Old 03-29-2006, 01:08 AM   #1
brad89
Guest
 
Posts: n/a
I was at work today, doing some monotonous vacuuming for Famous Barr, so I somehow drifted into thought on evolution. Although I know very little about it, I remember hearing somewhere about something called a pseudogene, pretty much a bunch of junk codons that don't code for anything useful or needed. I don't know how I seemed to just jump with this thought, but I wondered if pseudogenes could form mutations that cause benefits to the organism? I am pretty sure that a mutation to a gene will most likely be harmful to an organism, but if a mutation happened to a pseudogene, I figured it was "all to gain, nothing to lose." After all, if a pseudogene doesn't really code for anything, what would be the harm if it mutated into a real gene? I would think that if it, somehow, were to be harmful, that it would simply be naturally selected, but since it wouldn't affect any previously needed genetic material, the only possibility would be that it would be beneficial.

Perhaps my thinking is erroneous, however. I began to think of how it would interact spacially, like if a mutation would make a claw start growing out of an eyeball. I don't exactly know how this would happen, since I am by no means a biologist, but I remember hearing on some link that almost, what, 70% of the genome is made up of pseudogenes? Somewhat near that, but if a mutation occured on a pseudogene to change it into a gene, wouldn't this solve the problem of 'irreducible complexity'?

I also figured that pseudogene mutation may be able to speed up evolution because mutations are rampant in the gene pool. I just wondered if anyone with real knowledge in evolution and biology (perhaps Tenspace) could clear up my delusions on whether this could be true or not?

Thanks.
  Reply With Quote
Old 03-29-2006, 05:45 AM   #2
PanAtheist
Obsessed Member
 
PanAtheist's Avatar
 
Join Date: Oct 2004
Location: England
Posts: 2,017
Brad, I'm sure you would love learning about biochemistry - about how chemistry actually pull-offs aliveness.

It's about ten years since I did molecular biology, but I'll say this and hope it will be helpful (and not wildly untrue!)

I imagine that there are certain sequences in the DNA of the chromosomes which cause the sequences beyond it to act as a backbone for RNA building, and subsequent sequences which cause the disruption of such RNA building. Therefore only part of the DNA sequences present in the cell will be used as a backbone to create RNA strands - and these will have sequences matching only those parts of the DNA that did form a backbone.

I imagine that changing conditions in the cell can make some DNA sequences become backbones for RNA synthesis ("switching on") whilst others cease to be backbones for DNA sequences ("switching off"). Further, there will be some sequences of DNA that are *never* used as backbones in any normal circumstance. When I was at school we called this "junk DNA". (I have not heard the term "psuedogene", but I am guessing it is something similar.)

On top of this, only part of the RNA strands are going to be used as a templates for the construction of proteins. The RNA strands will have certain sequences which cause protein production to start and stop. Before and after these, the RNA sequences will again be like "junk". It is the protein which brings about actions in the organism.

If there is a "mutation" in the DNA sequences, which either creates a new "start here" sequence (where there wasn't one before) or destroys a "stop here" sequence, then what was "junk DNA" will suddenly be a sequence that is used to generate proteins. That proteins effect will depend upon the actual make-up of the sequences suddenly "released".

I can't think of any reason why its effect is more likely to be beneficial than harmful.
It's effect will be unpredictable (ie. random).

Healthy genes act as team-players. They are teamish!
Their winning plays are
salvations of an aliveness of which they are a part.
Only a fraction of genes are selfish/parasitic (and they
parasitize teams).
PanAtheist is offline   Reply With Quote
Old 03-29-2006, 06:05 AM   #3
a different tim
Obsessed Member
 
a different tim's Avatar
 
Join Date: Oct 2005
Location: Oxford, UK.
Posts: 2,330
You have two different things here I think - pseudogenes and junk DNA. I don't think there's any case of junk DNA mutating into a gene so far discovered. There are lots more ways to arrange a string of bases than there are ways to arrange them into ways that make sense as genes, so I'd think it would be unlikely from a purely probabilistic perspective. That really would be a hurricane-in-a-junkyard-making-a-747 level of probability.

Pseudogenes are slightly different in that they can code for proteins but are never expressed (e.g. the coding never actually takes place) - presumably they used to be genes and could be reactivated (as in the fully functioning, but not-expressed-in -nature, genes birds have for teeth - these can be activated in the lab producing actual hen's teeth). It is likely that such instances have been permanantly switched off by the actions of other genes but remain functional in themselves. Since these are more or less degenerate versions of once functioning genes I don't think they could be cited to explain irreducible complexity.

This is, however, not a problem as irreducible complexity is something entirely invented by ID advocates and no case of it has ever been observed (every case the ID people claim, like bacterial flagellae, has turned out to have plausible precursors). There is in fact no problem of irreducible complexity.

Pseudogenes and other non functional DNA strings do indeed mutate and presumably a pseudogene would become less likely to be functional with each mutation, eventually reaching the stage where even if it were switched on it wouldn't do anything useful. These mutations are not subject to selection as they have no phenotypic effect. Mutations therefore accumulate at a more or less constant rate and are useful as a a genetic clock to find speciation points and similar - small differences between two species "junk" DNA implies a recent divergence.

Interestingly, if creationism were true, there would be no reason to expect the phylogenetic tree given by DNA clocks to correspond at all with the family tree of life deduced from morphology. In fact short earth creationism would imply that as everything was created 6000 years ago, junk DNA from all animals and plants should be about equally different as they have all been mutating for the same period of time. Evolution on the other hand would predict that the trees should match quite closely, which in fact they do. I wouldn't try this on Salty and Jiminy though as they probably wouldn't even understand the concept.

