Intelligent Design

The spliceosome: a molecular machine that defies any non-design explanation.

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OK, let’s start with a very simple fact: eukaryotic genes have introns.

IOWs, they are not continuous. They are made of exons and introns: exon – intron – exon – intron – exon and so on. Exons code for the protein. Introns don’t.

So, when the content of the gene is copied to the mRNA, introns must be cut away, and only exons are retained, in order to be translated, so that the mature mRNA can be transferred to the cytoplasm and translated by the ribosome.

This process of removing introns is called splicing.

Now, a few clarifications:

a) Introns exist in prokaryotes too, but they are rather rare. For our purposes, we will only discuss introns in eukaryotes.

b) Introns exist in many different types of genes. For our purposes, we will discuss only those in protein coding genes.

c) The origin and possible function of introns is, still, a mystery.

d) Introns are usually longer than exons. In humans, for example, they amount to approximately 35% of the whole geneome, vs about 1.5% of coding exons.

e) However, the amount and length of introns can vary a lot in different organims. An extreme example is yeast (s. cerevisiae), whose genome contains a very small amount of introns (about 250 out of about 6250 genes).

When the gene if transcribed, both exons and introns are transcribed. A 5′ UTR (Untranslated region) and 3′ UTR, is also part of the pre-mRNA.

 

Fig. 1

Pre-mRNA is the first form of RNA created through transcription in protein synthesis. The pre-mRNA lacks structures that the messenger RNA (mRNA) requires. First all introns have to be removed from the transcribed RNA through a process known as splicing. Before the RNA is ready for export, a Poly(A)tail is added to the 3’ end of the RNA and a 5’ cap is added to the 5’ end. – By Nastypatty (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

So the question is: how are introns removed from pre-mRNA? IOWs, how is splicing achieved?

And there is more. As everybody probably knows, splicing is not always done in the same way. Different isoforms of the same protein can be obtained by alternative splicing, and they can have functional differences. I will not go into details about that, but here is the Wikipedia page about alternative splicing:

https://en.wikipedia.org/wiki/Alternative_splicing

So, how is splicing done, and how is alternative splicing regulated?

We know much about the first question, very little about the second.

There are three ways to perform splicing:

  1. Spliceosomal splicing
  2. Self-splicing
  3. tRNA splicing

The last two modalities are rare, and can be found both in prokaryotes and eukaryotes. I will not discuss them here.

So, the subject of this OP is spliceosomal splicing, which is restricted to eukaryotes.

Moreover, I will discuss only the major spliceosome, which is responsible for the vast majority of splicing in eukaryotes. It must be said, however, that also a minor spliceosome exists, and that it acts in a minority of cases.

So, the spliceosome.

The first important point is:

It is an amazing molecular machine. Even more, it is an amazing molecular cycle, involving many different stages each of which is an amazing molecular machine.

Let’s see. Here is a figure which summarizes the main stages of the spliceosome cycle:

 

Fig. 2

 

Spliceosomal splicing cycle – By JBrain [CC BY-SA 2.0 de (https://creativecommons.org/licenses/by-sa/2.0/de/deed.en)], via Wikimedia Commons

To make it simple, the spliceosome units are built upon 5 specific RNAs, called small nuclear RNAs (snRNA). These are, in humans:

U1 (164 bases), U2 (187 bases), U4 (145 bases), U5 (116 bases), U6 (107 bases)

They are transcribed from multiple gene copies. While their sequences are not particularly conserved (U6 being the most conserved of all), their secondary structure seems to be very conserved.

snRNAs are very important in the spliceosome, because they seem to be responsible for the catalytic activities.

Each of the 5 snRNAs forms a complex with proteins, and the complex takes the name of snRNP. The whole spliceosome includes at least 145 different proteins, maybe more, some of which are still not well known.

I will mention here some of the most important:

 

U1 snRNP:

U1 snRNP 70 kDa  (P08621, 437 AAs)

U1 snRNP A (P09012, 282 AAs)

U1 snRNP C  (P09234, 159 AAs)

Sm proteins: 7 small proteins (76 – 240 AAs) which form the “Sm core” ring in spliceosome subunits U1, U2, U4, U5, a ring which hosts the specific snRNA molecule.

 

U2 snRNP:

U2 snRNP A’ (P09661, 255 AAs)

U2 snRNP  B” (P08579, 225 AAs)

SF3a120 (Q15459, 793 AAs)

SF3a66 (Q15428, 464 AAs)

SF3a60 (Q12874, 501 AAs)

SF3b155 (O75533, 1304 AAs)

SF3b145 (Q13435,  895 AAs)

SF3b130 (Q15393, 1217 AAs)

SF3b49 (Q15427, 424 AAs)

SF3b14a/p14 (Q9Y3B4, 125 AAs)

SF3b10 (Q9BWJ5, 86 AAs)

Sm proteins

 

U4/U6 snRNP:

Prp3 (O43395, 683 AAs)

Prp31 (Q8WWY3, 499 AAs)

Prp4 (O43172, 522 AAs)

Cyph ( O43447, 177 AAs)

15.5 K (P55769, 128 AAs)

Sm proteins (for the U4 snRNA)

Lsm proteins: a number of proteins similar to Sm proteins (usually Lsm 2-8), which form a specific ring for the U6 snRNA.

 

U5 snRNP:

Prp8 (Q6P2Q9, 2335 AAs)

BRR2 (O75643, 2136 AAs)

Snu114 (Q15029, 972 AAs)

Prp6 (O94906, 941 AAs)

Prp28 (Q9BUQ8, 820 AAs)

52 K (O95400, 341 AAs)

40 K (Q96DI7, 357 AAs)

Sm proteins

 

Additional proteins in the U4/U6/U5 complex:

hSnu66 (O43290, 800 AAs)

hSad1 (Q53GS9, 565 AAs)

27 K (Q8WVK2, 155 AAs)

 

OK, these are only the main components, and the best understood. We are still far from the sum total of 145/150 proteins which are involved in the spliceosome cycle.

But how does it work?

Always in brief. Here is a typical exon-intron structure:

Fig. 3

 

Parts of an intron – By miguelferig (Own work) [Public domain], via Wikimedia Commons

 

GU, A and AG are nucleotides almost universally conserved in all introns, approximately at the positions shown in the figure, and which have a fundamental role in splicing. However, the real stuff is much more complex than this (see the splicing code section). GU (n. 4 in the figure) is near to the 5′ end of the intron, AG (n. 1) near to the 3′ end. The A (n. 3 in the figure) is called “the branch point”. The py-py-py (n. 2 in the figure) is the “polypyrimidine tract”.

a) The U1 subunit binds to the GU sequence at the 5′ splice site in the intron

b) The U2 subunit binds to the “branch point”.

c) The U4/U6/U5 binds to the complex.

d) Numeorus further modifications take place, causing the formation of a “lariat” (including the intron), which is then cleaved, while the two exons are ligated.

I will spare you the many complexities in all the various steps, which are well summarized (in a very simplified way) in this Wikipedia page:

RNA splicing

See in particular the “Formation and activity” section.

Or, if you like more detail, here:

Spliceosome Structure and Function

And here is a very good video on the whole splicing process in yeast:

 

 

Now, if somebody still has doubts about the complexity of this molecular machine/process, let’s consider some important aspects.

  • 1. The spliceosome is a molecular machine which appears in eukaryotes.

I quote from this paper (in the abstract):

Origin and evolution of spliceosomal introns

There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns.

The following Table shows how some of the main proteins involved in the spliceosome activity show practically no trace of homology in prokaryotes. I have included also included in the table two examples  which show low homologies due to some domain which is already expressed in prokaryotes: Prp4, whose 209 bits of homology are due to a specific domain, WD40, and Prp28, which exhibits 313 bits linked to the DEXDc domain. The point is: many of the spliceosome proteins are complete novelties in eukaryotes, but not all of them.

 

 Protein Bacteria Archea
U1 snRNP 70 kDa  (P08621, 437 AAs) 67
U2 SF3b130 (Q15393, 1217 AAs) 43.5
U4/U6 hPrp3 (O43395, 683 AAs)
U4/U6/U5 hSnu66 (O43290, 800 AAs)
U5 Prp8 (Q6P2Q9, 2335 AAs)
U5 Prp6 (O94906, 941 AAs) 100
U4/U6 hPrp4 (O43172, 522 AAs) 209 150
U/5 Prp28 (Q9BUQ8, 820 AAs) 313 286

 

I will analyze in more detail one of the most important proteins in the spliceosome, Prp8, in the last part of this OP

(Just a technical note: if you blast Prp8, you will find 3 hits which are obviously  an error due to unverified sequences, probably cases of contamination).

