Genetic Redundancy

[bigore]

I got this paper from an creationist friend, he says this is the ultimate proof that evolution in a darwinian way impossible is.

 

http://download229.mediafire.com/mnvwu4ljxxdg/tmd2zzzhmei/genetic_redundancy.pdf

 

I'm no biochemist or evolutionary biologist, but does he have a point or not?

[CharonY]

What kind of paper is this and what are the main points?

[Mr Skeptic]

I only skimmed it, but it seems its main points are that there is lots of redundancy in genetics, and that redundancy is the rule rather than exception. I think that evolution can explain that just fine -- transposons would make for many redundant genes, and in fact I think such redundancy is almost a necessity for evolution.

[iNow]

I'll teach you a little short cut. If it says "creationist," it's wrong.

 

With that said, if Mr Skeptics summary is accurate (I'm not going to bother with a PDF for a creationist claim), then this covers the redundancy argument:

 

http://www.talkorigins.org/faqs/comdesc/section4.html

[CharonY]

If anything redundancy is a point in favour of evolution. Created things usually tend not to have too many of those. I mean how many times did you shirt lose two buttons whereas there is only one additional spare was to be found. Not to mention the lack of thread, needle, a coffee, a hot meal, a non-time limited research position, a few mills to set up a lab, donuts and fresh air?

[Mr Skeptic]

An interesting read, iNow. I thought this little fact was particularly interesting:

Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10⁹³ possible functional cytochrome c protein sequences

It reminds me of when I read a creationist article concerning the probability of a particular protein forming. The probability was extremely low, but I knew that for the estimate to be meaningful, it would have to account for different but functionally identical proteins. I had no idea the sheer magnitude of functionally identical proteins there were.

[mrburns2012]

I read the article, and I thought it was an interesting read. The author seems educated; though he may be in denial, he isn't dumb. The meat of the article is basically this: because duplicated versions of genes exist, there must be some sort of natural selection to prevent them from disappearing/diverging. Yet when these same genes are knocked out on animal models, no phenotypic changes are observed (which isn't true). From these observations, the author concludes that the theory of natural selection is wrong, because natural selection isn't supposed to sustain nonfunctional genes.

 

With that said, his arguments are weak because he was cherry picking his data.

[Cap'n Refsmmat]

There's no selection pressure to eliminate duplicate genes, as far as I know.

[mrburns2012]

There's no selection pressure to eliminate duplicate genes' date=' as far as I know.

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The idea is that neutral genes tend to diverge presumably by spontaneous mutation. So, if duplicated genes are neutral, they'll diverge. If they're harmful, they'll be removed. If they're advantageous, they'll be very conserved. Because he sees that duplicated genes appear very conserved, he argues that there must be a selective advantage - so they aren't neutral genes. But knocking out these genes doesn't kill the animals, so he argues that they're neutral genes. Conservation of neutral genes is a paradox. That's his argument.

 

EDIT: By the way, duplicated genes can be harmful. A well known disorder is Trisomy 21. People with the condition have a significantly reduced fitness.

EDIT 2: Without examining data he's using, that's a perfectly reasonable argument.

Edited January 30, 2009 by mrburns2012

[iNow]

An interesting read, iNow.

 

Yeah, that talkorigins link totally spanks the claims in the article. You were right in your assessment posted above (I just went through it). Thanks for the head's up and quick help in this thread.

 

http://www.talkorigins.org/faqs/comdesc/section4.html

[bigore]

So if i understand this correctly genetic redundancy is not a problem for evolution.

 

I'm just curious, this is what is said in short:

 

- Every living organism has essential genes.

- Every living organism has lots of redundant genes.

- Essential genes cannot be removed without changing the phenotype.

- Redundant genes can be removed and do not change phenotype whatsoever.

 

So if redundant genes are not ALL necessary for the survival of the organism, the mutation rate should be higher, because there is no selection pressure. But that is what this article claims not to be true.

 

Redundant genes seemes to mutate at the same rate as essential genes. Why is that if there is no selection pressure on the redundant genes?

