In the 1970s, when scientists compared the sequences of DNA in genes with the sequences of RNA encoded by those genes, they made a puzzling discovery: the DNA of most genes in animals, plants, and other eukaryotes contains too much information. The extra segments of largely useless information were named introns, and they must be cut out of RNA before the protein is made. Exons are the portions of the gene that remain in the RNA after the introns have been removed.
- Relics of Eden
At every turn evolutionists are faced with inventing yet another story. But that’s ok because, to paraphrase dazz, they are used to it by now.
At some point in some lineage in the history of life it must have been advantageous to insert crap into the genome. But that’s simply not allowed, under the central dogma. Even so, some mechanism must have evolved to make it possible to insert crap into the genome, and then yet another mechanism evolved to remove the crap from the DNA so that protein could still be produced from genes in spite of the fact that genes had become filled with junk.
At some point, the evolutionary story stretches credulity.
Assume a gene without an intron. Now imagine a scenario in which some piece of crap of indeterminate length gets inserted into that DNA sequence. Imagine more than one. Imagine that protein manufacture continues unabated in spite of the insertion. Imagine now an imaginative mechanism arises to excise the crap out of the gene. Let your imagination run wild!
It’s simply difficult for me to believe that “it just happened, that’s all” is rational. It throws rationality, and science, out the window.
What is the most recent and the most plausible explanation for the rise and fall of introns?
They are an artifact of the Intelligent Design of organisms. They were required for alternative splicing which is an intelligently designed mechanism for producing more than one protein from any given gene.
That is the only plausible explanation for it
Not if you simply reverse the sketch you made. Self-splicing introns can insert themselves ‘selfishly’. They don’t benefit the organism, they benefit themselves, in much the same way a computer virus spreads on its own account, by hiding. Yes, yes, I know computer viruses are designed; save your energy on that score.
Unlike many transpososon-type elements, which can’t remove themselves, these introns are non-disruptive in genes provided they excise cleanly. Where they do excise cleanly, the opportunity exists for all sorts of crap to accumulate in the crevice so formed.
The mistake is in thinking that everything in a genome must be adaptive for the organism. Of course once you have such boundaries, you have the means to shuffle and drop exons, which can be adaptive.
A mechanism? Thought ID didn’t do mechanisms.
Which of the two explanations will look like a just-so story to Mung? Frankie’s “artifact of the Intelligent Design” or Allan’s well articulated, highly descriptive one?
Bets are open.
huh?
I should mention about 25% of the human genome is intron; less than 2% is exon. So if you wanted alternate versions of the proteins, you’d need c12 times as many alternate versions per gene to make the extra space cost-effective, compared to actually using it to ‘code’. And those alternate versions could be specifically tuned, which is not available when the same exons need to be used in many different proteins.
It’s not you, it’s him.
“It’s sooooo complex and I don’t understand it, therefore GAWDDIDIT!!”
Do these IDiots ever offer anything different?
Links from The Nature Institute”
Intron length affects timing of gene expression. Timing is very important during development. Does this demonstrate “selfish” intron behaviour?
A regulatory role for introns. Accidents put to good use.
Introns are not just paracitic insertions.
There are much more examples at the link I gave above.
And what about exitrons?
The usual line when experts unearth more details of processes is, “it seems to be more complex than we thought”, I would like to ask, more complex than who thought?
Charlie M,
Good stuff! A lot of that I had not seen before. Many thanks. God bless.
Sal
So they know what they are doing and why? Really? What happens when they get inserted into a coding sequence? I bet it messes it up.
And they just know when it’s time to get out? Really?
Hi Sal
I’m very happy to help. I knew this would be right up your street! 🙂
Dunning-Kruger Street
Umm Allan never said that nor how blind and mindless processes didit. So Allan’s well articulated, highly descriptive explanation doesn’t refute ID nor does it support evolutionism.
Introns splicing themselves in and then excising when the time is right- as if they know all of that. Evos will accept anything as long as they think it supports their position- even when it doesn’t. LoL!