  • 2. The spliceosome is a molecular machine which is universally present in eukaryotes.

All eukaryotes have introns, even if in very different degrees, and the spliceosome, even if in some organisms parts of the spliceosome complex can be lost. For a more detailed discussion, look at the Rogozin paper quoted above (Origin and evolution of spliceosomal introns), in particular the section:

Intron density, size and distribution in protein coding genes across the eukaryote domain

I quote this important conclusion:

As pointed out above, despite the existence of numerous, diverse intron-poor genomes, eukaryotes do not lose the “last” intron or the spliceosome although degradation of the spliceosome including loss of many components does occur, e.g. in yeast. The only firmly established exception is the tiny genome of a nucleomorph (an extremely degraded intracellular symbiont of algae) that has lost both all the introns and the spliceosome [7]; preliminary genomic data indicate that all introns might have been lost also in a microsporidium, a highly degraded intracellular parasite distantly related to Fungi [54].

So, whe can conclude that both introns and the spliceosome are a universal feature of eukaryotes, the few exceptions being simply cases of loss of information.

  • 3. The spliceosome is a molecular machine whose information is extremely conserved throughout eukaryotes, up to humans.

I have already mentioned that the 5 RNAs which form the core of the spliceosome are not extremely conserved at sequence level, even if they are extremely conserved at structure level.

However, many of the proteins that compose the spliceosome show an amazing sequence conservation throughout eukaryotes. Now, even if we cannot be certain of when eukaryoyes really emerged, and of their early evolutionary history (both issues being at present highly controversial), we can reasonably assume that protein sequences which are highly conserved in all eukaryotes have been conserved for something like 2 billion years (more or less). As anybody who has followed my previous OPs about information conservation in vertebrates certainly knows, that is an evolutionary time frame which certainly allows us to equal conservation to extremely high functional constraint.

But how conserved are spliceosome proteins? We can analyze a few of them with my usual methodology: looking at human conserved information. The results shows that many proteins involved in the spliceosome are amazingly conserved in all eukaryotes. While there are a few cases which have a rather different evolutionary history, this is by far the most common behaviour for spliceosomal proteins.

Here is a sample of some important sequences that show high homology with the human form in all major groups of single celled eukaryotes. The 5 groups of single celled organisms chosen here, indeed, cover rather well the whole range of single celled eukaryotes.

 

Fig. 4

 

These four important proteins, as shown, have an amazing amount of information shared with the human form, ranging from more than 1000 to more than 4000 bits. In bits per AA, the range goes from 0.88 to 1.80 bits per aminoacid (baa).  As can be seen, the highest homology is found in fungi, as expected, because fungi are the most likely ancestors of metazoa. The lowest homologies are observed in Naegleria (Excavata) or in Alveolata.

Of course, these proteins remain highly similar to the human form in the following evolutionary history in Metazoa.

So, we can safely state that most spliceosomal proteins, while emerging almost entirely in eukaryotes and showing only trivial homologies with prokaryotes, were probably already universally present in the Last Universal Eukaryotic Ancestor (LECA), and in a form already very similar at sequence level to what we observe in metazoa and in humans.

  • 4. The spliceosome is a wonderful example of irreducibly complexity.

OK, we have already said that splicing can be achieved in at least three different ways. For example, bacterial introns, although rare, are of the self-splicing type. So, we know that the generic function of splicing introns can be implemented in different ways.

But eukaryotic introns are of the spliceosomal type, and they are spliced only by the spliceosome.

We have also said that a minor spliceosome also exists. It shares some featues with the major spliceosome, but it is a different structure and acts on different, and much rarer, introns.

So, for the vast majority of eukaryotic introns, the major spliceosome, and only the major spliceosome, can effectively accomplish the splicing.

Now, I don’t mean here that the major spliceosome must always be absolutely complete, with all its 150 proteins, to be able to work. That’s not what I mean when I say that it is irreducibly complex.

Maybe in some organisms the spliceosome can be partially defective, and still work. It is difficult to say, because we still don’t understand the role of all the components of the spliceosome.

But however, as far as we can understand, most of the principal features must be present, because, as we have seen, the splicing is the result of a complex cycle, involving the RNAs and the subunits, and all stages are essential to the final result.

So, the spliceosome is certainly highly irreducibly complex, even if we may not be able to clearly identify the essential nucleus of molecules which is absolutely necessary to the minimal function.

Moreover, the spliceosome would be useless if spliceosomal introns did not exist, with their properties and code (see later), and spliceosomal introns could not exist if the spliceosome were not there to splice them, because otherwise transcription would be completely ineffective. So, in that sense, spliceosomal introns and the spliceosome are a good example of chicken egg paradox, or we could also say that they form an irreducibly complex system at a higher level. And remember, the whole system seems to have been already present, very much similar to its current form in humans, in LECA, as we have seen.

But, of course, our darwinist friends will simply say that they have co-evolved!  🙂

Moreover, we can and should ask ourselves: why is the spliceosome so complex? The answer is not easy, because we still understand very little, but it is certainly related to the complexity of the splicing code, and to the fundamental issue of alternative splicing.

The Splicing code.

To splice introns by localizing 5 (or a few more) conserved nucleotides and then cutting at the ends of a lariat and rejoining the two exons is certainly a complex task, but apparently not so complex  that one of the biggest and most impressing known molecular machines is needed for that. But the simple truth is that recognizing and appropriately splicing all introns is a much more complex task than that.

That is due to the simple fact that conserved nucleotides at the ends are not a sufficient signal to identify the segment that has to be spliced, and that a lot of other components (not always well understood) are necessary to that, and that the splicing is not made always in the same way, and that alternative splicing is a very powerful tool for transcription regulation.

The subject is very complex, and I will not deal with it in depth. However, Those interested could look at this recent review:

The splicing code.

Unfortunately, the paper is paywalled, but the abstract is very informative.

The complexity of the splicing code can give us some insight about the true reasons for the complexity of the spliceosome, and definitely supposrts the idea that the whole system, introns, splicing code and spliceosome, is irreducibly complex.

The Prp8 protein.

I will add a few words about this proteins, which is probably the most amazing component of the spliceosome, and well represents its essential features.

This protein has many amazing charactertistics:

a) It is, as far as I can say, the longest protein in the whole spliceosomal system, and a very long protein indeed: 2335 AAs.

b) It is completely absent in prokaryotes.

c) It is extremely conserved in eukaryotes, probably the most conserved protein in the whole spliceosomal complex (see Fig. 4). In Naegleria, we have 3345 bits of homology with the human protein, corresponding to 1.4 baa, while in fungi we have the amazing result of 4211 bits of human-conserved information, corresponding to 1.8 baa. IOWs, in fungi we already find almost 90% of the functional information present in human Prp8 (remember, the highest possible bitscore is about 1.2 baas), corresponding to 1995 identities (86%) and 2155 positives (92%): a result which is incredibly rare, considering that such information has been conserved for about 2 billion years.

Just to emphasize the importance of this fact, here is the blast between the human protein and the best hit in fungi (Basidiobolus meristosporus):

 

 

d) It is a protein which is extremely important for the function of the spliceosome. Here is a very good paper about this protein and its functional relevance:

Prp8 protein: At the heart of the spliceosome

I quote from the conclusions:

Prp8p is central to the expression of all nuclear intron-containing mRNAs. In higher eukaryotes, it is responsible for processing thousands of transcripts in alternative splicing pathways, and in both U2 and U12 spliceosomes. It is important for the pathology of human disease, as all eukaryotic pathogens and parasites require Prp8p to functionally express their genes, in some cases via the trans-spliceosome. Retinitis Pigmentosa, a human genetic disorder that causes progressive blindness, positions Prp8p as a target for therapeutic medicine.

Moreover, another way to assess the functional constraints of a protein is to check its tolerance to polymorphisms in humans. That can be done consulting a very recent and useful database, the ExAC browser, which reports data from about 60000 human genomes.

ExAC gives two important metrics to assess how much a protein is tolerant to polymorphisms and variants. I quote here from the site FAQ:

What are the constraint metrics?