 

By the way, i'm no creationist, this guy has more articles. But genetic redundancy is the Darwin's Death Blow as he calls it.

Edited January 30, 2009 by bigore

[bigore]

I totally agree with Mrburns 2012

 

But i like to go back on topic and like an answer to this question, preferrably with references.

 

- Every living organism has essential genes.

- Every living organism has lots of redundant genes.

- Essential genes cannot be removed without changing the phenotype.

- Redundant genes can be removed and do not change phenotype whatsoever.

 

So if redundant genes are not ALL necessary for the survival of the organism, the mutation rate should be higher, because there is no selection pressure. But that is what this article claims not to be true.

 

Redundant genes seemes to mutate at the same rate as essential genes. Why is that if there is no selection pressure on the redundant genes?

[mrburns2012]

Why is that if there is no selection pressure on the redundant genes?

 

You've provided a good summary:

 

- Every living organism has essential genes.

- Every living organism has lots of redundant genes.

- Essential genes cannot be removed without changing the phenotype.

- Redundant genes can be removed and do not change phenotype whatsoever.

 

The question is: are there's enough data in his paper (references and all) to support all (or any) of those conclusions? The answer is no. The section "Molecular switches" sounds bogus to me.

 

He basically claims that redundant genes KO mice show no observable phenotype throughout the paper. But when there are some, he shrugs his shoulders and pretty much says, "Well, they didn't die. That's good enough."

[Mokele]

Duplicated genes are far from a problem for evolution, and in fact can be a boon. Current evidence suggests that what gave vertebrates a 'leg up' back in the Cambrian was a whole-genome duplication, which allows the duplicated genes to diversify into new roles (in this case, a complex head). A second genome duplication seems to be behind jaws and paired fins, and teleost fish have had yet another (probably responsible for their incredibly complex skulls).

 

We've even watched it happening. Single-gene duplications are fairly common, about 1 in 100,000 divisions for yeast (probably similar for us), and don't require any specialized outside input. Deletions, too, but those are often lethal unless there's a duplicate.

 

 

The paper linked to is by someone who clearly has no knowledge of genetics, evolution, or any paper written on gene duplication in the past 40 years. This sort of stuff is covered in undergrad-level biology courses.

 

Mokele

[bigore]

Ok, the movement to pseudoscience seems a bit odd, but ok.

 

I don't think real biologists will look in this section, while my question is valid for biologists i guess.

 

Is Peter Borger right about the mutation rate of essential genes and redundant genes? I see an answer above about gene duplication. But that is what this article is about, gene duplication is not the only reason for redundant genes as stated in his referenses..

[Sayonara]

Off-topic trolling deleted and thread replaced in Genetics forum.

[Mokele]

Mutation rates are the same because mutations are simply a chemical process that doesn't distinguish based on gene function. Essential, redundant, and useless genes all mutate at the same rate, as do the areas between genes. Selection will weed out the mutations to essential genes, unless they're beneficial, but there is no reason to expect differences in mutation rate. Yet more evidence that Mr. Borger has no clue what he's talking about.

 

Mokele

[Mr Skeptic]

Is Peter Borger right about the mutation rate of essential genes and redundant genes? I see an answer above about gene duplication. But that is what this article is about, gene duplication is not the only reason for redundant genes as stated in his referenses..

 

Mutation rates can be different in different parts of the genome, but I don't know whether it is related to how vital the gene is, nor if the mutation rate itself is the same but the repair different. However, a mutation in a vital gene is far more likely to be acted on by natural selection, usually to remove it, so mutations accumulate more slowly in vital genes.

 

Without gene duplication, it would be nearly impossible for vital genes to evolve because most changes would be removed by selection pressures. However if there is a duplicate, both the duplicate and the original are more free to evolve since the other can cover for it in the case of an otherwise fatal mutation. A duplicate can end up changing enough to acquire a new function.

 

The selection pressure to delete a duplication would be quite small, especially in eukaryotes, though it could be significant for duplications of regulatory systems.