Pseudogenes: Molecular remnants of our evolutionary past

Genes provide the code that (mostly) makes us what we are. They are incredibly important in determining what we look like, how our bodies maintain themselves, and, in some cases, they even influence our behavior. However, genes can also ‘break’, and these broken genes can point towards major events in evolution. But before explaining any further, I’ll provide a refresher on how genes work.

Genes are stretches of a molecule known as DNA, short for deoxyribonucleic acid. The most important part of DNA is composed of four different molecules (bases), known as adenine, cytosine, thymine and guanine, usually represented as A, C, T and G.

DNA

In order for the code within genes to be read, they need to be copied or “transcribed” into an RNA (ribonucleic acid), a molecule that is very similar to DNA, but the T’s get changed into U’s (uracils). In every such molecule of RNA, every three letters is “translated” into a specific amino acid. For example, when an RNA reads “UUC”, it tells our cells to find a phenylalanine, “UGG” codes for tryptophan and “GAC” is for aspartic acid. So if a cell translates an RNA that says UUCUGGGAC, it will find these amino acids and put them together into a chain: phenylalanine + tryptophan + aspartic acid.

RNA translation

Chains of amino acids are then folded into particular configurations, making proteins. Besides building up strong muscles, proteins perform practically every function in our body, ranging from absorbing light in our eyes, fighting off infections, allowing for electrical impulses to travel in our nervous system and carrying oxygen in our blood.

Protein functions

So the recap: the code within our DNA gets copied into RNA, this is translated into amino acid chains that are folded into proteins, and these proteins do most of the work in making our bodies what they are. Hopefully it’s clear as to why the code in our genes is ultimately so important, and why certain mutations, or errors in the copying of DNA during reproduction, can have such drastic consequences.

In fact, such mutations can lead cause genes to ‘break’. To explain how, I’ll use an analogy from English sentence structure. Think of the following sentence as a gene:

The cat ate the dog.

There is a sequence of letters, just like DNA, and every three letters forms a word, analogous to codons. When you read these words, you recognize that they each have their own meaning, much like how codons ‘mean’ certain amino acids. Finally, the sequence of these words also have particular a meaning that changes if you moved them around, just like a sequence of amino acids forms a specific protein.

So how might mutations alter such a sentence? Let’s pretend that our sentence is from an ancient document that needs to be copied to be preserved, and every mistake made in copying is like a mutation that gets passed down into the descendant copy. First we can imagine a mutation where a single letter fails to be copied. In this case, we’ll delete the ‘t’ in cat.

The caa tet hed og.

As you can see, the sentence is no longer understandable. Now let’s mutate the original sentence by inserting a new letter before the ‘t’ in cat.

The caz tat eth edo g.

Again, this sentence is meaningless. We can also mutate the original sentence by taking the period, which tells the reader that the sentence has stopped, and moving it forward.

The cat. Ate the dog

Now there are two sentences, neither of which makes sense by themselves.

Genes can mutate in the same way, with insertions, deletions and early stops causing problems in the formation of the protein. In fact, many such mutational errors underly human diseases, such as amelogenesis imperfecta and retinitis pigmentosa. Accordingly, when these mutations happen in nature, we would expect them to be weeded out by natural selection. A mutation that causes your teeth or eyes to stop working properly will likely not help you survive and mate more, so why maintain it?

But what if it does? What if you’re an anteater that uses it tongue to rapidly capture ants and termites, and you swallow them so fast that you don’t need teeth? Would a mutated tooth gene be such a bad thing? Or what if you were a mole that spent nearly all of its life underground, hardly being exposed to the light of day? Perhaps having mutated vision genes isn’t an awful as it sounds for such an animal.

In such cases, scientists believe that natural selection no longer weeds out mutations in the underlying genes, allowing the genes to accumulate mutations that would be harmful to another organism, leading to a ‘broken’ gene. We call these genes pseudogenes, some examples of which you can see below.

Pseudogenes in tooth-reduced species
Pseudogenes in various mammals. Insertions (blue), deletions (red) and early stops (green) are shown.

So how are pseudogenes evidence for evolution, as opposed to Creationism? First, the presence of nonfunctional genes in the genomes of organisms seems to present a logical problem for creationism [1]: namely, why would a Creator create genes that don’t do anything? Wouldn’t it have been easier to create life without pseudogenes?

The astute observer will notice a parallel between pseudogenes and vestigial organs, anatomical traits that seem to serve no purpose to an organism. But Creationists reasonably point out that just because a gene doesn’t have a known function, doesn’t mean it is really nonfunctional [1,2]. Indeed, just like certain vestigial organs have been shown to possess functions, such as the human appendix, certain pseudogenes are known to have functions, such as regulating when certain genes are turned on or off.

But the importance of pseudogenes in the context of evolution and Creationism becomes apparent when we look at their distributions across various organisms. Who has them and who doesn’t matters quite a bit.

For example, mammals that lack enamel and teeth have pseudogenes for ENAM, a gene that is involved in the development of the enamel layer of our teeth. They don’t have a functional version anywhere in their genomes. By contrast, mammals that have enamel have an intact, functional ENAM gene, but do not have an ENAM pseudogene. So if ENAM pseudogenes are functional elements imbued by the Creator, why do they only exist in mammals without enamel and not those with enamel?

By contrast, evolutionary theory simply posits that mammals without enamel on their teeth, or that completely lack teeth, descended from mammals with enameled teeth and ENAM pseudogenes are simply the remnants of their past. What’s more striking is that researchers find fossil and other evidence to support the inferences of such pseudogenes.

As an expert on pseudogenes, you will get plenty of such examples in this blog, including from my own scientific research. Such genetic ‘fossils’ provide intriguing evidence of our evolutionary past.

References

1. https://creation.com/are-pseudogenes-shared-mistakes-between-primate-genomes

2. http://www.icr.org/article/adam-eve-vitamin-c-pseudogenes/

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One thought on “Pseudogenes: Molecular remnants of our evolutionary past

  1. Pingback: Developmental biology: When embryos point to evolution – Evolution For Skeptics

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