 19th 2010

On the subject of RTB I’m wondering what happened to the Biologos/RTB dialogue? In the comments section of the population size article Darrel wrote “We have told RTB that their thinking on this (and many other statements related to macro-evolution in general) does not in any way square with the science.” If this is true, then why have RTB’s recent writings on those topics not improved since this discussion? Dennis’s commentary on their podcast seems to be indicating they haven’t. Do they not care about accurately reporting the data or are they just incompetent? Which is worse?

Chris Massey - #14153

May 19th 2010


RTB’s approach is unlikely to improve. The problem is that RTB has a prior commitment to the notion that humans were specially created. They have ruled out the possibility of humans sharing common ancestry with other animals on theological grounds. So, unfortunately, when it comes to the science of common descent, they behave like YECers. They have no option but to look for some way to try to poke holes in the science rather than assessing it fairly.

But if you watch their videos on the issue of human evolution, one might also draw the “incompetent” conclusion.

Dennis Venema - #14155

May 19th 2010

What I find interesting about RTB is that their “clientele” are folks who accept some measure of scientific evidence (about the age of the cosmos, for example). So, in principle, their base can be appealed to on scientific grounds. This forces RTB to attempt to discredit common ancestry, population size data, etc based on (at least) an appearance of scientific merit (they can’t simply say that their theology precludes certain conclusions, like some YECs do).

Of course, when (if) their followers dig into the evidence…

I’d be curious to hear from commenters who were (once) followers of RTB but now accept common ancestry. What was the evidence that persuaded you?

Peter - #14158

May 19th 2010

Dennis, it seems to me that RTB’s theological objections to evolution are every bit as strong as AIG and ICR’s objections to an old earth. A while back I came across their resident theologian/philosopher Ken Samples’s discussions and writings on theistic evolution; he was less than complementary about it. Hugh Ross runs the show and clearly has no time for theistic evolution.

In many ways it’s quite a shame as RTB has done some excellent work in documenting the case for an ancient universe. Of late this article has been of particular use when discussing with YECs - http://www.reasons.org/special-edition-tnrtb-astronomers-assess-age-universe

It really documents how YEC arguments don’t stand up to scientific scrutiny and rely largely on pointing to unexplained gaps and anomalies.

Chris Massey - #14165

May 19th 2010


I sort of fall into that camp. I was born and bred a YEC. Then several years ago I came across some writings by Hugh Ross. I was impressed by his presentation of the evidence for an old earth. I had to admit that it appeared compelling. But I also felt safe because Ross offered a theory by which the days of creation could be reconciled with the 6 days of Genesis. Plus he believed that mankind were specially created. I was excited at the possibility of being able to accept the legitimacy of science (when it came to the big bang and the age of the earth at least) while still holding to the narrative of Scripture and the uniqueness of humanity.

In many ways I owe Mr. Ross a huge debt of gratitude. As a YEC, one grows up with a fear of science (although one doesn’t recognize it as fear). Ross helped me let my guard down and actually start listening to what scientists were saying. Of course it wasn’t long before I realized that Ross was holding out on me…that the evidence for evolution was equally overwhelming.


Chris Massey - #14166

May 19th 2010


I would say that the critical turning points were reading Kenneth Miller’s and Francis Collins’ books. And it was DNA that sealed the deal. One could explain the similarities between us and chimps based on common design. But common design couldn’t account for the fused chromosome 2, the common pseudogenes, common ERVs, etc. That’s why I think your area of study is so crucial to this debate. Our history is written inside every one of our cells.

Michael Thompson - #14183

May 20th 2010


I was wondering, does it really have to be one or the other?
I mean, I believe I am created by God, but i don’t feel I need to deny the biological processes that formed my body in nine months.
Can’t it be the same with mankind, can’t Ibelieve we are created by God by faith, without having to deny our biological history however long it has played out, as the evidence comes in?
If that is a bad analogy, please feel free to correct me! thanks!

Chris Massey - #14189

May 20th 2010


I agree with what you’re saying. Humans were indeed created by God. I used the term “special creation” because it is something of a term of art in the creation/evolution debate. “Special creation” is a doctrine that holds that humans (and usually all other “kinds”) were created by God suddenly without any biological history.

Karl A - #14192

May 20th 2010

On Denis Alexander’s recent post, Gingoro posted a question about the development of the eye, namely how much of that hypothesized pathway has been well explained by evolutionary biology.  In other posts, Rich has asked similar questions, basically asking “Where’s the beef?” with naturalistic evolutionary theory.  If they have been satisfactorily answered I (and they) have missed it.

I won’t repeat those questions here, but I do want to ask Dennis or Darrel about the role of genetics in potentially answering these questions.  It would seem, down the road a decade or six, genetics should be able to tell us in fairly fine detail, what the genome of the “common ancestor to A, B, C and D” looked like, and what functions those genes held.  Could one even dream that genetics could tell us things like what that ancestor looked like, what habits it had and what habitats it preferred?  Heck, geneticists already tell us that some Neanderthals had red hair!