For synonymous and missense, we created a signed Z score for the deviation of observed counts from the expected number. Positive Z scores indicate increased constraint (intolerance to variation) and therefore that the gene had fewer variants than expected. Negative Z scores are given to genes that had a more variants than expected.

For LoF, we assume that there are three classes of genes with respect to tolerance to LoF variation: null (where LoF variation is completely tolerated), recessive (where heterozygous LoFs are tolerated), and haploinsufficient (where heterozygous LoFs are not tolerated). We used the observed and expected variants counts to determine the probability that a given gene is extremely intolerant of loss-of-function variation (falls into the third category). The closer pLI is to one, the more LoF intolerant the gene appears to be. We consider pLI >= 0.9 as an extremely LoF intolerant set of genes.

Now, for Prp8 we get the following results:

Constraint
from ExAC
Expected
no. variants
Observed
no. variants
Constraint
Metric
Synonymous 366.6 460 z = -3.02
Missense 920.2 266 z = 10.55
LoF 92.6 8 pLI = 1.00

That means the following:

a) The number of observed missense variants is so low vs expected (266 vs 920.2) that the z value is 10.55 (IOWs, 10.55 standard deviations, more than 10 sigma). Believe me, this is a really exceptional result, most proteins are much more tolerant to missense variants.

b) The probability of loss of function is 1. That means that even heterozygous LoF is absolutely not tolerated.

This is an extremely functional molecule, if ever there was one!

A brief conclusion.

To sum up the meaning of this rather long discussion, I would simply say:

  1. The introns – spliceosome system is a molecular machine of amazing complexity. I have touched only its main aspects in this OP, but believe me, there are layers of complexity there that would require a whole treatise and that I have not even started to mention here.
  2. Whoever can really believe that all this can be explained by some RV + NS model is, IMO, really admirable for his faith in a wrong paradigm.

408 Replies to “The spliceosome: a molecular machine that defies any non-design explanation.

  1. 1
    mike1962 says:

    Excellent. Thank you

  2. 2
  3. 3
    Dionisio says:

    What a peasant surprise to find this OP here today!

    Such a fundamental topic of biology explained by the best teacher in town.

    Mile grazie!!!

  4. 4
    gpuccio says:

    mike1962, Truth Will Set You Free, Dionisio:

    Thank you for your kind words! They are always deeply appreciated. 🙂

  5. 5
    Dionisio says:

    The introns – spliceosome system is a molecular machine of amazing complexity. I have touched only its main aspects in this OP, but believe me, there are layers of complexity there that would require a whole treatise and that I have not even started to mention here.
    2.Whoever can really believe that all this can be explained by some RV + NS model is, IMO, really admirable for his faith in a wrong paradigm.

    No additional comments needed.

  6. 6
    Dionisio says:

    From the abstract of the pay-walled paper “The Splicing Code” referenced in the OP:

    […] the splicing code depends on a myriad of different factors that in part are influenced by the background in which they are read such as different cells, tissues or developmental stages.

    Given the complexity of the splicing process, the construction of an algorithm that can define exons or their fate with certainty has not yet been achieved.

  7. 7
    Dionisio says:

    gpuccio:

    Another chicken egg conundrum?

    […] spliceosomal introns and the spliceosome are a good example of chicken egg paradox, or we could also say that they form an irreducibly complex system at a higher level.

    Here’s a point where we may disagree:

    “our darwinist friends will simply say that they have co-evolved”

    Well, that statement left out an important term with strong explanatory power that they use in their [pseudo] scientific conclusions: ‘somehow’.

    A more accurate sentence would read thus:

    “our darwinist friends will simply say that they have somehow co-evolved”. 🙂

    BTW, does the term “co-evolved” imply convergent evolution or those are unrelated concepts?

  8. 8
    Dionisio says:

    @7 follow-up

    Off topic – quick digression

    Is the RNA polymerase associated with another apparent chicken egg paradox too?

    Just curious.

    Thanks

  9. 9
    gpuccio says:

    Dionisio:

    “our darwinist friends will simply say that they have somehow co-evolved”.

    Glad to accept the correction. You are a better darwinian exegete than I am! 🙂

  10. 10
    Dionisio says:

    Here are a few papers perhaps related to the interesting discussion that is about to start here?

    Intronic Splicing Enhancers, Cognate Splicing Factors and Context Dependent Regulation Rules
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753194/pdf/nihms399453.pdf

    SR Proteins: Binders, Regulators, and Connectors of RNA
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303883/pdf/molce-40-1-1.pdf

    Directional Phosphorylation and Nuclear Transport of the Splicing Factor SRSF1 Is Regulated by an RNA Recognition Motif†
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884534/pdf/nihms782152.pdf

    RNA and Proteins: Mutual Respect
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373437/pdf/f1000research-6-11393.pdf

    Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570092/pdf/gkx477.pdf

    AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105168/pdf/ncomms13347.pdf

    A-kinase anchoring protein AKAP95 is a novel regulator of ribosomal RNA synthesis
    http://onlinelibrary.wiley.com.....13630/epdf

  11. 11
    Dionisio says:

    gpuccio @9:

    I knew you’ll accept the correction, because that term may help to clarify the meaning of the sentence… or so they hope. 🙂

    BTW, I left out other important terms they use quite frequently in the recent research papers: surprisingly, unexpectedly, etc. 🙂

  12. 12
    Dionisio says:

    @10 follow-up

    Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175361/pdf/gkw831.pdf

    TDP-43 stabilises the processing intermediates of mitochondrial transcripts
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5550480/pdf/41598_2017_Article_6953.pdf

    Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563511/pdf/41467_2017_Article_370.pdf

    The fitness cost of mis-splicing is the main determinant of alternative splicing patterns
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663052/pdf/13059_2017_Article_1344.pdf

    RNAs: dynamic and mutable
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708131/pdf/13059_2017_Article_1361.pdf

    Intron retention enhances gene regulatory complexity in vertebrates
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688624/pdf/13059_2017_Article_1339.pdf

    IRFinder: assessing the impact of intron retention on mammalian gene expression
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353968/pdf/13059_2017_Article_1184.pdf

  13. 13
    Dionisio says:

    So, the subject of this OP is spliceosomal splicing, which is restricted to eukaryotes.

    So, the spliceosome. A few important points about it:

    1.It is an amazing molecular machine. Even more, it is an amazing molecular cycle, involving many different stages each of which is an amazing molecular machine.

    1. The spliceosome is a molecular machine which appears in eukaryotes.

    2. The spliceosome is a molecular machine which is universally present in eukaryotes.

    3. The spliceosome is a molecular machine whose information is extremely conserved throughout eukaryotes, up to humans.

    4. The spliceosome is a wonderful example of irreducibly complexity.

    The Splicing code.

    The Prp8 protein.

    a) It is, as far as I can say, the longest protein in the whole spliceosomal system, and a very long protein indeed: 2335 AAs.

    b) It is completely absent in prokaryotes.

    c) It is extremely conserved in eukaryotes, probably the most conserved protein in the whole spliceosomal complex

    d) It is a protein which is extremely important for the function of the spliceosome.

    Is there a main item #2 ?

    Is it (2) The Splicing code. ?

    (3) The Prp8 protein. ?

  14. 14
    gpuccio says:

    Dionisio:

    You are right, as always: I had lost control of my listing hierarchy. Maybe my OPs are becoming too long! 🙂

    So, let’s say that I cut the first 1., and leave the last two sections as added sections, and not parts of a list.

    Next time I will try to be more careful… 🙂

  15. 15
    gpuccio says:

    Dionisio:

    You provide a true treasure trove of papers about RNA-protein interaction, and the incredible multitude of factors involved in splicing regulation.

    The spliceosome is probably the common agent which regulates all final effects at the end of such a complex, and still poorly understood, network of fine interactions.

    DNA motifs, trans-acting proteins, RNA-protein complexes, all seem to have a vast and intricate role in this huge skein of parallel events that takes place in the nucleus and influences the final events of splicing and translation, that we often consider as simple outcomes of transcription.

    Alternative splicing and its regulation are really black holes in our understanding of how cells work. A fascinating world, which we can add to the already stimulating and frustrating complexities of epigenetic regulation, of transcription factor networks, of chromatin states control, and, why not?, of morphogen gradients formation and regulation! 🙂

    And I apologize for all that I am forgetting…

  16. 16
    Dionisio says:

    gpuccio,

    The OP couldn’t be better in substance. It’s very insightful (I call it juicy!). Highly informative. Well structured.
    Just one minor detail, which you just mentioned.
    The first 1. wasn’t necessary.
    As you know, I look at your papers very seriously.