Sometimes they say “common design.”
Which explains everything that common descent does just by invoking it. The lack of “common design” (differences indicating divergence) that also matters to common descent is simply ignored.
OK, not really different, but at least another complete failure to deal with the issues that in fact don’t support their claims.
Glen Davidson
GlenDavidson,
Of course you could discuss the research relevant to the thread or at least show that you are interested in it.
Glen:
Godthe Designer likes a little variety, except when he doesn’t. He also likes introns, except when he doesn’t.Glen the equivocator strikes again! How are you defining common descent, Glen? I ask because when it isn’t in caps then all you are talking about is humans giving rise to humans- ie a typical family tree.
LoL! So a common design excludes divergence? Really?
LoL! The blind watchmaker likes very little variety except when it doesn’t. It also likes introns, except when it doesn’t. Too bad the blind watchmaker can’t account for introns in the first place.
Why? Did Mung explain anything, or just complain about evolution?
Sorry, one needs to say something useful if one expects interest. You should try it.
Glen Davidson
LoL! All Glen and the rest do is complain about ID and never explain anything in terms of blind and mindless processes
And yet you and yours never do. Perhaps YOU should try it.
That will never happen, Charlie. These guys aren’t interested in research and science. Dogma never is
Mung says,
The Central Dogma of Molecular Biology is,
I don’t see how inserting crap into a genome violates the Central Dogma. Perhaps Mung can explain ?
The function of spliceosomal eukaryotic introns is multi-purpose. We are discovering function after they are expressed, but they have important function before they are expressed as reconfigurable parking lots and highways for molecular machines like regulatory proteins.
Much of the ncDNA before it is transcribed can be viewed as spacers and parking lots which also have epigenetic RAM in the form of histones (and occasionally DNA mehtylations). And how they function as a spacer or parking lot depends on the cell type, and there are at least 213 canonical cell types, but possibly thousands of cell types in actuality (skin cells, nerve cells, bone cells, sperm cells, etc.)
So intron length is more than just about timing. It affects the way the Origami Code of higher order chromatin structure works between cell types to create configurations like the one below.
Depicted below shows how DNA can serve as parking lots for molecular machines in gene expression. The location of the parking lots changes depending on cell type, and thus also the spacer locations. The spacer locations help isolate one transcription area from other transcription areas. These transcription areas go by names like Topologically Associated Domains (TADs) or transcription factories.
Depicted below are molecular machines known as regulatory proteins parking on non-coding DNA. The complexity boggles the mind!
CharlieM,
Hi Charlie
Thanks for the info on introns. This helps the case for their function in the genome. Drosophila has a gene that takes 16 hours to express in development. This is due to the length of genes introns.
The previous diagram has a really groovy description on the STC blog:
http://schaechter.asmblog.org/schaechter/2014/02/on-finding-jewels-in-the-junk.html
Here are some more thoughts from the STC blog. They obviously put the complexity of eukaryotic spliceosomal introns in context:
The complexity the Intelligent Designer put in the eukaryotic animal cell boggles the mind.
Prions transfer their spatial shape, ie information, to other proteins causing them to also change shape
Many of the parking lots in the picture here:
lie within the introns.
Here is a description of the discovery some parking lots (aka ENHANCERs) lying within introns. These introns coordinate the configuration and movement of these “parking lots” (enhancers).
http://www.pnas.org/content/106/47/19934.full
Hopefully, those introns don’t look so junky now! They look like amazing robotic arms positioning molecular machines in just the right place to do the right job.
The intron (and other ncDNA) positioning of molecular machines to make proteins reminds me of the man-made analogue of robotic arms positioning and operating tools in the making cars.
Frankie,
Did you actually read what you responded to? You know what a self-splicing intron is?
Mung says,
I can understand why the origin of introns might seem impossible to people who haven’t learned (or don’t bother to learn) basic biochemistry and molecular biology.
Mung asks,
If you don’t know the answer then why not just ask for help instead of prefacing your question with your view that the answer is probably irrational? You don’t know the answer so don’t assume that nobody else does either.
