Is There “Junk” in Your Genome? Part 4

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February 17, 2012 Tags: Genetics

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

Is There “Junk” in Your Genome? Part 4

One of the challenges for discussing evolution within evangelical Christian circles is that there is widespread confusion about how evolution actually works. In this (intermittent) series, I discuss aspects of evolution that are commonly misunderstood in the Christian community. In this last of several posts on “junk DNA”, we explore how unitary pseudogenes serve as signposts to the evolutionary history of a species, and continue to confound antievolutionary groups.

In our previous post, we examined processed pseudogenes – transcribed gene copies that randomly insert into genomes. Unitary pseudogenes, however, are different: unlike processed pseudogenes, they are unique sequences in genomes, and not copies. They have the features one expects of “real” genes: regulatory sequences, introns, and protein coding sections – but with mutations that prevent them from being transcribed or translated. Like buildings in various states of repair, there is a similar range for unitary pseudogenes. If they have only been recently inactivated, they will be largely intact – like a recently abandoned building with a few broken windows. Others are further along in their degradation, like a stone building without a roof and grass growing up through the floor. Some are so far gone that one needs to peel back the turf to search for what remains of the foundation. Despite their various states of disrepair, they remain recognizable – in some cases, they can persist for millions of years before they slowly mutate beyond recognition.

The reason for these defective genes is straightforward: the organism that had the original mutation that removed the function of the gene was not significantly impacted by the loss. One example I have previously discussed is the human GLO pseudogene. The functional GLO gene is part of the biochemical pathway for making vitamin C, something that humans and other primates are not able to do: if we don’t get enough in our diet, we get scurvy. In an environment with adequate dietary vitamin C, however, the loss of the GLO gene is no big deal – and mutations that remove its function would not have been a disadvantage. The mutations that remove GLO function in humans are the same mutations we see in other species – they are an example of mutations in a nested hierarchy, the type of pattern that relatedness produces. This indicates that the mutations happened once, in a common ancestral species, and have been inherited by several species that descend from that ancestor, ours included.

So, what’s a defective gene like you doing in a species like this?

While it makes sense that mammals ought to be able to make vitamin C (even if humans and other primates cannot), in some cases pseudogenes seem much more “out of place.” One example from the human genome that we have discussed in the past, is the vitellogenin gene, a gene required for egg yolk formation in egg-laying organisms. This gene is present in the human genome as a pseudogene, even though humans are placental mammals – human embryos are nourished through a placenta, not egg yolk. This pseudogene was located in the human genome by predicting that its genomic location relative to its neighboring genes would be retained for a long time, even after its inactivation. Accordingly, researchers found a functional vitellogenin gene in the chicken genome, and noted the genes on either side of it (let’s just call them “Gene A and Gene B” for convenience). Gene A and Gene B are also side by side in the human genome, so the researchers looked between them for the signs of vitellogenin gene remains – and found them in that precise spot, still visible despite approximately 300 million years since we last shared a common ancestor with chickens:

Other examples like this abound: whales, for example, have unitary pseudogene remnants of genes devoted to an air-based sense of smell, even in cases where the whale species in question does not have an olfactory organ. A second example from whales are pseudogene remnants of visual pigments adapted for wavelengths of light found in terrestrial settings, not aquatic environments. These examples make perfect sense in light of the terrestrial ancestry of whales, but are challenging to account for from an antievolutionary perspective.

Pseudogenes: evolution’s silver bullet?

Unitary pseudogenes with shared mutations in nested hierarchies among related species are far from the only evidence for evolution, and are not even necessarily the line of evidence most convincing to specialists. Specialists can see the broad pattern of multiple lines of converging evidence that support common ancestry to an extent non-specialists cannot easily appreciate. Unitary pseudogenes, however, are valuable tools for demonstrating a sampling of those lines of evidence, and providing a window into the world of comparative genomics that, to paraphrase Dobzhansky’s famous quote, would make absolutely no sense except in the light of evolution.

Yes, the implications of unitary pseudogenes such as these are easy for even non-specialists to grasp: whales have the defective remnants of genes adapted to terrestrial vision and air-based smelling because they descend from terrestrial ancestors. Placental mammals, including humans, have a defective remnant of a gene used to make egg yolk because they descend from egg-laying ancestors. Unitary pseudogenes share identical mutations across related species because they were inactivated in a common ancestor, and were inherited by every species that descended from that ancestral species.

No special training in genetics is required to appreciate the strength of the evidence that these examples provide. Nor does it require special insight to see that attempts made by antievolutionary groups to refute this evidence face an uphill battle. Its daunting nature notwithstanding, some have undertaken just that task, since the evidence is too compelling to ignore, and too risky to leave unanswered.