  17. 17
    gpuccio says:

    Dionisio:

    “As you know, I look at your papers very seriously.”

    I know. You are my best editor. 🙂

  18. 18
    Mung says:

    All this congratulatory back-slapping makes me sick. I predict gpuccio will eventually run from this thread like he ran from the last one.

    Apart from that. Good to see you again gpuccio.

    a) Introns exist in prokaryotes too, but they are rather rare. For our purposes, we will only discuss introns in eukaryotes.

    Is that because introns in prokaryotes are self-splcing? We don’t need no stinking spliceosome.

  19. 19
    Mung says:

    Here is a figure which summarizes the main stages of the spliceosome cycle

    How many random accidents did it take to cobble all that together Mr. Dawkins?

  20. 20
    J-Mac says:

    I was just reading up on that including alternative splicing, dual coding genes and duons.

    If someone says these were not designed, no miracle will persuade him…Amazingly clever designs in DNA…

    Great job gpuccio!

  21. 21
    J-Mac says:

    Mung,

    Anything is possible when one is delusional, as are Dawkins and his followers…

  22. 22
    Dionisio says:

    Mung @19:
    Perhaps we don’t know exactly how many, but it could have been a few changes here and there…despacito, until the whole thing worked, as it’s commonly done in the Boeing assembly facilities.
    You may want to look at the evo-devo Despacito thread to see how simple that is.
    🙂

  23. 23
    gpuccio says:

    Mung:

    “Is that because introns in prokaryotes are self-splcing? We don’t need no stinking spliceosome.”

    Yes! Introns in prokaryotes are rare and self-splicing.

    No stinking slpiceosome needed, at all! 🙂

  24. 24
    gpuccio says:

    J-Mac:

    Indeed!

    Sometimes I am really amazed at the unending layers of new complexity that open themselves almost daily in biology. That seems never to end.

    I hope some day people will awake from their strange hypnosis, and realize what should already be obvious and self-evident to all: the wonderful, thrilling amount of intelligence and design in the biological world.

  25. 25
    Arthur Hunt says:

    Hi gpuccio,

    You did not mention the single most important thing about the spliceosome and splicing.

  26. 26
    bill cole says:

    The spliceosome along with chromosome structure and the nuclear pore complex makes the eukaryotic cell one of natures most spectacular origin events.

  27. 27
    Belfast says:

    Not quite off topic is the question of Darwinists’ possibility given enough time …
    Just this day I was questioning a maths expert and asked him “if they ask you -but it IS possible to accept A=B? – what is your reply?

    “Certainly it is theoretically possible, but to ACCEPT that possibility which is one in a hundred you would have to dismiss the fact that the odds are 99 to 1 that A does not equal B, and you would have to give a convincing reason for rejecting.”

  28. 28
    gpuccio says:

    Arthur Hunt:

    “You did not mention the single most important thing about the spliceosome and splicing.”

    Hi, Arthur Hunt, welcome to the discussion.

    Should I ask what it is?

  29. 29
    gpuccio says:

    bill cole:

    Yes, the nuclear pore complex is another amazing example.

    Really a simple thing, the transition to eukaryotes! 🙂

  30. 30
  31. 31
    Dionisio says:

    @12 follow-up

    Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424149/pdf/ncomms15134.pdf

    The intron in centromeric noncoding RNA facilitates RNAi-mediated formation of heterochromatin
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322907/pdf/pgen.1006606.pdf

    A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoietin
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737145/pdf/gkv1168.pdf

    Mechanisms and Regulation of Alternative Pre-mRNA Splicing
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526142/pdf/nihms710140.pdf

    A mechanism underlying position-specific regulation of alternative splicing
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716086/pdf/gkx901.pdf

  32. 32
    ET says:

    Arthur Hunt:

    You did not mention the single most important thing about the spliceosome and splicing.

    Yes, he did- it is in the title. 😎

  33. 33
    ET says:

    Perhaps Art is talking about alternative splicing- something else blind and mindless processes don’t have an answer for:

    Most strands of unspliced mRNA, otherwise known as pre-mRNA, have about a dozen introns that can be removed. Yet the spliceosome doesn’t always link together the remaining exons in a straightforward manner. Sometimes the spliceosome intentionally skips an exon, or it reorders the exons, or it unexpectedly leaves an intron in the mix. On average, this variable editing process produces about 10 different proteins for every gene that we have. “Alternative splicing allows us to make the most out of every gene,” says Joan Steitz at Yale University School of Medicine. “Splicing is the reason we can have the same number of genes as the fruit fly Drosophila and yet be more complicated.”

    From Uncovering the Spliceosomes’ secrets

    But you did mention that- alternative splicing- in your OP…

  34. 34
    gpuccio says:

    ET:

    I think Arthur Hunt should clarify his thoughts himself. If he likes, of course.

    I will not try to guess, even if I have some idea…

  35. 35
    ET says:

    Yes, normally I would agree, however this is Arthur Hunt we are talking about. He wants to refute your claim by showing you don’t know what the single most important thing about spliceosomes and splicing is. Cuz if you don’t know that then your argument fails cuz you don’t know jack about it.

  36. 36
    Mung says:

    Arthur Hunt:

    You did not mention the single most important thing about the spliceosome and splicing.

    I am always eager to learn.

    What is the single most important thing about the spliceosome and splicing?

  37. 37
    Eric Anderson says:

    gpuccio,

    Excellent work highlighting this incredible system.

    But everyone knows such a functionally-complex, information-rich, integrated system could only come about through a long series of accidental particle interactions. Yeah, that’s the ticket . . . 🙂

    —–

    Thanks for taking time to lay out the details. Great resource.

  38. 38
    Dionisio says:

    @3 correction

    Someone pointed to this error:

    “peasant surprise”?

    Well, I have no idea what that could mean.

    It was supposed to read ‘pleasant surprise’ instead.

    My typo.

  39. 39
    gpuccio says:

    Dionisio:

    “Peasant surprise” = the simple, sincere and unadulterated surprise that a true peasant feels daily in front of the wonders of nature.

    You are always very creative with your typos! 🙂

  40. 40
    gpuccio says:

    ET:

    “Yes, normally I would agree, however this is Arthur Hunt we are talking about.”

    Yes, it is Arthur Hunt. I know.

    I should probably be happy that he has found time to read my OP, even to comment here, however briefly.

    In a sense, I am.

    But in another sense, a very important sense for me, I stick to a principle that has always guided me in all my discussions here. Here, in this blog which is intended to discuss science, all are equals, in the sense that all are important (or no important) for what they say, not for who they are.

    That is in no way a lack of respect for scientific expertise, or for academic role. I fully respect all those things.

    But, in a scientific debate, only ideas are important.

    So, if Arthur Hunt (or anyone else) wants to “refute” my claims by a single unsupported statement, he is of course perfectly entitled to do that.

    And I am perfectly entitled not to worry about that.

    But, as I have said, I will not debate my imaginary guess of what he would say. I like discussion, but not unilateral discussion.

    I really hope that Arthur Hunt will find the time, or the motivation, to make his statement a little more “explicit”. But that’s completely up to him.

  41. 41
    gpuccio says:

    Eric Anderson:

    “Excellent work highlighting this incredible system.”

    Thank you! And you are right, the system is really incredible.

    “Thanks for taking time to lay out the details.”

    They say that the devil is in the details. Isn’t it strange that nobody seems to wonder about the incredible amount of conserved information in proteins like Prp8, for example? And that the transition from prokaryotes to eukaryotes is still “explained” mainly as an endosymbiosis event (which could at best partially explain the origin of mithocondria and chloroplasts), while nobody seems too worried about the amazing informational novelty implied by structures like the spliceosome, the nuclear pore, and many others?

    In this case, details are simply the truth that nobody wants to consider.

  42. 42
    gpuccio says:

    ET:

    Here is another interesting passage from the page you linked at your #33:

    Many of the 200 proteins involved in the spliceosome regulate the process in unknown ways. Some of these regulators act as communication vectors between the spliceosome and other complex cellular processes: For example, researchers have found that when the spliceosome jams in yeast cells, protein messengers signal for the cell to switch the kinds of genes made available to RNA polymerase for transcription. Thinking about all these connections “can make your eyes cross,” Sharp says.