Karl A - #14193

May 20th 2010

However, I presume that the genome of every single generation of, say, human ancestors, will not be reconstructible from the genetic record - it couldn’t be that detailed, could it?  There also may be issues of “noise” in the record, or sample limitations, I don’t know.  I’m guessing there will be considerable gaps as the ancestral paths of extant species are reconstructed.

How much can we reasonably expect specifically from genetics in the area of answering Gingoro’s and Rich’s questions?

Janet - #14194

May 20th 2010

Thanks to everyone who responded to my questions.  Your comments have all been very helpful.

In response to Dennis, I wouldn’t say that I was ever a follower of RTB, but one of Hugh Ross’s books was instrumental in my turning from the YEC understanding of my youth to an old-earth position.  My journey toward acceptance for common descent began when I attended a creation/evolution debate at my university.  I came away with a strong feeling that, while the creationist was a much more polished presenter and debater, the evolutionist had much better, more persuasive data.  I still wasn’t convinced, but was becoming more open to the idea.  Then a few years later I ran across a book by Alistair McGrath, which led me to Faith of a Physicist by John Polkinghorne.  I wasn’t totally comfortable with Polkinghorne’s theology but was impressed with his ideas, and for a few years I read everything of his I could get my hands on.  And then the DNA evidence, which I really saw for the first time in Collins’ book, sealed the deal, as Chris said.

Janet - #14198

May 20th 2010


So now I’m trying to find a position in between ID and EC.  One of my hang-ups is how to think of God’s interaction with the world in the context of the evolutionary process.  Sometimes full-blown EC seems to present a fairly hands-off, deistic type of God.  I know that’s not what the BioLogos team believes, but I think that’s an area that could be fleshed out more.  But that’s getting off-topic…

BTW, Michael, I like your analogy and think it’s helpful.

Karl A - #14202

May 20th 2010

I should add that addressing my questions above would IMO make a great topic for a future post, albeit more speculative than your posts to date.  If you wanted to do that rather than a more off-the-cuff answer now I would be plenty satisfied!

Scanman - #14386

May 21st 2010

Chiming in on the ID comments above…

As a Theistic Evolutionist…it is immediately implied that we are also ID’ers.

God directed evolution…(which implies some sort of supernatural interference/influence on environmental pressures) is Intelligent Design.

I see no reason that supporters of Biologos should take any issue with Intelligent Design…only maybe with the intolerance of many ID proponents (which include those of the YEC camp).


Dan Baright - #15775

June 1st 2010

E. O. Wilson once reported estimates of extant species range from 10 to 100 million.  The number of ancient common ancestors “predicted” by Evolution must be huge!  And yet, to my knowledge, not even one has ever been identified nontrivially and then stood the test of time.  Next, the lineages of these hypothetical common ancestors must be separated from the lineages of the even far greater numbers of lineages of the fellow members of their species.  Surely it isn’t a reasonable hypothesis that all lineages are extinct except the ones with the particular common pseudogenes now under study.

The more parsimonious hypothesis is that it has not been common ancestors that are responsible for the common back stories but rather mathematical-physical-chemical necessities in conjunction with common global environments, including horizontal gene transfers, over the eons.  The fossil record and other geology indicate histories based on global biogenesis and parallel developments (as suggested by Louis Agassiz prior to Darwin) rather than Evolution and its long chains of singularities, i.e., common ancestor couples.      (cont.)

Dan Baright - #15776

June 1st 2010

(cont. from above)

Regards current CHEMICAL homologues, consider H1N1 (swine flu virus) and the apparent short time it has taken to incorporate into its own genome genetic material from humans, birds, and swine.  Vice versa, researchers might discover, or at least contemplate, alternate causes (modern and ancient) of synteny in primates.  Example: See “HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots” by A. Schroder, P. Shinn, H. Chen, C. Berry, J. Ecker, and F. Bushman in “Cell,” Vol. 110, Issue 4, pp. 521-529. (Abstract is on the web.)

See also: Lynn Margulis’s book, The Symbiotic Planet (1999, p.9), regards a special laboratory case of fruit fly speciation as reported by Niles Eldridge.

Dan Baright - #16137

June 3rd 2010

ERRATA:  In my previous post I misspelled the last name of Niles Eldredge.  My apologies.

jmvdm - #72479

September 6th 2012

Hi Dennis,

I have a question about the Gulop pseudogene that I hope you may be able to answer. This is about the familiar argument that humans and chimps share seven mutated loci in their Gulop gene and that these mutations are identical in their location and molecular character. The cnclusion that they have a common ancestor depends to some extent on how this compares with the Gulop genes in other primates such as Gorillas and Orangutans. For instance, to state the obvious, if they also had that same Gulop gene then the most recent common ancestor of humans and chimps would not be the first one to carry that pseudogene. It might also be the case that the Gulop gene of Gorillas and Orangutans share some of the seven mutations, but not all. Is there any information on this? What is your opinion?


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