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Signature in the Pseudogenes, Part 2

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May 17, 2010 Tags: Genetics

Today's entry was written by Dennis Venema and Darrel Falk. You can read more about what we believe here.

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.

Notes:

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).

References:

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


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.
Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.

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Alex - #13999

May 18th 2010

...
- All of this is becoming clear in the literature and the insurmountable problems recognised.
- Scientists in private conversations increasingly admitting the failings of Darwinism. If the shackles of metaphysical naturalism and censorship were removed, up to 60% of scientists would reject the entire paradigm.

If this is even partially correct then Darwinism has had its day. Change is evidently underway so why attempt to reconcile Christian belief with a failed system?


Karl A - #14006

May 18th 2010

Quote from Alex 13999 “If the shackles of metaphysical naturalism and censorship were removed, up to 60% of scientists would reject the entire paradigm.”

Quote from Karl A “Up to 47.9% of all statistics are made up on the spot.”

Fun aside, how does one go about figuring that percentage out?


Karl A - #14011

May 18th 2010

I very much enjoyed following the back/forth that followed Dr. Giberson’s recent post “Would you like fries with that theory?”  Nothing stimulates vigorous discussion like writing a post that could be considered extreme and polarizing!

The following will be a sophomoric attempt to reflect some of the things I learned reading Rich’s posts and the responses to them, on the current post.  I think some fairly broad-brush accusations have been made here (again) against ID by some of the commenters, and I’m uncomfortable with that.

Here goes.  First off, I think this series by D & D is fantastic – cogent, clear and compelling.  Second, lest anyone wonder, I consider myself an evolutionary creationist.  Common descent seems very difficult to argue with at this point.  Yet I found some of Rich’s arguments compelling.  Particularly compelling was his point that, if we want to categorically say that (divine?) design cannot ever be detected (scientifically or otherwise), we had better be prepared to justify that on theological and/or philosophical grounds. (I don’t want to go to the opposite extreme of some ID proponents and categorically say that design *must* be detectable otherwise God is impotent, either.) 

(cont.)


Karl A - #14012

May 18th 2010

I would much prefer to take a more neutral position, that God can do what God wants, and we get the frustrating privilege of observing his actions “through a glass darkly”.  How activist has God been in shaping the course of evolution and, more broadly, the development of the universe?  Is any one of us prepared to say we have that subject nailed down?

Another subject of Rich’s posts (I think) comes down to, how much of the course of evolution can be plausibly explained naturistically by the current scientific consensus?  Rich says there is much more sizzle than steak.  Now, it certainly seems that genetics is filling in a lot of blanks – in today’s post, how proto-mammals lost the working egg yolk gene for example.  While I agree that the search for theistic primary causes has a pretty low batting average, should I be afraid of leaving the door open for someone to find evidence of God adding information or design to the process?  I don’t want to be on the wrong side of the adage “The one who says something cannot be done should not get in the way of someone who is actually doing it.”

Let me know what I’m misunderstanding.

Peace.


Merv - #14014

May 18th 2010

Alex (13999), could you give any examples or expand upon the private conversations where scientists are admitting failings of Darwinism?  I’m suspecting that such conversations may often refer to specific areas that don’t fit with other areas or where unanswered questions still remain.  Such things are different than “rejecting the entire paradigm”.  But quote mining can make them sound like the same category.  Obviously they can’t have been “too private” to be able to be referenced as a statistic. 

—Merv


Marshall - #14015

May 18th 2010

Hi Karl,

I share the position you suggest—not saying God’s design must or must not be detectable, but that God will do as he pleases and we’ll never figure it all out.

For me, I don’t see reason to expect God to intervene at certain points within biology, nor do I find the suggested barriers of natural processes compelling. ID advocates are often quick to point out that the design they detect doesn’t necessarily point to God, and I think they’re right to do that. Design at that level, if not a result of natural processes, is potentially the result of advanced aliens or supernatural entities other than the ultimate Creator. It doesn’t require God to tinker with genes—scientists can do that in the lab as well.

This is why I find the intelligent design of the universe as a whole, and the elegance of the natural processes within it, to be better “design” arguments than looking for certain unexplained transitions within biology. The former are things that truly are beyond the power of any created being. I’d need to see evidence for an instance of design injection before accepting it—a gap in our knowledge isn’t enough—but my theology doesn’t require the existence or absence of such events.


Esley Heizer - #14020

May 18th 2010

Alex - as a scientist who works in molecular evolution none of my colleagues, that I know personally, reject evolution or have any problem with it. It is the core around which biology is built. Without evolution the whole field falls apart. Yes we still have things we need to understand and there is much yet to discover. However the chances of anything undiscovered destroying the theory of evolution is so minuscule that it is pointless to discuss. The theory of evolution is not going anywhere and is just going to become stronger as time passes.


unapologetic catholic - #14027

May 18th 2010

“Particularly compelling was his point that, if we want to categorically say that (divine?) design cannot ever be detected (scientifically or otherwise), we had better be prepared to justify that on theological and/or philosophical grounds.”

Why don’t we hear from anybody who disagrees with this propsition?  I certainly don’t and I haven’t heard anybody else even claiming that is their position.  The key words are “cannot ever.”  There is no reason to think divine design or any other divine intervention couldn’t be detected.  There are reasons to think certain things “did not” happne that way but no strong reason to think it “had to happen” that way.