Allan Miller gave you the answer in comment #2. The first introns were undoubtedly group II self-splicing introns. Tom Cech got the Nobel Prize in 1989 for discovering them. The chemical reactions of self-splicing are the same as those of spliceosomal introns.
Modern spliceosomal introns appear to have arisen from these original self-splicing introns through an intermediate stage where the group II intron acted in trans to assist removal of introns that had gradually lost the ability to self-splice.
Protein factors that enhanced the efficiency of this reaction evolved and eventually the RNA acquired mutations making it dependent on those proteins for activity. At this point the primitive spliceosome became irreducibly complex.
Over time the original group II intron evolved into the five small RNAs we see today in the spliceosome. Those five snRNAs still retain similarities to the original group II self-splicing intron revealing their origin. The hypothesis is known as “Five Easy Pieces.”
All of this information, and much more, can be found with a little effort. Or you could just ask people who know about biochemistry and molecular biology. It’s never a good idea to assume you can challenge evolution just because of personal ignorance.
Costa, M., Walbott, H., Monachello, D., Westhof, E., and Michel, F. (2016) Crystal structures of a group II intron lariat primed for reverse splicing. Science, 354:aaf9258. [doi: 10.1126/science.aaf9258]
Doolittle, W. F. (2014). The trouble with (group II) introns. Proceedings of the National Academy of Sciences, 111:6536-6537. doi: [doi: 10.1073/pnas.1405174111]
Lynch, M., and Richardson, A. O. (2002). The evolution of spliceosomal introns. Current opinion in genetics & development, 12:701-710. [doi: 10.1016/S0959-437X(02)00360-X]
Martin, W., and Koonin, E. V. (2006). Introns and the origin of nucleus–cytosol compartmentalization. Nature, 440:41-45. [doi: 10.1038/nature04531]
Rogozin, I. B., Carmel, L., Csuros, M., and Koonin, E. V. (2012). Origin and evolution of spliceosomal introns. Biology direct, 7:11. [doi: 10.1186/1745-6150-7-11]
Roy, S. W., and Gilbert, W. (2006). The evolution of spliceosomal introns: patterns, puzzles and progress. Nature Reviews Genetics, 7:211-221. [doi: 10.1038/nrg1807]
Sharp, P. A. (1991). ” Five easy pieces.” Science, 254:663-664.
Will, C. L., and Lührmann, R. (2011). Spliceosome structure and function. Cold Spring Harbor perspectives in biology, 3:a003707. [doi: 10.1101/cshperspect.a003707]
stcordova,
Ah Jeez, I can hardly be bothered any more. Reams and reams and reams of brain-dump, pretty pictures, it’s all rilly complex therefore ….
You don’t have to post as if your eternal life depended on it, Sal. Discussion has become nigh impossible. You all think everything was designed. I think we got that.
https://en.wikipedia.org/wiki/Intron
You don’t say.
The book cited in the OP called them junk.
When it’s pointed out that stuff is complex in opposite ways to which we could expect stuff to be complex they fall strangely silent. I think I see an OP coming up…
Larry Moran,
This is from the op.
Yet the argument you make is for the origin of spliceosome removed introns. What about the origin of group 2 introns?
The complexity the Intelligent Designer put in the simplest eukaryotic cell boggles the mind!
Regarding introns as spacers, it might be instructive to go back to an exchange between Jonathan Wells and Steve Matheson, Arthur Hunt and Larry Moran seven years ago (my how time flies!).
http://www.evolutionnews.org/2010/06/the_factfree_science_of_mathes035521.html
Nope nope nope. As we know now, these “spacers” may not be so inert after all, but more akin to information bearing robotic arms used to position proteins that service the genes. We are starting to realize this because introns also harbor HISTONES!
As pointed out in the STC blog, alteration of these histones on ncDNA allows them the DNA/chromatin complex to be spatially manipulated. In combination with histone modification, proteins, RNA transcripts, these “spacers” are transformed into robotic arms that service the gene (as shown above).
