Is Functional Information Functional?

Self splicing introns don’t work in the nucleus of a eukaryotic cell as I have shown you due to Mg++ content. I do like the story of the “invading introns”. :slight_smile:

You’re right here, my wording was incorrect. Indeed, it is not the case that the constrained part of a protein is made of AAs that are all absolutely required for the function. The right way to put it would have been to say that the constrained part of a protein is made of AAs that all contribute to the function to the point that any change occurring in the sequence of that constrained part would be negatively selected.

“…any change occurring in the sequence of that constrained part would be negatively selected” would be utterly and spectacularly wrong. You have cited no data nor even argued that extant proteins must occupy activity maxima. That’s just one of the many false assumptions built into @gpuccio’s hypothesis.

Would you like to see the data falsifying your assumption? That’s right in the middle of my area of experience.

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So the confidence level in your estimate is so small it’s indistinguishable from zero.

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Bill, do you know the organism that was used when self-splicing introns were discovered? There was a Nobel Prize awarded for this work (Tom Cech). Google it, I think you will be surprised.

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Thanks Curtis.

The first example, discovered by Thomas Cech, was a ribosomal RNA found in a protozoan. Since then, hundreds of examples have been identified in genome sequences of many organisms. The example shown here, from PDB entry 1u6b , is part of a bacterial transfer RNA that must be spliced before it can adopt its functional form. In the illustration, the large structure in green is the intron, which uses a GTP and two magnesium ions to remove itself. The two exons that will be spliced together are colored red and blue–note that only a small piece of each exon is included in the structure.

This agrees with what I have previously read that a Magnesium plus rich environment is required for splicing. The eukaryotic cell nucleus (where most intron splicing occurs) is not Magnesium rich as such needs the spliceosome to remove introns.

Amazing that Bill can read an entire science article and ignore every last word except the one or two buzzterms he’s looking for, then declare he was right all along. :slightly_smiling_face:

Bill forgot the link but above passage comes from here

Self-splicing RNA

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No problem, Bill. I was just hoping you would read enough to back off the claim. Cech discovered self-splicing introns in Tetrahymena - which, as a protozoan, is eukaryotic. Yes, magnesium ion is essential to activity, but it obviously does take place in the eukaryotic nucleus.

I greatly value your participation here, and your persistence in voicing your viewpoint is highly admirable. I am hoping you will begin to scrutinize your claims with greater thoroughness and thus, increase the impact of your contributions.

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Consider that the nucleus is thought to have evolved partly as a consequence of endosymbiosis, among other things to keep splicing and protein biosynthesis separate.

The necessity of the spliceosomal complex is, in this model, a response to a selective pressure to remove deleterious introns that had lost their ability to splice themselves out of beneficial genes. So some introns lost the ability to splice themselves out due to deleterious mutations, which incurred a selective pressure to remove them, while others were coopted to remove the ones incapable of splicing. Elaboration of the splicing mechanism and the spliceosomal complex, in turn is one of the selective pressures that drove evolution of the nucleus and the spatial, compartmentalized separation of protein biosynthesis and splicing.

I highly recommend this fascinating article:
Martin W, Koonin EV. Introns and the origin of nucleus-cytosol compartmentalization. Nature. 2006 Mar 2;440(7080):41-5. PubMed PMID: 16511485.

Abstract

The origin of the eukaryotic nucleus marked a seminal evolutionary transition. We propose that the nuclear envelope’s incipient function was to allow mRNA splicing, which is slow, to go to completion so that translation, which is fast, would occur only on mRNA with intact reading frames. The rapid, fortuitous spread of introns following the origin of mitochondria is adduced as the selective pressure that forged nucleus-cytosol compartmentalization.

Can be accessed for free here. If the link doesn’t work, you can try google scholar for a free pdf.

I appreciate you citing this author. I also appreciate Rums persistence as I discovered the Magnesium problem in a discussion with him. I still think we have a chicken and egg problem with the spliceosome. We need one to make one at least in the eukaryotic cell nucleus.

What is the current thinking on the origin of the nuclear pore complex?

I don’t know. :slight_smile:

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You would need to show that this was the case in the ancestors of modern eukaryotes.

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And you need a movie of a prokaryotic cell evolving into a eukaryotic cell :slight_smile:

So you have no evidence that the ancestors of eukaryotes lacked the correct Mg++ for self splicing introns.

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What you need is evidence that the spliceosome pieces were spliced outside the cell nucleus were originally self splicing introns lost their self splicing capability as a result turned into spliceosomal introns.

Oh and then got the code to be able to travel inside and outside the cell nucleus through the nuclear pore complex. 200 spliceosomal genes all evolved this code for both their RNA and AA version. Amazing stuff. Another chicken and egg problem emerges; what came first the nuclear pore complex opening and closing based on a code or the code being part of RNA and proteins?

Even though God is an enormous concept he may be the most parsimonious explanation of this marvelous technology.

If you find the movie on this one you are golden. Unless it is from a lab outside space-time :slight_smile:

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Heh. Bill still pitching God Of The Gaps even though science rejected the idea as worthless three centuries ago.

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Since I have made no claims about the origin of the spliceosome, why would I need to do that. I don’t know how that system came about. You are making the claim that the system couldn’t evolve, so the burden of proof lies with you.

You need to show that all 200 genes were required in the first eukaryotes with spliced introns, or in their ancestors.

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I am making the case that a separate origin is a better explanation than it evolving.

You continue to use the straw-man fallacy…“could not evolve”.

This is something that made me very suspicious of Darwin’s argument when I first looked into the issues with the theory. His argument was impossible to falsify and allowed stories to support the theory.