  43. 43
    Dionisio says:

    @25:

    What kind of mysteriously convoluted way to say something?

    Melodrama, tragicomedy, psychodrama?

    Not sure.

    🙂

  44. 44
    PaV says:

    Arthur Hunt is very involved with plant t-RNA, and maize mitochondria. So, therein must lie the “most important thing about the spliceosome and splicing.”

    I suspect his ideas run along these lines.

  45. 45
    Eric Anderson says:

    gpuccio @41:

    “They say that the devil is in the details.”

    Yep. And the failure to look at the details is critical to the evolutionary story.

    The impression of evolutionary theory’s explanatory power is inversely proportional to the specificity of the discussion.

  46. 46
    gpuccio says:

    PaV:

    I know that Artur Hunt is very involved in those issues, and he is certainly a great expert about RNA in general.

    However, the page you linked seems to be about self-splicing introns, that I have explicitly not discussed in my OP, and that do not require the spliceosome.

  47. 47
    gpuccio says:

    Eric Anderson:

    “The impression of evolutionary theory’s explanatory power is inversely proportional to the specificity of the discussion.”

    Definitely!

    I must say that i find very little explanatory power in it even at very generic levels, but certainly as soon as we start to deal with details even that vague illusion of credibility soon disappears! 🙂

  48. 48
    Mung says:

    It seems to me that the spliceosome is something that was simply cobbled together by evolution. It certainly doesn’t look like something put together by an intelligent designer.

  49. 49
    PaV says:

    gpuccio:

    This might be what he thinks you’re overlooking: i.e., that the spliceosome can simply be viewed as a ‘part’ of an ‘intron.’

    Whether a Ferrari is stored in your garage, or is found in the dealer’s showroom, doesn’t affect the presence of design one wit.

  50. 50
    Arthur Hunt says:

    Hi all,

    Thanks for your patience, and for the discussion. Always interesting to see how others view these things.

    Of course, I was referring to the fact that the spliceosome is a ribozyme. At the heart of the splicesosome sits what is essentially a self-splicing intron. I know the subjiect of self-splicing introns is discouraged in this discussion, but it seems odd to me to rule as off limits the heart of the matter, as it were.

    I should point out that I am simplifying this somewhat, to encourage discussion and research. I apologize if this is not kosher (in a manner of speaking).

    I won’t be able to do a running discussion but I will check in periodically to answer questions and maybe move things along.

  51. 51
    Arthur Hunt says:

    I will add one thing to stir the pot. I think that the fact that the spliceosome is at its core a catalytic RNA calls into question assertions about the irreducible complexity of the complex. For reasons I hope are obvious.

  52. 52
    Dionisio says:

    The software product that my former employer successfully sold to many design engineering organizations, was in its core simply a bunch of bits and bytes somehow put together.
    That’s all. Nothing really special about it that could classify it as the product of an intelligent mind.
    That would be utterly ridiculous, to say it nicely.

    🙂

  53. 53
    Dionisio says:

    Things like this:

    https://www.kodugamelab.com/

    are just a bunch of bits and bytes somehow put together. Pure physics.

    That’s all. Nothing really special about it that could classify it as the product of an intelligent mind.
    That would be utterly ridiculous, to say it nicely.
    🙂

  54. 54
    gpuccio says:

    Arthur Hunt:

    Thank you for the clarification.

    A few quick thoughts about that point. I will probably come back more in detail tomorrow.

    1) In my OP, I say:

    To make it simple, the spliceosome units are built upon 5 specific RNAs, called small nuclear RNAs (snRNA). These are, in humans:

    U1 (164 bases), U2 (187 bases), U4 (145 bases), U5 (116 bases), U6 (107 bases)

    They are transcribed from multiple gene copies. While their sequences are not particularly conserved (U6 being the most conserved of all), their secondary structure seems to be very conserved.

    snRNAs are very important in the spliceosome, because they seem to be responsible for the catalytic activities.

    So, I would not say that I “did not mention the single most important thing about the spliceosome and splicing.” I did mention very clearly that the catalytic activity in the spliceosome seems to be mainly due to the RNA component.

    You say:

    “I know the subject of self-splicing introns is discouraged in this discussion, but it seems odd to me to rule as off limits the heart of the matter, as it were.”

    But that is not true at all. My intention has never been to discourage anything in this discussion. For the sake of simplicity, I have restricted my discussion in the OP to the major spliceosome, because I believed that the OP was long and complex enough that way. But of course I am very interested in any aspect of the issue in the discussion here. So, your comments are absolutely welcome.

    Of course, you say something more, beyond the simple fact that the spliceosome is a ribozyme (at least in part). You also say:

    “At the heart of the splicesosome sits what is essentially a self-splicing intron.”

    Now, I have nothing against that concept, but as I had not the time to deepen this aspect, I would like to profit of your knowledge, and I ask you: is there evidence that the snRNAs in the spliceosome are derived from, or anyway similar to, self-splicing introns components?

    Again, I have no problems in admitting that the RNA part of the major spliceosome can be derived from self-splicing introns, but I would like to know if there is evidence of that, at sequence level or at structure level.

    However, even if that is true, you can certainly see that my discussion in the OP is mainly focused on the protein component of the major spliceosome. That is essentially the information component that I have tried to analyze.

    So, even if the RNA part can be traced to something that already existed in prokaryotes, my discussion about the protein part remains, IMO, completely valid.

    There can also be no doubt, IMO, that the eukaryotic spliceosome has a functional complexity that is completely different from that of self-splicing introns. That is what I am debating here.

    Regarding irreducible complexity, I invite you to read again what I wrote in the OP:

    OK, we have already said that splicing can be achieved in at least three different ways. For example, bacterial introns, although rare, are of the self-splicing type. So, we know that the generic function of splicing introns can be implemented in different ways.

    But eukaryotic introns are of the spliceosomal type, and they are spliced only by the spliceosome.

    We have also said that a minor spliceosome also exists. It shares some featues with the major spliceosome, but it is a different structure and acts on different, and much rarer, introns.

    So, for the vast majority of eukaryotic introns, the major spliceosome, and only the major spliceosome, can effectively accomplish the splicing.

    Now, I don’t mean here that the major spliceosome must always be absolutely complete, with all its 150 proteins, to be able to work. That’s not what I mean when I say that it is irreducibly complex.

    Maybe in some organisms the spliceosome can be partially defective, and still work. It is difficult to say, because we still don’t understand the role of all the components of the spliceosome.

    But however, as far as we can understand, most of the principal features must be present, because, as we have seen, the splicing is the result of a complex cycle, involving the RNAs and the subunits, and all stages are essential to the final result.

    So, the spliceosome is certainly highly irreducibly complex, even if we may not be able to clearly identify the essential nucleus of molecules which is absolutely necessary to the minimal function.

    As you can see, I am not denying in any way that splicing can be performed by simpler and different structures. I also explicitly quote here self-splicing introns as an example of a different way to achieve splicing.

    My point is that the whole system which implements splicing for eukaryotic spliceosomal introns is a new and different entity, and that it is irreducibly complex.

    I have also specified that I don’t mean by that that all the components of the system are indispensable to achieve the function. But it is difficult to deny that some important irreducible core must be present to implement all the subtle and necessary aspects of eukaryotic splicing in most of eukaryotic genes.

    I hope that this helps to clarify my views. I am certainly looking forward to further contributions from you. As I have said, I do love discussion.

  55. 55
    Dionisio says:

    My questions @43 remain unanswered.

    But now, it seems like @25 was barking up the wrong tree?

    🙂

  56. 56
    Arthur Hunt says:

    gpuccio,

    Sorry that I overlooked your description. I need to read more slowly. Many apologies.

    There is indeed an abundance of evidence for the proposition that the structural and catalytic components of the spliceosome and group 2 introns are basically the same. I suspect (but haven’t tried to check it out) that google will help you track this down.

    As far as the proteins of the spliceosome are concerned, I guess if totally unrelated proteins in prokaryotic systems can also facilitate the activity of the core of the splicing enzyme, then maybe the uniqueness of proteins that make up these complexes is not so great as you are asserting.

  57. 57
    Dionisio says:

    Reading more slowly won’t fix the “overlooking” problem. Paying attention to the words might help.