Now why the extra complexity for eukaryotes? Prokaryotes don’t go through so much trouble. But this is like asking why are Rube Goldberg machines complex when the task can be done more simply. The issue is, like the peacock’s tail, the extravagance of the Rube Goldberg machine seems to go beyond mere survival.
Prior to Darwin’s time, extravagances in biology were seen as something that was put there in order to make observers wonder at the genius of the Rube Goldberg Machine Maker in the sky. In Darwin’s time, it was the peacock’s tail that was the symbol of extravagance. The peacock’s tail made Darwin sick. In the present day, we have so many more things that ought to make Darwin sick, like functional introns!
One benefit of this extra complexity enables dynamically changing expression levels between cell types in multicellular animals. It would appear the Intelligent Designer had method in his madness. Praise be!
Therefore, at least in this case we’ve established how introns can be functional. There’s hardly been any discussion about the 3D aspect of introns as robotic arms for molecular machines.
Sheesh, I’d think you’d be a little more appreciative of the new perspectives I’m offering. So much focus on transcription and just quoting snippets here and there without much mechanical insight.
Now we know a lot more than we did in 2010 when the intron debate between Wells and Matheson, Hunt and Moran took place.
Introns compose 30% of the genome or so. I don’t think it’s quite so easy to write them off today like Matheson did 7 years ago. One can see, given what I laid out above, it probably will be a lot harder to write them off after a few more decades of research.
7 years is a long time to start setting the record straight on the old intron debate between Wells and Matheson, but better late than never.
It’s because evolution cannot think about design in the same way designers like us can. You seem afraid to address this head on.
I don’t think the origin of introns is impossible, I just find it miraculous. I mean, what are the odds? 🙂
I’ll tell you what Larry, I’ll pull out some biochem and molbiol texts and see what they say about when, how, and why introns evolved. That’s a step in the right direction isn’t it? However, my experience has been that such books don’t cover evolution. They tend to stick to the facts.
Simplicity and elegance are strived for in design. Complexity can be implemented with simple, discrete components that are loosely coupled.
You designer designs utterly unlike any human designer. And yet you use human designed artifacts as evidence for design in biology. Those robot arms, are they goldberg style contraptions? Is the software that runs them? No, and no.
You are worshipping a process. The irony is strong.
It’s called science. We learn more, people change their opinions. What you are doing is not science, it’s some weird score settling combined with some sort of sense of resentment.
Always worth checking the primary source when Sal is quoting.
stcordova,
Introns can be functional. This does not make every base in every intron functional. This is exactly the same argument you’ve used on LINEs, SINEs, everything else. One functional sequence, and that’s 25% of the genome accounted for …
I’m not going to get you to see this, and I am getting pretty bored saying it.
These aren’t ‘new perspectives’. It’s just Google-copy-paste. I (and anyone else), am perfectly capable of going out and reading the literature (well, anyone except colewd, apparently!). The purpose of your posts, though, seems more to dazzle than to inform.
Yes, you provided a caveat and that begs the question- you said:
And my response was- So they know what they are doing and why?
That should create havoc for the gene involved.
Only what is written. But yes, self-splicing introns are just another biological feature that blind and mindless processes cannot account for.
Mung,
It’s that pathetic detail thing again, isn’t it? Sequences, dates, organisms, inside leg. Now! Or I say …. Designed. Somehow.
It’s never stopped me before!
You already sound like Sal. YEC is calling! You know you want it!
Testable hypotheses. Else all you have is just another creation myth.
This is surreal- just because we can observe something, ie self-splicing introns, and it’s actions follow all of the rules of biochemistry that is not evidence that self-splicing introns arose via natural selection, drift or constructive neutral evolution. It is only evidence for their existence, what they can do and how they do it.
The irony- Somehow evolved by means of blind and mindless processes vs Designed. Somehow.
Darwin set the standard evolutionists must meet. And there isn’t anything in any subsequent version that supersedes it.