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Pseudogenes: Pseudo-functional or key regulators in health and disease


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#1 Kay

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Posted 29 April 2011 - 02:02 AM

Pseudogenes: Pseudo-functional or key regulators in health and disease?

Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs and David Raul Francisco Carter

Author Affiliations

School of Life Sciences, Oxford Brookes University, Headington, Oxford, OX3 0BP, United Kingdom

Abstract

Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.


RNA Society
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#2 Netsach Yisrael

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Posted 29 April 2011 - 01:15 PM

Thanks! I saw the same abstract here at Uncommon Descent, but I haven't been able to read the paper.

Does the paper draw the conclusion that there are no "shared errors" in our and apes' DNA? Do the authors support the idea that pseudogenes, etc., are not actually "errors," but rather purpose-designed elements of our genetic makeup? Do they explain in the paper how this disproves evolution?
Democracy: the theory that the common people know what they want, and deserve to get it good and hard. --H. L. Mencken

#3 Kay

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Posted 29 April 2011 - 01:22 PM

Thanks! I saw the same abstract here at Uncommon Descent, but I haven't been able to read the paper.


I am pleased that you are at least looking at other viewpoints :sarah:

I must say that @ uncommondescent there is civility in the discussions, reasoning and intelligence :doh:

However, I came across it from another source - when I was researching ERV's and pseudogenes last evening, and the publication was of interest.

I tend to have a wide range of sites and sources I look at ...

Does the paper draw the conclusion that there are no "shared errors" in our and apes' DNA? Do the authors support the idea that pseudogenes, etc., are not actually "errors," but rather purpose-designed elements of our genetic makeup? Do they explain in the paper how this disproves evolution?


You can purchase the paper for a minimal cost if you aren't subscribe to the Journal ... think from a European source if need be for about 10 Euros.

I also don't think anything at all was mentioned in regard to either proving or disproving evolution - was it?

Then, in view that you raised this - one wonders whether they are "shared errors" ... ?

More recently I came across comment about GULO - whether the claimed "errors" were errors in a sense.

Why?

The statement was made that no research had yet been undertaken whether insertions, so called "errors", were in actual fact regulators (not in these exact words but inferred), again, no research - just assumed that they were "shared errors".

It almost seems to echo the assumption of "junk DNA"?

Thought I had bookmarked the comments ... apparently not ... if I come across the article again in my travels I will post the link here.

Though back to the comments:

Or are several of those who now hold to Theistic Evolution in the brotherhood now jumping the gun ... now that's another story - shock, horror! - gossiping among yourselves, because it seems to be the case, anything published here.

I did a trial run with another article, although, for Coyne, as Uncommon Descent described - there appears to be "Trouble in Paradise" :P
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#4 The Barbarian

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Posted 29 July 2011 - 02:00 AM

I was an undergraduate in the 1960s when I was first made aware that some (maybe much) non-coding DNA (that's what scientists call it) had functions. A quick search turns up a paper about the function of non-coding DNA in 1975, about 36 years ago.

#5 The Barbarian

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Posted 29 July 2011 - 02:07 AM

It's hard to believe that any "designer" would make a functional feature that depended on destroying the functionality of another feature. The GULO gene has been deactivated in a wide variety of organisms, but the mode of deactivation has sorted out according to evolutionary history. This is pretty good evidence that it's merely the removal of a metabolically demanding function that is unnecessary in many organisms due to a diet that provides sufficient vitamin C.

On the other hand, there are numerous instances of a gene being deactivated by mutation for one function and picking up another. Evolution is very opportunistic, and it might well be that some of these "broken" genes might have a different function today.

Hard to see any "design" in that, though.

#6 Kay

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Posted 29 July 2011 - 02:19 AM

Barbarian

Evolutions "poster boys":

GULO - well, that has been done to death - but who has determined that it is "broken"?

GULO - in humans, there is a much more efficient system to take-up vitamin C.

The DNA - non-functional - again, done to death.