"You care for nothing but shooting, dogs and rat-catching, and will be a disgrace to yourself and all your family"
a different tim is offline   Reply With Quote
Old 03-29-2006, 05:34 PM   #4
brad89
Guest
 
Posts: n/a
Oh, well maybe from now on before I come here with my idiot spare time theories I should actually learn about biology. I just don't know enough yet to actually cook up any real questions, so I guess the whole pseudogene thing is bunk. Sorry to waste your time, and thanks for clearing that up!
  Reply With Quote
Old 04-06-2006, 10:56 AM   #5
aurora
Guest
 
Posts: n/a
I'm a genetics student and just took a course last semester on molecular evolution, so I really should be able to answer this. Unfortunately I suffer from the all too common student syndrome of forgetting everything the moment you leave the exam room. Because of that I can't provide specific details or examples, but I can say that definitely POSSIBLE for a pseudogene to undergo a mutation that makes it functional again.

Pseudogenes arise from copies of functional genes, and since there are now two copies of the same gene, one of them is free to mutate and do whatever it likes. As long as none of these mutations are detrimental to the organism, the second gene is not selected against, and eventually becomes a pseudogene when it no longer codes for a functional protein. Since it is not selected against however, the psuedogene remains in the genome, and continues to accumulate mutations... and it is possible that one of these mutations may once again give it a function, although of course beneficial mutations in any situation are rarer than harmful ones.

'Junk DNA' is mostly repetitive DNA (the same three nucleotides being repeated, for example), I'm pretty sure that we even studied an example of junk DNA becoming a functional gene. Like a previous poster said, the probability of a stretch of repeated nucleotides encoding something functional is pretty low, but as long as the 'right' mutation occurs, anything is possible.

I hope that made sense, and anyone who knows more about the subject please correct anything that's wrong
  Reply With Quote
Old 04-06-2006, 11:56 AM   #6
4thgeneration
Guest
 
Posts: n/a
Quote:
brad89 wrote
I was at work today, doing some monotonous vacuuming for Famous Barr, so I somehow drifted into thought on evolution. Although I know very little about it, I remember hearing somewhere about something called a pseudogene, pretty much a bunch of junk codons that don't code for anything useful or needed. I don't know how I seemed to just jump with this thought, but I wondered if pseudogenes could form mutations that cause benefits to the organism? I am pretty sure that a mutation to a gene will most likely be harmful to an organism, but if a mutation happened to a pseudogene, I figured it was "all to gain, nothing to lose." After all, if a pseudogene doesn't really code for anything, what would be the harm if it mutated into a real gene? I would think that if it, somehow, were to be harmful, that it would simply be naturally selected, but since it wouldn't affect any previously needed genetic material, the only possibility would be that it would be beneficial.

Perhaps my thinking is erroneous, however. I began to think of how it would interact spacially, like if a mutation would make a claw start growing out of an eyeball. I don't exactly know how this would happen, since I am by no means a biologist, but I remember hearing on some link that almost, what, 70% of the genome is made up of pseudogenes? Somewhat near that, but if a mutation occured on a pseudogene to change it into a gene, wouldn't this solve the problem of 'irreducible complexity'?

I also figured that pseudogene mutation may be able to speed up evolution because mutations are rampant in the gene pool. I just wondered if anyone with real knowledge in evolution and biology (perhaps Tenspace) could clear up my delusions on whether this could be true or not?

Thanks.
A lot of certain genomes appear to be NCR (non-coding regions) or intergenic regions. However, recent research has revealed that a bunch of what was thought to be "junk DNA" is actually ultra-conserved from the simplest animals all the way up. The question you should be asking is, if it is so fastidiously conserved.....wtf does it do? Although it isn't totally clear, it is probably involved in regulatory functioning. I think better microarrays with more overlapping IGR's will probably help us to understand its function in the future. What a pain in the ass this is going to make functional genomics......
  Reply With Quote
Old 04-06-2006, 12:53 PM   #7
Tenspace
I Live Here
 
Tenspace's Avatar
 
Join Date: Jan 2005
Location: Rocky Mountains, USA
Posts: 10,218
Ready for my junk DNA theory?

Junk DNA == /dev/null

It's the genome's garbage collection system.

"Science and Mother Nature are in a marriage where Science is always surprised to come home and find Mother Nature blowing the neighbor." - Justin's Dad
Tenspace is offline   Reply With Quote
Old 04-06-2006, 03:06 PM   #8
4thgeneration
Guest
 
Posts: n/a
Why is it so conserved then? I'm thinking functional RNA.
  Reply With Quote
Old 04-07-2006, 01:46 AM   #9
a different tim
Obsessed Member
 
a different tim's Avatar
 
Join Date: Oct 2005
Location: Oxford, UK.
Posts: 2,330
Quote:
brad89 wrote
Oh, well maybe from now on before I come here with my idiot spare time theories I should actually learn about biology. I just don't know enough yet to actually cook up any real questions, so I guess the whole pseudogene thing is bunk. Sorry to waste your time, and thanks for clearing that up!
No, no, keep asking questions! They're good questions.

How can you tell a good question? Because you learn something from the answer. And sometimes the answer, as with this example of conserved "junk" DNA (and, yeah, why is it conserved?) can lead to more interesting things. I wouldn't have found out about conserved junk DNA if you hadn't asked that question.

So carry on.

"You care for nothing but shooting, dogs and rat-catching, and will be a disgrace to yourself and all your family"
a different tim is offline   Reply With Quote
Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Forum Jump


All times are GMT -7. The time now is 10:50 AM.


Powered by: vBulletin - Copyright ©2000 - 2019, Jelsoft Enterprises Ltd.
Copyright © 2000 - , Raving Atheists [dot] com frequency-supranational frequency-supranational