    It seems like I’m not alone in the poor reading comprehension club. 🙂

    BTW, the suspicion @55 was valid.

  58. 58
    gilthill says:

    gpucio,

    Another wonderful post! It’s so enjoyable and stimulating to read you.

    A brief comment on the chicken and egg paradox regarding spliceosome introns and the spliceosome that you mention in section 4. We all know that biology offers a myriad of examples of such paradoxes. But these paradoxes are intractable paradoxes only in the context of naturalism. Open the door to a mind/intelligent agent and these paradoxes vanishes immediately for intelligent agents have this unique power to design and implement systems having the appearence of a chicken egg paradox.

  59. 59
    gpuccio says:

    gilthill:

    Thank you for your kind words.

    Of course a global design can explain that kind of logical dependencies. If a new plan is conceived as such, as a whole, and then implemented, even if in steps, then all different parts can be implemented at the same level of efficiency. We can have different implementations for similar functions, with different levels of complexity, but in each plan the different parts (which build up the irreducible complexity of the whole) will be harmoniously present.

    I think I will go into greater detail about that in my answers to Arthur Hunt (as soon as I find a little time! 🙂 )

  60. 60
    gpuccio says:

    Arthur Hunt:

    “Sorry that I overlooked your description.”

    Thank you for the acknowledgement. It is appreciated.

    Good to hear from you. I will soon answer your interesting points, but some further research is appropriate for that, so it could take a little time.

    Not too much, I hope! 🙂

  61. 61
    gpuccio says:

    Dionisio:

    “It seems like I’m not alone in the poor reading comprehension club.”

    We have all been in that club, from time to time!

  62. 62
    Mung says:

    Arthur Hunt:

    I will add one thing to stir the pot. I think that the fact that the spliceosome is at its core a catalytic RNA calls into question assertions about the irreducible complexity of the complex. For reasons I hope are obvious.

    Hi Art, Thanks for your reply.

    Are you seriously proposing that if we remove the catalytic RNA at the core of the spliceosomal complex that the remainder of the complex would continue to perform the same function, iow, that the catalytic RNA is superfluous?

  63. 63
    gpuccio says:

    Mung:

    No, it would seem that he is proposing the opposite, that the proteins are not so essential. Or at least not so “unique”.

    I will try to write a more detailed answer about that.

  64. 64
    Mung says:

    gpuccio:

    No, it would seem that he is proposing the opposite, that the proteins are not so essential. Or at least not so “unique”.

    So you think that he is proposing that the proteins are superflous to the function of the spliceosome complex, remove them all and everything would still work like before?

    I have another hypothesis: that Art doesn’t understand what it means to say a molecular machine is irreducibly complex. After all these years.

  65. 65
    Eric Anderson says:

    Arthur Hunt @50:

    Thanks for sharing some more information about the spliceosome. I had a question about this statement:

    Of course, I was referring to the fact that the spliceosome is a ribozyme. At the heart of the splicesosome sits what is essentially a self-splicing intron.

    1. Are you saying the intron splices itself out of the sequence?

    2. What does an intron in the “heart of the spliceosome” have to do with removing the introns in the relevant sequences?

    3. I presume you aren’t suggesting that introns in genes are self-splicing?

    Thanks for any further clarification you can offer.

  66. 66
    gpuccio says:

    Eric Anderson:

    Self-splicing introns are self-splicing. Spliceosomal introns (the vast majority of introns in eukaryotes) are not.

    I will try to add some details about these issues in my next posts.

  67. 67
    Mung says:

    …it became clear that one kind of intron (the spliceosomal introns), as well as the cellular machinery that removes them (the spliceosome), are ubiquitous in eukaryotic genomes.

    – The Origin and Evolution of Eukaryotes. p. 295.

  68. 68
    Mung says:

    ..spliceosomal introns appeared abruptly at the time of the origin of eukaryotes (and thus are quite ancient even if not primordial), and originated from preexisting self-splicing introns, which were likely present at very early stages of life.

    – The Origin and Evolution of Eukaryotes. p. 296.

    Personally I think they are primordial and not just ancient.

  69. 69
    gpuccio says:

    Arthur Hunt (and all interested):

    So, I will start from your #56, and try to clarify my views on the issues you have mentioned.

    I apologize in advance because I will have to clarify many aspects that you certainly know better than me. I will do that so that all can follow the reasonings (at least I hope so). The subject, of course, is not so simple. I hope you will correct me if I say something wrong or imprecise.

    Moreover, as you are admirably brief in explaining your points, I will have to interpret, in some degree, what you say at #56, so that I can try to comment on the relevant ideas. Of course, again, if I am misunderstanding your points I apologize, and you are welcome to clarify and correct.

    So, I would divide your argument in two related, but different points.

    1) The relationship between self-splicing introns and the RNA component of spliceosomal introns.

    You say (in response to a previous request of mine):

    There is indeed an abundance of evidence for the proposition that the structural and catalytic components of the spliceosome and group 2 introns are basically the same. I suspect (but haven’t tried to check it out) that google will help you track this down.

    2) The role of proteins in the spliceosome:

    You say:

    As far as the proteins of the spliceosome are concerned, I guess if totally unrelated proteins in prokaryotic systems can also facilitate the activity of the core of the splicing enzyme, then maybe the uniqueness of proteins that make up these complexes is not so great as you are asserting.

    Now, point 1 is much simpler, while point 2 requires some interpretation, and a more detailed answer.

    So, I think that I will proceed this way: I will give first some information about self-spicing introns, so that all can follow the discussion. Then I will address point 1, and finally point 2.

  70. 70
    Mung says:

    In fact, LECA had not only one complex spliceosome, but two.

    – The Origin and Evolution of Eukaryotes. p. 302.

    Compound miracles! Is it any wonder Eukarya is considered a distinct domain of life?

  71. 71
    Eric Anderson says:

    gpuccio:

    Thanks. I look forward to the additional information when you get a chance.

    In particular, I’d be curious as to whether there are experiments showing that the self-splicing introns splice themselves out of an RNA sequence without involvement of any other cellular machinery. Specifically, does the RNA sequence need to be folded correctly before the self-splicing occurs? Or could we just put an RNA sequence in a beaker and the intron would splice itself out?

  72. 72
    ET says:

    Arthur Hunt:

    I think that the fact that the spliceosome is at its core a catalytic RNA calls into question assertions about the irreducible complexity of the complex.

    Not if one understands the concept. You still have to account for that catalytic RNA and self-splicing introns.

    Good luck with that

  73. 73
    Mung says:

    A book on The Origin and Evolution of Eukaryotes that fails to elucidate the origin and evolution of the spliceosome complexes.

    Imagine that gpuccio.

    These subsets of snRNAs are nonetheless evolutionarily related to one another and probably originated by gene duplication some time before LECA (Russell et al. 2006).

  74. 74
    Mung says:

    Eukaryotes invest very heavily in the spliceosome: about 1% of known human and yeast genes encode products deployed in splicing.

    The Origins of Genome Architecture. p. 238

    That’s a pretty amazing addition to the genome. And all by “accidental” mutations. Sure. And Santa is going to give you the desires of your heart too. Believe it.

  75. 75
    gpuccio says:

    Arthur Hunt (and all interested):

    I will start form this statement you made:

    “At the heart of the splicesosome sits what is essentially a self-splicing intron.”

    It is true that in my OP I have mentioned self-splicing introns, but I have not discussed them. That was essentially for the sake of brevity, and because my focus was on spliceosomal introns.

    However, now it’s time to deepen the discussion.

    So, I have made my homework, and I will refer in the following discussion essentially to a recent paper
    (2015):

    “Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution”

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394904/pdf/nihms673151.pdf

    which seems to be a very good summary of what is known about the issue.

    The paper is open access, so everyone interested can check the details directly.

    I will also draw some information from this paper of 2011:

    Group II Introns: Mobile Ribozymes that Invade DNA

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140690/pdf/cshperspect-RNA-a003616.pdf

    Open access too.

    First of all, there are two different types of self-splicing introns: group I and group II.

    Again, for the sake of brevity, I will not discuss here group I, because group II is the category which is more directly implied in the possible origin of spliceosomal introns and of the spliceosome, as we will see.

    I will start with a very important concept: these are essentially retrotransposons.