Alex - #14029

May 18th 2010

Merv, I can only refer you to the podcast which I linked to of the show in which this is discussed. It is my understanding though that many are afraid of the consequences of coming out as a Darwin skeptic in scientific circles. Fear of reprisals is largely what is holding together the Darwinian ‘consensus’. The instances of discrimination towards those who have done so in the past are well known. Despite this, the data can only be ignored for so long. The generation of upcoming scientists will also have no need to cling to the outdated paradigm, as they have not spent their careers attempting to defend it at all costs. They are free to follow the evidence where it leads. Once the present climate of fear is removed, the barriers will be overcome and the dam will break.


Chris Massey - #14032

May 18th 2010

Alex,

Be careful what you read or listen to. People with fringe views who are unable to provide credible evidence for their theories and, as a result, are unable to gain traction for their theories within the scientific community, frequently claim a conspiracy to stifle their views. In reality, scientists thrive on challenging established views. Scientists who buck the trend are not discriminated against if their science is rigorous and they adequately respond to their critics. Those are the sort of scientists who win Nobel prizes.


Merv - #14034

May 18th 2010

... removal of the climate of fear ...  ... following the evidence where it leads ...  Those are things we all should agree on.  As to whether the consensus floods in the direction you are thinking it will if/when barriers come down;  that may not happen in the direction sought.  And which side is attempting the erection of the most barriers?  But hey!  We should all be seeking truth wherever it leads, right?

—Merv


Glen Davidson - #14035

May 18th 2010

Fear of reprisals is largely what is holding together the Darwinian ‘consensus’.

Behe’s take is quite the opposite (link gives context):

MB: I think that the main reason for the disparity is the difference in the philosophies of the elite elements of society versus ordinary people. Much of the elite in our society (such as academics, media, entertainment industry, and so on) is secularized, and an idea like Darwin’s theory is congenial to their view of the world. The bulk of ordinary people, however, are religious and their views are not constricted by the need to explain everything in the world by chance and natural law. So when they view the evidence for Darwin’s theory, most people are unpersuaded by it.

Source

It’s worth about as much as the “fact” that 60% of scientists would abandon evolution if they could, as he doesn’t even pretend to explain why most good religious biologists like Giberson, Falk, and Collins accept evolution.  But at least he steers clear of the Expelled-type hysteria about persecution.

Glen Davidson


John VanZwieten - #14036

May 18th 2010

Since we seem to have some commenters here who are familiar with YEC literature, I’m wondering if there are articles published where YEC scientists found a specific pseudogene (or found anything new, really) where they expected to find it based on their paradigm.


Glenn - #14077

May 19th 2010

RTB had a recent human origins podcast discussion in which they spent some time critiiquing the Biologos articles on ancestral human population sizes. They don’t mention Biologos by name but the “online articles” they refer to are almost certainly this one.


Dennis Venema - #14111

May 19th 2010

Thanks for the heads up, Glenn. I’ll try listen to it later.


Janet - #14121

May 19th 2010

I’ve taken a look at this Answers In Genesis link on pseudogenes, and listened to a bit of the RTB podcast that Glenn mentioned.  As a non-biologist, it’s difficult for me to know whether any of the arguments AIG and RTB make are valid.  For example, the AIG article says “There is always an element of subjectivity in the process of aligning sequences of homologous (orthologous) DNA” and “Evolutionists must essentially ‘shop around’ for the closest match in trying to deduce the orthologous pairings of pseudogenes from primate to primate.”  Is this true?  Is it a legitimate point?

When seeing arguments and counter arguments like this, how can we non-specialists determine who’s closest to the truth?  It’s easy for me to see why people who follow these organizations would not accept evolution.


John VanZwieten - #14124

May 19th 2010

Janet,

I had some of the same thoughts when reading various links on pseudogenes.  At some point our non-biologist eyes just glaze over.

This article provides what I think is a pretty good standard for assessing such articles:  to what extent do the authors really seem to be wrestling with the data, and to what extent do they seem to be obfuscating it?

Professor Wood over at Bryan College is a YEC who seems to me to wrestle with data.  I haven’t found much at AIG that didn’t seem to be way on the obfuscation end of things.


Malcolm - #14126

May 19th 2010

Indeed, Todd Wood’s paper on human and chimp genomes contains the phrase “it is difficult to explain why pseudogenes with the exact same substitutions or deletions would be shared between species that did not share a common ancestor.”


Dennis Venema - #14136

May 19th 2010

Brief comment: Todd Wood isn’t willing to use those arguments in an attempt to refute common ancestry, because (as a biologist) he knows those arguments don’t hold water. If indeed those arguments were valid, he would use them.

I’ve listened to a bit of the RTB podcast now. Rana’s arguments are weak. He avoids the point that the three different methods we discuss are based on different assumptions. The SNP/HapMap data, for example, is not based on a ‘molecular clock’ at all - it’s based on recombination frequency. The point is that three different methods with independent assumptions all give the same answer. If Rana is going to object to this work, he needs to show why the methodologies underlying these three models is in error. I see no attempt to do that, at least in that podcast.

He also promotes the mitochondial Eve/Y chromosome Adam data as a way to explain population sizes - this is greatly in error. The method of transmission of these forms of DNA make them unsuitable for population size estimates. For that, you need to examine autosomal chromosomes, like the three methods Darrel and I discussed in our post.


unapologetic catholic - #14146

May 19th 2010

“Evolutionists must essentially ‘shop around’ for the closest match in trying to deduce the orthologous pairings of pseudogenes from primate to primate.”  Is this true?  Is it a legitimate point?”

No, it’s a misrepresentation of fact.


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