Bringing it together: antievolutionary approaches to pseudogenes, unitary and otherwise, miss the mark

Now that we have covered significant ground with respect to what various classes of pseudogenes are and how they arise, we are now able to properly evaluate antievolutionary arguments put forward in an attempt to discredit these lines of evidence for evolution. Attempts to discredit unitary pseudogene evidence generally have one or both of the following two approaches, which we will evaluate in turn:

Approach 1: Discuss rare examples of processed pseudogenes that have acquired function, and imply that all pseudogenes, including unitary pseudogenes, will similarly be shown to have function.

This approach is a fairly common one in the antievolutionary literature, and examples abound. We have examined previously how processed pseudogenes may, in rare cases, acquire a function and come under selection. Note well: the vast, vast majority of processed pseudogenes are not functional and are slowly mutating beyond recognition as DNA not under selection. While rare examples that have acquired function are very interesting from a scientific perspective, they do not “confer functionality” on the remainder of processed pseudogenes, let alone on unitary pseudogenes.

The other issue with this argument is that in many cases we know what the function of the unitary pseudogene once was. We know what the function of vitellogenin is, for example – and we can find this gene in modern-day egg-laying animals. When we see the remnants of this sequence in the human genome it is a stretch to argue that it has another, as of yet unknown function. When we see the human pseudogene sitting between two other genes in the human genome the same order as we observe in the chicken genome, it stretches credibility well past the breaking point.

Approach 2: Claim that unitary pseudogenes with mutations shared across species are the result of non-random mutations that occurred independently in the two species, and are not inherited from a common ancestor.

This argument, though having an appearance of validity, is similarly doomed to frustration. While mutations are not entirely random (certain regions of the genome mutate more readily than others) there is no known mechanism that could create the precise, repeated pattern of shared mutations we observe between related species. The most significant attempt to mount this type of argument against unitary pseudogenes in general was directed at the GLO pseudogene, and I have already discussed the specific details of why that attempt was inadequate. No refinement of that argument, to my knowledge, has been put forward since.

In summary, pseudogenes in general, and unitary pseudogenes in particular, remain a significant thorn in the side of antievolutionary groups. In the next post in this series, we’ll cast our net wider and explore an example of how multiple, convergent lines of evidence support evolution, often in unexpected ways.

For further reading:

http://biologos.org/blog/signature-in-the-pseudogenes-part-1
http://biologos.org/blog/signature-in-the-pseudogenes-part-2
http://biologos.org/blog/a-tale-of-three-creationists-part-3


Dennis Venema is Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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beaglelady - #68064

February 18th 2012

Excellent post as usual, Dennis.  It’s a tad difficult to explain the vitellogenin gene any other way, unless God intends for us to go back to laying eggs some day.


dont_blame_me_blame_evolution - #68100

February 19th 2012

Speaking of “laying eggs”, some new news from the humbling world of science…

 

Apparently, now, after 130 years of teaching in one direction, science is doing a 180 on the function of sex in evolution:

Biology textbooks maintain that the main function of sex is to promote genetic diversity. But [some researchers] propose that although diversity may result from a combination of genes, the primary function of sex is NOT about promoting diversity. RATHER, it’s about keeping the genome context—an organism’s complete collection of genes arranged by chromosome composition and topology—as UNCHANGED as possible, thereby maintaining a species’ identity.” http://www.sciencedaily.com/releases/2011/07/110707161037.htm

 

As beaglelady might say, “amazing.”

 

 


Dennis Venema - #68078

February 18th 2012

Thanks - always nice to know that I have the BL seal of approval!


Yes, among unitary pseudogenes the human vitellogenin one is my favorite example. I don’t think I’ve ever seen an antievolutionary organization try a hand at explaining it away. They typically use “safer” examples like GLO or the olfactory receptor ones - ones that at least make sense for a mammal to have. I’d love to see RTB or AIG put their thoughts on this one into print.  

beaglelady - #68086

February 19th 2012

And all I can hear over here are crickets.  But I’m sure someone will take up the challenge.


dont_blame_me_blame_evolution - #68104

February 20th 2012

And all I can HEAR over here are crickets.”

My imagination is extra active tonight. Everything I see and HEAR bespeaks evolution.

I’m curious about hearing, and how it evolved.

What I see in nature, especially in biology, is what some call “information.” Actually, I don’t think “information” does justice to what really appears to be going on. I think “directions” is better. As in, the “directions” to assemble that new HDTV stand. If you think about it, we take for granted how involved “directions” actually are. And I don’t mean just how many steps and screws are required. See, directions require

1) A directOR, who has a goal in mind, for some reason


2) A “language” of direction


3) The directIONS, the detailed, directIVE information


4) A recipient of the directions

5) The recipient’s ability to receive, understand (possibly after translation of the language of the directions) and act upon the directions

6) Successful execution of the directions by the recipient.

How all this could happen by accident (or by random mutations or by natural flow or by some other means excluding intelligent action) has always mystified me.