    Let’s read the very beginning of the first paper:

    Group II introns are remarkable mobile retroelements that use the combined activities of an autocatalytic RNA and an intron-encoded reverse transcriptase (RT) to propagate efficiently within genomes. But perhaps their most noteworthy feature is the pivotal role they are thought to have played in eukaryotic evolution. Mobile group II introns are ancestrally related to nuclear spliceosomal introns, retrotransposons and telomerase, which collectively comprise more than half of the human genome. Additionally, group II introns are postulated to have been a major driving force in the evolution of eukaryotes themselves, including for the emergence of the nuclear envelope to separate transcription from translation.

    But where can group II introns be found?

    From the second paper:

    2.1. Phylogenetic Distribution
    Group II introns have been found in bacteria and in the mitochondrial (mt) and chloroplast (cp) genomes of fungi, plants, protists, and an annelid worm (Belfort et al. 2002; Lambowitz and Zimmerly 2004; Toro et al. 2007; Vallès et al. 2008). Group II introns are rare in archaea, with the few found there likely acquired from eubacteria by relatively recent horizontal transfers (Rest and Mindell 2003). In eubacteria, group II introns are present in ?25% of sequenced genomes, generally in small numbers, and typically as active retroelements with functional ribozyme and RT components. By contrast, group II introns in organelles frequently have degenerate RNA structures and either lack ORFs or encode degenerate IEPs that no longer promote intron mobility (Michel and Ferat 1995; Bonen 2008; Barkan 2009). Such immobile group II introns are inherited vertically and rely on host-encoded splicing factors (see later). Group II introns have not been found in the nuclear genomes of eukaryotes, but their hypothesized descendants, spliceosomal introns and retrotransposons, are highly abundant in eukaryotes, together comprising more than half of the human genome.

    More in next post.

  76. 76
    Mung says:

    Are the spliceosomes molecular machines? Michael Lynch seems to think so.

    An unexpected layer of complexity in the evolution of the spliceosome was introduced with the discovery that many eukaryotes harbor not just one, but two, such molecular machines (Hall and Padgett 1994; Burge et al. 1998; Patel and Steitz 2003).

    The Origins of Genome Architecture. p. 240

  77. 77
    gpuccio says:

    Mung:

    Yes, 150-200 proteins involved in the spliceosome, out of about 20000 genes, is about 1%.

    A remarkable investment indeed! 🙂

  78. 78
    Mung says:

    Love your posts gpuccio. Always intriguing (though boring and repetitious).

    Thank you and Merry Christmas!

  79. 79
    Mung says:

    gpuccio:

    Again, for the sake of brevity, I will not discuss here group I, because group II is the category which is more directly implied in the possible origin of spliceosomal introns and of the spliceosome, as we will see.

    I, otoh, don’t see the relevance of Type II self-splicing introns to the origin of the spliceosome. I cannot seem to find any connection between the two. 🙂

  80. 80
    Mung says:

    How might the major and minor spliceosomes have arisen?

    The Origins of Genome Architecture. p. 240

    Oh goody! Yes, how? Will Christmas come early this year?

    😀

  81. 81
    Dionisio says:

    As Eric Anderson wrote @71, I look forward to reading what gpuccio will explain on this fascinating subject.
    Thanks.

  82. 82
    Dionisio says:

    gpuccio @75:

    However, not it’s time to deepen the discussion.

    However, now it’s time to deepen the discussion.

  83. 83
    Dionisio says:

    gpuccio @75:

    As usual, very pedagogical approach to present complex biological information. Thanks.

    This thread is very informative.

    One thing I did not like about this comment @75 is that it finishes suddenly with this announcement:

    “More in next post.”

    Now we have to wait for the next episode.

    🙂

  84. 84
    ET says:

    gpuccio:

    Yes, 150-200 proteins involved in the spliceosome, out of about 20000 genes, is about 1%.

    Thanks to the spliceosome we know the 20,000 is a base number as there are more than 20,000 proteins. In other words it isn’t “one gene = one protein” scheme, as was once thought. And that scheme was presented because, given blind watchmaker evolution, no one could have ever predicted that cells contained spliceosomes and alternative splicing was the norm. But now that we know all of that of course blind and mindless processes didit.

  85. 85
    Eric Anderson says:

    Mung @74:

    It is interesting how preconceptions can cause people to be a sloppy with their language. Quoting:

    An unexpected layer of complexity in the evolution of the spliceosome was introduced with the discovery that many eukaryotes harbor not just one, but two, such molecular machines (Hall and Padgett 1994; Burge et al. 1998; Patel and Steitz 2003).

    No change in the “evolution” was introduced. However the spliceosome came about, it came about. Nothing about its history changed with our discovery of additional complexity in the system. 🙂

    Furthermore, contrary to what evolutionists typically believe from the assumptions they bring to the table, the discovery of additional challenges to the evolutionary story doesn’t mean the new discovery helps us better understand the evolutionary story. What an objective observer might very well conclude is that the evolutionary story is headed down the wrong path altogether.

    What they should have said is:

    “The discovery that many eukaryotes harbor not just one, but two, spliceosomes means our made up story about the evolution of the spliceosome isn’t correct. So we’ll have to come up with another made up story.”

    There. Fixed it for them.

  86. 86
    gpuccio says:

    Arthur Hunt (and all interested):

    Now, let’s try to summarize the main points about group II self-splicing introns:

    1) They are essentially retrotransposons, mobile elements

    2) They can be found in bacteria, rarely in archaea, and in the organelles of eukaryotes (mitochondria and chloroplasts), where they are often degenerate.

    3) They are not found in the nuclear genome of eukaryotes.

    Now, what is the structure of these special introns?

    Look at Fig 1 in the first paper I quoted. You will see the secondary structure of the RNA derived from a group II intron, organized into six domains (DI – DVI).

    Now, here it gets complicated. The intron-transcribed RNA is indeed a ribozyme, and has a catalytic activity which can self-splice it from the transcribed mRNA. The catalytic activity is especially implemented by the DV domain, but also other domains contribute.

    But the DIV domain is also special, because it includes an ORF, which encodes for a protein, called IEP (intron-encoded protein).

    This protein does three different things, by three different domains:

    a) A reverse transcriptase domain (RT), which can copy the RNA to DNA for retrotransposition

    b) A maturase domain which helps the ribozyme catalytic site to effecting the self-splicing

    c) A DNA binding domain and an endonuclease domain which intervene in the final phase of retrotransposition, when the new DNA is inserted in the genome (retro-homing).

    Not so simple, is it? 🙂

    OK, so to sum up:

    – the ribozyme activity in the transcribed intron itself effects the splicing (self-splicing). This process is rather complex, and is mediated by a complex tertiary structure, where the active site is mainly represented by DV.

    – however, the splicing probably need, in vivo, the intervention of the IEC, the protein encoded by DIV of the same intron, with its maturase acticity which helps stabilize the splicing by the ribozyme. In that sense, the ribozyme and its encoded protein act as a ribonucleoprotein complex.

    – moreover, the IEC, with other domains, can also intervene as a reverse transcriptase and endonuclease to allow retrotransposition and retro-homing of the intron code.

    Well, to onlookers: I told you it was not simple.

    I apologize again to Arthur Hunt for having to explain these basic points before going on with my reasonings. Any correction or integration will be welcome.

    I would leave it at that for today. I will go on tomorrow.

    As a final thought, I give you the Uniprot description of the function of a typical IEC, a protein encoded by the DIV of a group II intron.

    It is one of the best known, LtrA. In particular, the following relates to the LtrA in Lactococcus lactis, P0A3U0, a 599 AAs long protein. Here is the function section from Uniprot, which illustrates well many of the concepts I have described before:

    Multifunctional protein that promotes group II intron splicing and mobility by acting both on RNA and DNA. It has three activities: reverse transcriptase (RT) for intron duplication, maturase to promote splicing, and DNA endonuclease for site-specific cleavage of recipient alleles. The intron-encoded protein promotes splicing by facilitating the formation of the catalytically active structure of the intron RNA. After splicing, the protein remains bound to the excised intron lariat RNA, forming ribonucleoprotein particles, and cleaving the antisense strand of the recipient DNA in the 3′ exon. After DNA cleavage, retrohoming occurs by a target DNA-primed reverse transcription of the intron RNA that had reverse spliced into the sense strand of the recipient DNA. It also contributes to the recognition of the DNA target site and acts as a repressor of its own translation.

    Moreover, just to have some idea of how conserved is this Ltra protein in bacteria, I have blasted the protein from Lactococcus lactis against a different group of bacteria, Proteobacteria.

