tgamble

"Ways in which pseudogenes do not match the evolutionary paradigm
http://www.godandscience.org/evolution/pseudogenes.html

An article by Gary Gilbert published in the October, 1992 Spectrum magazine presented the beta globin pseudogene as compelling evidence for human's and ape's evolution from a common ancestor. Gilbert suggested pseudogenes, and other non-coding DNA, are molecular potsherds that can be used to reconstruct a species' evolutionary history, requiring that this DNA really have no function, but continues to be produced as a partial record of what once was an important adaptation. Many studies have been carried out regarding different pseudogenes. A study done by Gonzalez et al.1 looked at ribosomal DNA (rDNA) in chimpanzee, gorilla, orangutan, gibbon, and rhesus monkey rDNA. The 2-kb pseudogene was present in the apes but not in Old World monkeys. Some of the Alu elements of the gene were shared by all the primates studied, one was absent only from the rhesus monkey rDNA, and another was absent from both gibbon and rhesus rDNA. This kind of random inclusion of Alu elements does not support the simple evolutionary paradigm of common descent.

Another study by Minghetti and Dugaiczyk2 examined the enolase pseudogene, present in humans and four other primates, including the baboon, an Old World monkey. The accepted value of 5 x 10-9 nucleotide substitutions per site per year as the evolutionary rate for pseudogenes would lead one to conclude this pseudogene arose 14 million years ago. However, evolutionary theory states Old World monkeys diverged from the hominid lineage some 30 million years ago. It is difficult to explain how the sequence substitution rate would vary from one pseudogene to another, since they are non-coding, and therefore should not be subject to any form of natural selection.

What is common to all these pseudogene studies is that the pseudogenes from humans and apes are not identical. One would expect some similarity, since 98% of our genome is identical to that of chimpanzees. What is the purpose of this non-coding DNA? In humans, 97% of the genome is non-coding, suggesting that it must serve some purpose. Even evolution would not be expected to produce a species which has an efficiency of only 3%. Natural selection should have removed all this useless DNA. Much of the non-coding DNA that was once considered nonfunctional is actually highly functional. In fact, recent studies show that some of this non-coding DNA can control expression of other DNA, and other non-coding DNA probably serves to give structure to DNA and the chromosomes."

I fail to see how "not indentical" takes us to "we should expect some similarity" implying that there is nonse. They are located in the same place and it's the same crippling mutation isn't it? What else is there that doesn't make it identical?

"Much of the non-coding DNA that was once considered nonfunctional is actually highly functional."

Why do I seriously doubt that this statement is true?

Any help on this would be greatly appretiated! Thanks

pz

Because pseudogenes are nonfunctional, we expect them to accumulate mutations more rapidly than functional genes -- there is no longer any selection for a particular operational sequence. They just steadily accumulate garbage changes until they are obliterated.

The statement that much of the non-coding DNA is functional is on a par with the reasoning in the rest of that quote. The fact that there is so much of it is not evidence that it is functional. We know that roughly twice as much DNA is dedicated to regulatory function as is strictly coding, but that still doesn't amount to much.

I just find it weird that creationists are so obviously perturbed by this bit of information from the HGP. I guess their sense of a designer is not someone who is wasteful and heaps up lots of junk, or thinks 'just good enough' is acceptable. Too bad. Reality slaps 'em in the face once again.

theyeti

Arrghhh! Yet another creationist mixing up his pseudogenes and Alu elements. This is simply a non sequitur. The issue is about pseudogenes and then he drags Alu elements into it in order to draw attention away from the pseudogene data. Alu elements are capable of retrotransposition, and are thus known to copy themselves all over the genome, so to see one or two inserted into the middle of a pseudogene is unsurprising. Furthermore, the anecdotes that they cite don't even come close to contradicting a common descent hypothesis. 1) Alu elements appearing in all primates suggest that they were present in the common ancestor of all primates, regardless of when any given pseudogene may have arisen. 2) The loss of an Alu element in the rhesus monkey just means that this lineage lost an Alu element. So what? 3) The absence of an Alu element in both rhesus and gibbon means that the common ancestor of both probably lost an Alu element. I suspect that these two group together phylogenetically; if one of these two has a closer relative that contained the Alu element, and the same Alu element was also found in an outgroup, then that would be weird. But there is no indication that this is what happened.

It's very easy to explain how the rates vary. Mutation is random, not uniform. Given a large number of DNA sequences, they will tend to fit a normal distribution curve (i.e. Bell curve) in regards to mutation rates. Some will mutate very little, while others will mutate a great deal. The majority will be somewhere in between. This is why effective molecular clocks must incorporate data from many genes in order to find the average. Given that the measured rate of mutation did not vary much from the proposed divergence time, this appears to be well within what's expected (from my non-phylogeneticist's point of view) from noise. The fact that this example appears to be cherry-picked only underscores this.

Nor should they be.

And they are very similar. If they weren't, no one would be able to pick them out with a BLAST search or isolate them in the lab with the appropriate primers.

Quite the contrary, the large percentage of non-coding DNA suggests nothing other than the fact that it's unlikely that all of it is functional.

This ignores two things:

1) Much of this DNA is able to make copies of itself throughout the genome; hence, there is a mechanism for its spread that is independent of the good it does the host.

2) The metabolic load of carrying around extra DNA is extremely low for a muticellular organism. There is no reason for natural selection to remove it absent deletion bias.

First of all, there has only been a tiny percentage of DNA that was once considered non-functional that was later found to be functional. And calling it "highly" functional is a bit of an overstatement. It's been discovered that removing some introns or Alu elements, in a tiny percentage of cases, can be detrimental; but that does not imply function anymore than the detriment in removing a bullet from an internal organ implies that the bullet has a function. What is also true is that recent studies have shown that about 6% of DNA with unknown function is highly conserved, which implies that it is functional. But here's the catch: the only reason to assume this is Darwinian evolution. And finally, while some DNA is certainly important for structural purposes, this doesn't change the fact that the sequence is unnecessarily similar in closely related species, such as humans and chimps. This is what makes the pseudogene case so important -- even if a stretch of DNA containing a pseudogene did have a structural function, it still wouldn't explain the sequence of the pseudogene shared between two species.

theyeti