No-one is saying that it was never ever said in the past, that "some" thought there may have been some function - but limited - anyway, I will get the quotes out, Collins, Dawkins etcetera, because they have been the most vocal in that regard - Francis Collins recently, changed his mind.
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#7 The Barbarian

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Posted 29 July 2011 - 02:58 AM

GULO - well, that has been done to death - but who has determined that it is "broken"?


It's had a mutation. It no longer does in those organism, what it does in animals that don't have the mutation. That's what geneticists mean by "broken."

GULO - in humans, there is a much more efficient system to take-up vitamin C.


Yep. We eat it. Fruit-eating organisms get plenty in their diet. So it was an advantage to having it broken; no need to commit resources to an unneeded function.

The DNA - non-functional - again, done to death.


Yep. The old story that scientists didn't know about functional non-coding DNA is silly.

No-one is saying that it was never ever said in the past, that "some" thought there may have been some function - but limited


There is certainly some that is non-functional. Scientists have removed huge sections of non-coding DNA in some organisms, with no observable results at all.

anyway, I will get the quotes out


Don't do it for my sake. Quote-mining never did anything for me.

Collins, Dawkins etcetera, because they have been the most vocal in that regard - Francis Collins recently, changed his mind.


Collins seems to have been consistent on this. He acknowledges that much of non-coding DNA is not functional, but also acknowledges that scientists have found that a good deal of it does have a function.

Which is what the evidence shows.

#8 Kay

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Posted 29 July 2011 - 05:35 AM

The Barbarian - the comment isn't "quote mined" - it is from his books ... and it shows a change of mind 4 years apart.

And let's drop the "quote mine" also "flat-earthers" etcetera and the usual jargon - thanks - because we are not playing that game here :)

The section really is for Christadelphians to discuss the various issues, though other comment is welcome - but one get's rather weary of the "broken record" of GULO - Chromosome 2 - etcetera.
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#9 The Barbarian

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Posted 29 July 2011 - 12:46 PM

The Barbarian - the comment isn't "quote mined" - it is from his books ... and it shows a change of mind 4 years apart.


Any quote out of context is quote-mined. I've read Collins' works and neither of these, in isolation precisely says what he says. And in the body of his work,I don't see any change WRT non-coding DNA, except for the amount of it.

And let's drop the "quote mine" also "flat-earthers" etcetera and the usual jargon - thanks - because we are not playing that game here :)


We should always discourage quote-mining. It is not a good game to play. I think that the number of flat-Earth creationists is so tiny today as to be negligible, however.

The section really is for Christadelphians to discuss the various issues, though other comment is welcome - but one get's rather weary of the "broken record" of GULO - Chromosome 2 - etcetera.


I prefer evidence to quotes. However, if you don't want me to be here, I can leave. A mod has only to ask, and I'll go, even if I've broken no rules.

#10 Kay

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Posted 29 July 2011 - 02:38 PM

The Barbarian

As owner of this board, you can participate (and I am certain that other Administrators will agree with me) - but don't use the usual "name calling" etcetera from sites who don't believe in God or His creation.

This is a Bible Discussion Forum.

The FACT is that Collins changed his mind, no quote mining - it is just plain and simply a fact that he did.

As mentioned, GULO, has been done to death ... and I would prefer to side on the side of God - for whatever reason, the structure is how He decided to set it up - man's opinion is worth little, or his second guessing God ... who is man, or his opinion about creation when compared to the Creator and the Creator's attestation.
"seek ye first the kingdom of God, and his righteousness" Matthew 6:33

#11 The Barbarian

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Posted 29 July 2011 - 04:01 PM

As owner of this board, you can participate (and I am certain that other Administrators will agree with me) - but don't use the usual "name calling" etcetera from sites who don't believe in God or His creation.


For me, it's not just a belief. I know Him.

This is a Bible Discussion Forum.

The FACT is that Collins changed his mind, no quote mining - it is just plain and simply a fact that he did.


Have you actually read the entire book and article from which you're taking these bits, or have you taken this from somewhere else?

As mentioned, GULO, has been done to death ...


