Is There Evidence of Function for Pseudogenes in Mice? - Evolution News & Views

Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

Evolution News and Views
Junk DNA NEWS
 

Is There Evidence of Function for Pseudogenes in Mice?

Over the past year or so I've corresponded with a pro-Darwin graduate student in biology at a major public research university on the east coast. Unfortunately, I had to end the correspondence because, despite my repeated pleas for civility and personal forgiveness towards him, he simply could not restrain himself from personal attacks against me. Though I ended any personal correspondence with this Darwinist, he recently asked me a question worth answering here on Evolution News & Views. To give some background, his question asks how I calculated that a mouse "pseudogene," if it were truly a non-functional pseudogene, would tend to be rewritten by neutral mutations in about 125 million years:

I had a question about a figure you derived in your review of Carroll's book [The Making of the Fittest]. Could you explain how you arrived at the figure 125 mya?:

"Carroll claims that the mutation rate for mice is 2 x 10^-9 per base pair per generation, and other sources indicate that mouse generation time is 3 months. This means that a non-functional mouse 'pseudogene' should be completely rewritten in about 125 million years. According to Neo-Darwinists, humans and mice supposedly shared a common ancestor between 75 and 125 million years ago, which means that any such shared 'pseudogenes' could have been 60%-100% rewritten by neutral mutations. Could we still recognize a 'pseudogene' [were it] 60% rewritten? 75%? 100%?"

The calculation is fairly simple to perform, and I'll break it in 3 steps:

(1): Mutation rate = 2 * 10-9 mutated-base-pair / generation = 0.000000002 mutated-base-pair / generation.

(2): 0.000000002 mutated-base-pair / generation * 4 generations / year = 0.000000008 mutated-base-pair / year.

(3): Take the inverse to make the units "years per mutated-base-pair" (i.e., how long will it take to guarantee that a given base pair is mutated or "rewritten"), and you get 125,000,000 years per any given mutated-base-pair.

One can also frame the calculation slightly differently by recognizing that there are 4 generations per year for mice:

0.000000002 mutated-base-pair / generation * 125,000,000 year * 4 generation / year = 1 mutated-base-pair.

The implications of this calculation are as follows: Sean B. Carroll constantly says in his book The Making of the Fittest that in biology, the rule is "Use it or Lose it." The converse would seem to also be true: if you haven't lost something, then that implies you're probably still using it, and it has function. So why do so many allegedly non-functional "pseudogenes" persist in mice and humans?

In short, if humans share pseudogenes with mice, then according to the standard Darwinian story, those pseudogenes have been sitting around in the genome doing absolutely nothing for around 125 million years. If these pseudogenes are really doing nothing, then they should no longer exist in the mouse genome, as mutation rates and statistical averages would dictate that a functionless stretch of mouse DNA should have been completely rewritten due to random, neutral mutations over such a long time period.

If the rule is "use it or lose it," then the fact that these "pseudogenes" haven't been lost implies that they may actually be performing some function in the cell. The Washington Post recently reported that "the vast majority of the 3 billion "letters" of the human genetic code are busily toiling at an array of previously invisible tasks." The argument presented here provides evidence that pseudogenes may not all be simply functionless "junk"-DNA, but like most other types of non-coding-DNA, they too are toiling at some task.