Back to HEARING (crickets or anything else)…

Notice the language here: “The research provides a new mathematical framework for understanding sound processing and suggests that our hearing is highly optimized in terms of signal coding—the process by which sounds are TRANSLATED into information by our brains—for the range of sounds we experience. The same work also has far-reaching, long-term technological implications, such as providing a predictive model to vastly improve signal processing for better quality compressed digital audio files and designing brain-like codes for cochlear implants, which restore hearing to the deaf.” http://www.sciencedaily.com/releases/2006/02/060227185506.htm

Jesus Christ!! (Help us and save us.) I never realized how high-tech HEARING was!

[Disclosure: I don’t know if these researchers were “evolutionary scientists”. I do know they didn’t use the E-word in this article. Perhaps they didn’t think it was necessary, or that it would just raise quarrelsome questions.]

“He who has ears to hear, let him hear.” [Mat 11:15]


Terrance - #68111

February 20th 2012

I came across this little video from RTB on genomics - http://www.reasons.org/videos/genomics - but that’s about all I could find . It looks like they’ve updated their whole site since I last saw it.


dont_blame_me_blame_evolution - #68119

February 20th 2012

Terrance,

Good video. The only thing I would disagree with is the “wash,” that is, that we can’t prove whether genomic similarity is due to common ancestry or due to common designer.

The question implied by my post was ‘how can you have this amazingly complex, direction-rich biological software absent an intelligent software programmer?’

Check this out. http://www.evolutionnews.org/2011/08/stephen_meyer_gives_the_positi048951.html

Lots of other videos with Meyers are available on youtube. Wonderful stuff.

 


melanogaster - #68209

February 22nd 2012

“Lots of other videos with Meyers are available on youtube.”

Does Meyer get the most important, fundamental evidence right?

Cal - #68087

February 19th 2012

I’m sure this point has been raised, countless times before, but two balls seemed to be served by this post.

What I mean is that ok, this unitary psuedogene for egg laying is a sign of evolution to be the case. That’s alright. What I take issue is the careless use of language as ‘defective’. Maybe inactive or not-required, but this speaks of sloppiness in Creation. Can we assert so boldly that there is nothing left to uncover as to its purpose.


Uncle Bonobo - #68095

February 19th 2012

“sloppiness =/= “nothing left to uncover.”




melanogaster - #68210

February 22nd 2012

“What I take issue is the careless use of language as ‘defective’.”

Cal, it’s not careless in that context. It is unequivocally defective as a vitellogenin gene. That doesn’t preclude it from having another function.

“Maybe inactive or not-required, but this speaks of sloppiness in Creation. Can we assert so boldly that there is nothing left to uncover as to its purpose.”

Dennis isn’t making such an assertion. We can, however, note that no one on the creation/ID side of the political debate feels that uncovering such functions are worth their own time or effort. That speaks volumes, don’t you think?

dont_blame_me_blame_evolution - #68096

February 19th 2012

Haven’t read this latest from Dennis. Probably won’t. If I asked him questions about this one he’d probably just direct me elsewhere, and not answer my questions, as was the case before (see page 2 of “Behold the Man”).

Maybe I’ll read it if PNG, Uncle Bonobo, Papalinton and David Evans tell me this is the one; the best evidence they’ve come up with for evo.

Meanwhile, I’m watching “60 Minutes” right now. Interesting episode. Says a lot about how advanced the commonly-accepted, consensus science actually is. Also, makes one wonder whether science is really as “self-correcting” as some here at BioLogos have said.

Leslie Stahl says this is EXPLOSIVE!

http://www.cbsnews.com/8301-505269_162-57380096/inside-60-minutes-placebo-story/

 


melanogaster - #68185

February 21st 2012

“Haven’t read this latest from Dennis. Probably won’t.”


No need to belabor the obvious. Then why comment?

“I’m curious about hearing, and how it evolved.”

I don’t think you are. But prove me wrong! Demonstrate some curiosity about hair cells with some questions (not quotes) about them that can’t be traced to a creationist web site.

I’m interested in how you think hearing was designed.

dont_blame_me_blame_evolution - #68186

February 21st 2012

“I’m interested in how you think hearing was designed.”

Very carefully.


melanogaster - #68208

February 22nd 2012

You’re not curious. 


Please explain the differences in regeneration capability between avian and mammalian hair cells. Creationist web sites won’t help you there, but curiosity, which you claim to have, will.

dont_blame_me_blame_evolution - #68098

February 19th 2012

Right now, I’m watching something even better... The Simpsons.


Tim - #68177

February 21st 2012

Dennis,

There is some small amount of yolk in mammalian embryos that I believe goes by the name of deutoplasm.  Does this have any relevance to vitellogenin genes?


Dennis Venema - #68183

February 21st 2012

Hi Tim,


Humans are nested within the amniotes, so some hints of amniotic life are to be expected even if placental mammals don’t fully embrace the amniotic lifestyle any longer. Humans also have a yolk sac, but it does not fill with yolk as it does in egg-laying species - though it retains some functions in hematopoiesis (the generation of the first blood cells). Vitellogenin is used as a carrier for transferring yolk components en masse, something that humans don’t do (or need to do). Thanks for the question. 

Tim - #68192

February 22nd 2012

Thank you Dennis!


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