Pseudogene, relic or functional?

I was cruising through the trueorigins.org rebuttal of Theobold's 29 evidences and read some stuff that I haven't seen debated recently, specifically redundant pseudogenes. To allow a little more room for varied debate (even though it will probably veer away at some point) I will list 2 points with my own comments. I will exclude material from the talkorigins.org site (29+ Evidences for Macroevolution: Part 4) with the understanding that everyone is familiar with it, if not go to the link.Briefly, the argument for redundant pseudogenes as evidence supporting evolution is that closely related species (phylogenetically) will have similar redundant pseudogenes as per common anscestory. Also, the redundant gene loses function due to mutation, becoming the pseudogene, as long as its duplicate continues functioning.1. This is the form that most counter-arguments on the site take and I find this one particularly lacking. First, pseudogenes themselves are not predicted, true. However, evolutionary theory does not have to predict pseudogenes themselves, but rather the relationship between pseudogenes of different species. Secondly, evolution DOES predict that two organisms will have representative pseudogenes in the same chromosomal position if they recently diverged from a common ancestor with the gene duplication given the rarity of gene duplication. Also, the non-existence of identical pseudogenes between phylogentically distant organsisms as a potential falsification is not discussed by the trueorigins.org author.2. The loss of the primary function in the pseudogene due to mutation speaks of its vestigial nature. The pseudogene's genetic ancestory is quite apparent due to its sequence homology to known functional genes, but its new role as a pseudogene dramatically differs from its previous function. This is no different than wings on an ostrich or the blind eyes of a mole. The previous specificity of unaltered pseudogene homolog is totally lost in the mutated, redundant pseudogene. The question becomes, if pseudogenes have any function whatsoever, is that function immediate or an adaption to the alteration after the fact. Also, is that function needed for phenotypic differences? For me, the argument that pseudogene function is a necessity for the organism seems to fall short.NOTE: bibliography citations are included and readers should reference http://www.trueorigins.org/theobald1e.asp for complete citation.

The first and presumably only pseudogene known to have a function was discovered earlier this year, in Nature, 423, 91 - 96 (01 May 2003). Abstract: As active as genome research is, and with maybe 20,000 pseudogenes in humans, I'd have to think that a few more examples would have shown up by now if their having a function was terribly common. Sure, others will turn up that do something, but pseudogenes like the human or chimp urate oxidases are so obviously "broken", and recently broken, variants on their functional analogues in monkeys that it's pretty obtuse to deny their relatedness.Oh, and trueorigins argument #1 is startlingly lame - could we call it a pseudoargument?

Pseudogenes are largely inevitable because of another dominant component of just about any genome you can find except for bacteria. Retrotransposons. Given the RT activity of LINE-1 elements alone I am surprised that there are not more pseudogenes....and the copies made by retrotranposition will almost always be messed up because 1. RT polymerases are more inaccurate for the most part than DNA polymerases 2. As with expermimental RT you will tend to do a good job transcribing the 3' end of the transcript but the polymerase tends to fall off at as it moves to the 5' end leading to truncated copies of the original RNA.A much stranger kind of pseudogene are mtDNA insertions or NUMTS where recent studies suggest the main source of NUMTs is not due to RT but rather large chunks of the mtDNA genome actually getting out of the mitochondria, travellig intact through the nuclear membrane and then integrating randomly in the genome....however, these are actally very useful tools for studying evolution, particularly phylogenetics (assuming you don't mess up and mis identify the NUMT as bona fide mtDNA). The nuclear copies will take on the slower mutation rate of the nuclear genome and the mutations will be distributed more randomly since the pseudogenes are no longer constrained by natural selection...it makes for a good comparative tool i.e. internal outgroup in principle, for phylogenetic analysis.

I don’t see why evolution does not predict pseudogenes. Or if it (somehow) does not, it doesn’t predict vestiges either.Surely evolution does expect that, if some feature is no longer required, it could become sidelined, and then reduced due to the cost of maintaining it.If a wing is no longer needed for flight (or even, if flight is dangerous, eg insects on windswept islands, eg the Kauai flightless stag beetle), then evolution predicts it might become reduced.And in exactly the same way, if a gene is no longer required -- eg the vitamin C synthesising gene in apes, which get enough vit C in their diets -- then if it gets accidentally turned off by a mutation, that could happen to no detriment to the organism... and the gene -- now a pseudogene -- could sit in the genome unnoticed by anyone except geneticists.I suppose these might more correctly be called postdictions, since we knew about them already... but then, variation plus heredity plus limited resources -- Darwin’s original observation -- predicts adaptation, and Darwin was fully aware of adaptation before he worked out the mechanism. So, pre- or post-, either way, they are what we might anticipate from the known mechanisms.On the other hand (not meaning to change the subject ), the creation ‘hypothesis’ does not predict the huge range of poor, sadistic and ludicrous designs that we find in nature. We have no creationary reason to anticipate them...Cheers, DT

Transferring to a different field, in a very strict sense astronomy does not predict comets. There is nothing in astronomy that requires comets to be present in a solar system. However, we know that comets do exist and their presence is well within current theories in astronomy.What the author of trueorigins.org missed is that the Theory of Evolution states mechanisms. For something to be "predicted" it has to be consistent with the mechanisms of evolution.

