You seem to have lost me too @Rumraket.
I’m very surprised by you two being perplexed about this. Here’s an article discussing mechanisms for intron proliferation:
Yenerall P, Zhou L. Identifying the mechanisms of intron gain: progress and trends. Biol Direct . 2012;7:29. Published 2012 Sep 10. doi:10.1186/1745-6150-7-29
To my knowledge it has been documented by phylogenetic analysis that younger genes generally have fewer introns than older genes(reference below) (the implication being that introns are capable of invading new genes), and that there is an overall trend for gene age to positively correlate with intron numbers. I often come across articles discussing introns as a type of mobile genetic elements, and they’re also typically mentioned in discussions concerning selfish DNA in general.
Edit: I should say that since multiple different means by which introns can be gained have been proposed, it would be an oversimplification to say all introns could be said to fit the bill of a kind of transposable/selfish genetic element. But there has definitely been considerable discussion around the concept of introns as selfish transposable elements, particularly concerning the mechanisms thought to be responsible for the origin of eukaryotic spliceosomal introns from prokaryotic group-II self-splicing introns during eukaryogenesis.
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Honestly, the programming analogy is a terrible one.
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Would I guess correctly that “young” genes are ones that are not shared deep into a common ancestry tree? I’m wording this poorly I realize.
Interesting stuff.
Are any of them? To my knowledge introns don’t code for reverse transcriptase or any of the other proteins needed for a transposon. Are introns even copied from one locus to another?
Some introns (Group-II self splicing introns) encode the Prp8 protein (which also functions in the spliceosomal complex), which actually appears to have evolved from retroelement-encoded reverse transcriptases.
Abstract
Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may not be sufficient for the nucleotidyltransferase activity. The RT domain is followed by an uncharacterized sequence region with relatives found in fungal RT-like proteins. This part of Prp8 is predicted to adopt an α-helical structure and may be functionally equivalent to diverse maturase/X domains of retroelements and to the thumb domain of retroviral RTs. Together with a previously identified C-terminal domain that has an RNaseH-like fold, our results suggest evolutionary connections between Prp8 and ancient mobile elements. Prp8 may have evolved by acquiring nucleic acid–binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example—the other one being telomerase—of the RT recruitment from a genomic parasite to serve an essential cellular function.
Group II introns in particular appear to be very active in plant mitochondrial genomes:
Apparently some are, though the mechanisms facilitating this are still apparently shrouded in mystery.
This why I first analogized introns to deactivated, formerly self-replicating computer viruses. We can discard the computer code analogy, but I think the widespread presence of introns in eukaryotic genomes really are best explained as the remnants of ancient group-II selfish genetic elements that invaded the endosymbiotic host’s genome during the process of eukaryogenesis, most of which eventually lost their ability to self-splice and proliferate, which in turn facilitated the evolution of the spliceosomal complex as a mechanism necessary for their removal from mRNA, with some few remaining introns still occasionally being (somehow) capable of facilitating their own insertions.
Now this does not seem to be able to explain all recent intron gains (for some reason introns are still continuously gained), and other mechanisms for intron emergence also appear to have evolved.
Back from Tennessee. Saw many/most of the posts. Thanks for your input! I don’t see anything compelling, to conclude that Eliminating Virus, would be a good idea.
I would be interested in your take on this, when you get a chance:
IF a Designer says… “you will surely Die”, what difference does it make, how the Designer “picks you off”? Your followup post, seemed to be trying to get God off the hook!
Here is a small point that you may not like… when you say to me… “though your numbering is a charming but confusing mess”… I am just telling you, that type of line, just makes it easy for me to discount your “good data”!
Now some Fun info.
Facebook and Blogs, obviously have “clarification posts” going on all the time.
I appreciate the Design Features on this Blog (I need to start using them), many help facilitate and Focus on key areas of the post.
My Numbering Technique, is just a way that allows people to Focus on certain areas of the post.
I hear you, that you feel it is confusing.
Since you are a programmer… would give you some pushback on rebelling against numbers:
- In the 1970’s I had to program using a “card”, there were Numbers (in order) all over it… why?
- In the 1980’s I had a Green Screen to code on… in the 1990’s, they switched to 4 colors… why?
- Every line, in All computer code, is numbered… why?
- When I go to Home Depot, they are numbers everywhere… why?
- When I go to the Grocery Store, and ask Where is the Peanut butter, the stocker says Aisle 14
- Etc.
Since people are actually concerned about “Numbering”, and “Capitals”, and even “Commas”, let me ask this additional question.
IF this Rock is found on Mars, and a similar Rock is found 1 mile away,
and then 2 similar Rocks are found an additional mile away,
and then 3 similar Rocks are found an additional mile away,
and then 5 similar Rocks are found an additional mile away,
and then 8 similar Rocks are found an additional mile away…
Can I infur Anything, from a Science standpoint about this “pattern”?
Thanks again for taking the time to answer my previous points!