There are many other examples. Would you like to see some different ones?

and I would prefer to side on the side of God


It would be easy if He told us all the details, but He didn't. So we have to go take a look and find out.

for whatever reason, the structure is how He decided to set it up - man's opinion is worth little, or his second guessing God ... who is man, or his opinion about creation when compared to the Creator and the Creator's attestation.


Which is why we should go with whatever evidence He gives us. God is truth. Christians should embrace the truth no matter where it goes, in the confidence that He would not lead us otherwise.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined1. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts2, 3, 4 can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially 'disposable DNA' in the genomes of mammals.

Clearly Collins was right that large amounts of non-coding DNA has no function. He is also right in asserting that much of it does have a function, something known from the 1970s. I don't see a contradiction here.

#12 nsr

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Posted 29 July 2011 - 05:09 PM

It would be easy if He told us all the details, but He didn't. So we have to go take a look and find out.


Do we have to? I tend to think that if God doesn't tell us something, either explicitly or by enabling us to deduce it from his word, then it means one or more of the following:
- we don't need to know.
- he doesn't want us to know.
- we can't know.

In this case, I think probably all three are true. It makes no difference to our salvation. I think we are probably far, far too primitive to understand how God does any of his supernatural work. If our scientific understanding can't explain how Jesus did something relatively simple like healing, turning water to wine, or walking on water, then how can it possibly grasp how God created life?

Discussions about the means by which God brought about life on earth always, and I mean always lead to the most unChristlike behaviour on both sides of the discussion, and never ever achieve anything remotely like edification.
"But you have come to Mount Zion and to the city of the living God, the heavenly Jerusalem, to an innumerable company of angels, to the general assembly and church of the firstborn who are registered in heaven, to God the Judge of all, to the spirits of just men made perfect..." (Heb 12:22-23)

#13 The Barbarian

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Posted 29 July 2011 - 07:25 PM

Do we have to? I tend to think that if God doesn't tell us something, either explicitly or by enabling us to deduce it from his word, then it means one or more of the following:
- we don't need to know.
- he doesn't want us to know.
- we can't know.


I think He gave us intelligence and curiosity for a reason. He didn't tell us about atoms, or disease microbes, or solid-state physics, among others. All of these have turned out to be good to know about.

It makes no difference to our salvation. I think we are probably far, far too primitive to understand how God does any of his supernatural work.


Yep. But He did grant us the ability to learn how nature works. Thank Him. This would be a sad and dull place with no mysteries to solve.

If our scientific understanding can't explain how Jesus did something relatively simple like healing, turning water to wine, or walking on water, then how can it possibly grasp how God created life?


He gave us a hint in Genesis. He used natural means to produce living things.

Discussions about the means by which God brought about life on earth always, and I mean always lead to the most unChristlike behaviour on both sides of the discussion, and never ever achieve anything remotely like edification.


It can. But if you accept that it really doesn't affect our salvation, and that God is truth, then finding out isn't a bad thing.

#14 nsr

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Posted 29 July 2011 - 08:46 PM

I think He gave us intelligence and curiosity for a reason. He didn't tell us about atoms, or disease microbes, or solid-state physics, among others. All of these have turned out to be good to know about.

Sorry, but Scripture says nothing about our intelligence and curiosity being used to find the truth. It's the opposite: we have to humble ourselves, admit how feeble our intelligence actually is, seek the things which God commands and not the things we find interesting, and listen to what God says.

Yep. But He did grant us the ability to learn how nature works. Thank Him. This would be a sad and dull place with no mysteries to solve.

I'm sure it would, but see above.

He gave us a hint in Genesis. He used natural means to produce living things.

I don't think he gives us any hints regarding how he did it. Remember, the Bible wasn't just written for scientists living in the 20-21st centuries. I am extremely sceptical of the idea that modern man is able to use modern thinking to deduce and understand the Bible in a way that ancient man couldn't.

It can. But if you accept that it really doesn't affect our salvation, and that God is truth, then finding out isn't a bad thing.