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I was cruising through the trueorigins.org rebuttal of Theobold's 29 evidences

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Yes, the problem with Ashby Camp's rebuttal is that he doesn't understand the points that Theobold is making in his essay. In fact, I rarely read any of Camp's arguments to the end, because once it became clear that he wasn't really arguing the point the rest of the argument became irrelevant to Theobold's point.One thing that Camp does not seem to understand, and this shows up a lot in his "rebuttal", is that the predictions of evolution must be constrained by current scientific knowledge and known facts and discoveries. As you state, Loudmouth, it is true that ToE does not predict pseudogenes; but it does make predictions about pseudogenes once they have been discovered.

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As active as genome research is, and with maybe 20,000 pseudogenes in humans, I'd have to think that a few more examples would have shown up by now if their having a function was terribly common. Sure, others will turn up that do something, but pseudogenes like the human or chimp urate oxidases are so obviously "broken", and recently broken, variants on their functional analogues in monkeys that it's pretty obtuse to deny their relatedness.

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If I understand the creationist position, then we have:God created species that can be placed on a "phylogenic" tree because (insert your own opinions about the aesthetic sensibilities of the creator here);
The molecular "phylogenies" match the traditional taxonomic phylogenies because the more similar species are the more similar their biochemistries must be (God is presumably remarkly unimaginative or lazy);
pseudogenes and "retroviral insertions" also support the traditional phylogenies;
therefore, conclusion/prediction pseudogenes must have biochemical functions that are presently unknown.Yes, it's impossible to "prove a negative", but the longer we wait, the more it seems that this basic prediction of creation "science" can be considered falsified.

What of pseudogenes such as the faulty GLO vitamin C synthesising gene we and the other apes possess? (See http://www.jbc.org/cgi/reprint/269/18/13685.pdf)It’s pretty bleedin’ obvious that this one doesn’t work, otherwise we would be unable to suffer from scurvy.If the claim is that pseudogenes are intentional on the part of the creator, what was he up to there?Cheers, DT

Hi Oolon. Getting bored at II?

Hi Morpho!Well it has been pretty quiet apart from "Charles Darwin"... And of course I'm looking for a chance to publicise / use my website now I've finally done it Actually, it seems a bit quiet all over atm. Where are all the nice chewable creationists these days?Cheers, DT / Oolon

Chiroptera:(suggesting a creationist explanation )The molecular "phylogenies" match the traditional taxonomic phylogenies because the more similar species are the more similar their biochemistries must be (God is presumably remarkly unimaginative or lazy);Judge:
Why would this make God unimaginative or lazy?
On the surface this argument seesm to make some sense. Similar creatures would have similar biochemistries.The whole can be greater than the sum of the parts. Viewed on their own the same genes may appear exactly the same from organism to organism, but in conjunction with the rest of the whole they may not be exactly the same.what do you think?

The use of the words "unimaginative" and "lazy" were meant to be facetious. But it does seem that if God wanted to confound the future Darwins she could have given the different species radically different biochemistries that would none the less produce the species we see. We are, after all, talking about an omnipotent, omniscient being.But the overall point of the post is that the creationist argument is that the reason phylogenies based on biochemistry match, to a large degree, the phylogenies based on traditional taxonomy is that similar species must have similar biochemistries. But pseudogenes, if they indeed do not have a function, contradict this; since they do not have a function, there is no reason for similar species to have similar pseudogenes (or even to have any pseudogenes at all, come to think of it). This is why the creationists want to claim that pseudogenes must have yet undiscovered functions.As I stated, it is impossible to prove a negative - we cannot prove that most pseudogenes have no function. But the longer that we look for functions and fail to find them, it seems that it becomes less and less credible that a function exists.

Chiroptera:But pseudogenes, if they indeed do not have a function, contradict this; since they do not have a function,Judge:
I'm not sure I follow you here. Are you saying pseudogenes do or do not have a function?Secondly is it not possible that those pseudogenes which appear today not to have a function, once had a function?thanks for your time.

One pseudogene (in mice) has been shown to have a function - Hirotsune, et al., Nature. vol 423, pp 91-96 (2003). It regulates messenger RNA stability of its coding homolog. It's the only one yet known to do anything, "Although nuch effort has been devoted to understanding the function of pseudogenes..."
There are about 20,000 pseudogenes in humans, and every one of them once had a function, back in some ancestral species where they were still coding genes. But after they get "broken" by mutations, they don't seem to do much other than serve as filler.

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There are about 20,000 pseudogenes in humans, and every one of them once had a function, back in some ancestral species where they were still coding genes. But after they get "broken" by mutations, they don't seem to do much other than serve as filler.

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What is interesting, is when a pseudogene is clearly analogous to a functioning gene in a very closely related species (according to traditional taxonomy) there are very few mutations that have "broken" it. On the other other hand, the further back in the family tree the gene used to function, the more mutations there are, and the exact mutations in related species match where they lie on the phylogenic tree; I'll post this link again: 29+ Evidences for Macroevolution: Part 4It's the same question again: if species have similar genes because they are morphologically similar, and if pseudogenes used to have a function, why were they "broken" in similar ways in similar species? They "functionality" argument doesn't work in this case.