I have never seen anything good come out of these discussions. I'm actually quite astounded by the arrogance of man in thinking he can work out "how God did it". As I said, if science can't explain the miracles of Jesus, why should we believe it can explain the creation, a far greater event on a far greater scale?
"But you have come to Mount Zion and to the city of the living God, the heavenly Jerusalem, to an innumerable company of angels, to the general assembly and church of the firstborn who are registered in heaven, to God the Judge of all, to the spirits of just men made perfect..." (Heb 12:22-23)

#15 The Barbarian

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Posted 30 July 2011 - 12:09 AM

Barbarian observes:
I think He gave us intelligence and curiosity for a reason. He didn't tell us about atoms, or disease microbes, or solid-state physics, among others. All of these have turned out to be good to know about.

Sorry, but Scripture says nothing about our intelligence and curiosity being used to find the truth.


1 Corinthians 12:8 To one indeed, by the Spirit, is given the word of wisdom: and to another, the word of knowledge, according to the same Spirit; [9] To another, faith in the same spirit; to another, the grace of healing in one Spirit; [10] To another, the working of miracles; to another, prophecy; to another, the discerning of spirits; to another, diverse kinds of tongues; to another, interpretation of speeches.
[11] But all these things one and the same Spirit worketh, dividing to every one according as he will.


For us, the study of his creation glorifies God and makes clear His divine providence and wisdom.

Barbarian observes:
Yep. But He did grant us the ability to learn how nature works. Thank Him. This would be a sad and dull place with no mysteries to solve.

I'm sure it would, but see above.


I like His POV in 1 Corinthians.

Barbarian observes:
He gave us a hint in Genesis. He used natural means to produce living things.

I don't think he gives us any hints regarding how he did it.


He says the Earth and water brought forth living things. Seems right to me. Not a lot of technical detail, but a clear demonstration that nature is His, and the way He does many things.

Remember, the Bible wasn't just written for scientists living in the 20-21st centuries.


Of course. He didn't describe the way cell membranes came about for example. He kept it simple, but accurate.

I am extremely sceptical of the idea that modern man is able to use modern thinking to deduce and understand the Bible in a way that ancient man couldn't.


Modern science has come around to the same opinion about the origin of life. Not bad.


Quote
It can. But if you accept that it really doesn't affect our salvation, and that God is truth, then finding out isn't a bad thing.

I have never seen anything good come out of these discussions.


Maybe not here. Some boards have unbelievers, and sometimes, as was the case with C. S. Lewis, reason can be a way to come to him. Not many, but over the years, several atheists or agnostics have told me that my talks with them have led them to believe. A good thing, even if I'm not the most productive evangelist.

I'm actually quite astounded by the arrogance of man in thinking he can work out "how God did it". As I said, if science can't explain the miracles of Jesus, why should we believe it can explain the creation, a far greater event on a far greater scale?


As Einstein said, the most incomprehensible thing about nature is that it is so comprehensible to us. We were made to know and understand it.

Edited by The Barbarian, 30 July 2011 - 12:15 AM.


#16 Netsach Yisrael

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Posted 10 August 2011 - 09:08 PM


It would be easy if He told us all the details, but He didn't. So we have to go take a look and find out.


Do we have to? I tend to think that if God doesn't tell us something, either explicitly or by enabling us to deduce it from his word, then it means one or more of the following:
- we don't need to know.
- he doesn't want us to know.
- we can't know.


No, we don't have to. But to avoid being hypocritical, we should avoid taking advantage of modern medicines, paternity tests, and other technology--because if you really want to have those things, then you actually do "have to" after all. None of them would be possible without "looking and finding out."
Democracy: the theory that the common people know what they want, and deserve to get it good and hard. --H. L. Mencken

#17 nsr

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Posted 10 August 2011 - 09:24 PM

And there's a perfect example of why these discussions never lead to mutual edification.

I'll be closing this thread if that's all right, Kay.
"But you have come to Mount Zion and to the city of the living God, the heavenly Jerusalem, to an innumerable company of angels, to the general assembly and church of the firstborn who are registered in heaven, to God the Judge of all, to the spirits of just men made perfect..." (Heb 12:22-23)




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