    I got a best hit of 419 bits, and a range of 372 – 419 bits in the first 100 hits.

    That means that the intron-encoded protein shows a good, but not really impressive, conservation in bacteria, at a level of about 0.6 – 0.7 bits per aminoacid (baa), at least in the limited comparison I have done.

    I would like all to remember this, because I think it will have some importance in the future discussion about spliceosomal proteins.

    OK, that’s all for the moment.

  87. 87
    gpuccio says:

    ET:

    Yes, of course, but let’s just say that it is about 1% of protein coding genes! 🙂

  88. 88
    gpuccio says:

    Mung, ET, Eric Anderson, Dionisio and others:

    I am postponing all discussion about the “origin of the spliceosome” and its relations with group II introns, because I believe that we have to have clear and detailed ideas on a number of important things before.

    Just have a little patience! As you can see, the subject is rather complex. 🙂

  89. 89
    Mung says:

    gpuccio:

    3) They [group II self-splicing introns] are not found in the nuclear genome of eukaryotes.

    Lynch agrees:

    No group II intron has been found in a eukaryotic nuclear gene. (p. 244)

    Ir’s amazing, all those mitochondrial genes that moved into the nuclear DNA, but none with a group II intron. What are the odds.

  90. 90
    Mung says:

    gpuccio:

    Just have a little patience! As you can see, the subject is rather complex.

    ok. Guess I’ll have to break out my copy of Intervening Sequences in Evolution and Development. Chapter 6 is “Different Types of Introns and Splicing Mechanisms.”

    🙂

  91. 91
    FourFaces says:

    Whoever can really believe that all this can be explained by some RV + NS model is, IMO, really admirable for his faith in a wrong paradigm.

    You are very kind. Personally, I call such a person a jackass. But that’s just me.

  92. 92
    DATCG says:

    Thanks Gpuccio on another engaging post. I look forward to Arthur Hunt’s input regarding #50 #51 #56 assertions as well.

    As we track through this discussion, I wonder how many assumptions come from the heart of the matter, that are made for blind, unguided evolution to progress to the Spliceosome?

    Will we get detailed step by step evolutionary progress of interdependent systems coordination and organization?
    Driven by unguided, gradual step by step “process” or the usual narrative that “could have” or “may have likely” happened?

    I’m intrigued that this may offer up something unique in both sides of the discussion.

  93. 93
    Mung says:

    It is now clear that introns are not all alike, even in the most general terms.

    Intervening Sequences in Evolution and Development. p. 112

    gpuccio,

    If you let me know which kind of introns and/or which aspects of the spliceosomes you are studying deeper I’ll see what I can contribute.

    So far you appear to be spot on. Good work.

    Cheers

  94. 94
    DATCG says:

    #44 PAV, thanks for book link.

  95. 95
    Mung says:

    DATCG:

    Will we get detailed step by step evolutionary progress of interdependent systems coordination and organization?

    My experience is that you’ll find far more discussion of how the different sorts of introns evolved with far less devoted to to the origin and evolution of the spliceosomes.

    They will cover one and pretend to have thus addressed the other.

  96. 96
    DATCG says:

    Found link, is this the correct Arthur Hunt?

    Arthur Hunt – UKY Research Gate Profile

  97. 97
    DATCG says:

    #95 Mung, yes, it’s my expectation as well.

  98. 98
    gpuccio says:

    Arthur Hunt (and all interested):

    So, let’s take again the discussion.

    I think we have enough data now to answer point 1.

    Your point was:

    “There is indeed an abundance of evidence for the proposition that the structural and catalytic components of the spliceosome and group 2 introns are basically the same.”

    and, (which is more or less the same):

    “At the heart of the splicesosome sits what is essentially a self-splicing intron.”

    Is that true?

    In the light of what we know, I would definitely say: yes!. With some reservations that I will clarify.

    In my comment #54 I had already stated that I had nothing against this concept, I just needed more information. After some research, I can say that the concept is correct.

    Let’s see some details:

    a) We have seen that the ribozyme catalytic activity in the group II intron RNA is mainly localized in one domain, DV. Well DV is also the only domain whcih is highly conserved, and at the same time the only domain which has high homology with one of the spliceosomal RNAs U6. On the other hand, U6 is also the most sequence conserved spliceosomal RNA, and directly involved in the catalysis. So, we can certainly say that this important piece of the complex is shared between the group II ribozyme and the spliceosomal catalytic site, both at sequence and at structure level.

    b) The rest of the RNA component is rather different in the two context, at sequence level. But we can accept that there is a very strong structure similarity, and that essentially the catalysis works in a very similar way in group II introns and in the spliceosome.

    I must say that the more i read about group II self-splicing introns, the more I become convinced that they are a fascinating structure, and that they could make a very good argument for ID, in their own right. 🙂

    However, let’s not digress!

    For those who are interested in the basic structural features of the catalytic site, I would recommend this very good, although very technical, video:

    https://www.youtube.com/watch?v=ESXo3fTThBI

    Now, a few more points:

    c) Although the structural working of the catalytic site is highly comparable, it is however realized in very different ways in the two contexts.

    In group II intron RNA, indeed, almost everything depends on the six domains in the one molecule, which fold into a very complex 3D structure. For example, the main role of scaffold here is implemented by DI, the biggest domain. Moreover, the only protein contribution is provided by the IEP, with its maturase activity.

    On the contrary, in the spliceosome we have five different RNA molecules, only one of which really corresponds to one domain in the group II intron RNA, and each of these five snRNAs is part of a complex with its specific proteins, a lot of them. The global interaction of all these ribonucleoproteins in some way reconstructs the structure of the catalytic site.

    Even if we consider only the final shared catalytic activity, I would definitely say that the two contexts are very different, and that going from the first to the second is no simple matter, and requires a lot of engineering.

    More in next post.

  99. 99
    Mung says:

    And of course, given an hypothesis of intelligent design, one might expect to find such re-use.

  100. 100
    gpuccio says:

    Mung:

    Yes, of course!

  101. 101
    nkendall says:

    Great article. Thanks for taking the time to put this together.

    As a broad-brush analysis that is intuitive for most let me offer the following.

    Suppose we put together an analogy between the complexity of the spliceosome and the English text necessary to describe it in detail. In this back of the envelope exercise I have made every effort to be charitable to Neo Darwinism–extraordinarily charitable.

    In Stephen Meyer’s book, “Darwin’s Doubt” he quotes Michael Denton as saying that the ratio of meaningful English sentences or phrases of 100 characters to character phrases that are unintelligible is 1 / 10^100.

    The article here references the paper: “Spliceosome Structure and Function”, stripped of the TOC and Bibliography, this paper is about 65,000 characters. There are many pictures. It has been said that a picture is worth a thousand words. I think that is an understatement in this case. But let us say there are 10 pictures and assign 1000 words to each; each word has 4-5 letters. So roughly, let’s say there are 100,000 English letters needed to describe the spliceosome based on this one article. A very low estimate for the adequacy of human informational conveyance especially considering we don’t know everything there is to know about how the spliceosome works. But let’s go with that anyway. Let’s further assume that 100 characters is about the minimum distinct informational quantity that can be meaningful. Let’s say that we have as many monkeys typing new English text phrases as we have grains of sand on earth (10^19) and that each monkey was turning out a new 100 character string each second. There have been about 10^18 seconds since our planet was born. So there could be only about 10^37 total 100-character English sentences/phrases generated since the birth of our planet using these assumptions. And let’s further assume that every valid (meaningful) 100 character English phrase generated by our monkeys just happened to be suitable as a new (i.e. non-redundant) useful explanation for a spliceosome–in other words, let’s factor out natural selection completely. These are all preposterous assumptions of course and all wildly favorable to Neo-Darwinism.

    Even with these assumptions the probability of obtaining a text to describe the splicesome would fall short by about 66 orders of magnitude. 10^103 – 10^37

    Conclusion: Neo-Darwinism is a canard. But it is only the second greatest intellectual canard in human history. The greatest intellectual canard in human history is the metaphysical doctrine of materialism. It is the assumption of the truth of materialism that necessitates Neo-Darwinism and it is the believed truth of Neo-Darwinism that forms the necessary condition to support materialism. Together they form a grand intellectual tandem canard–a magnificent intellectual catch-22 and a supreme example of human gullibility.

    Be well all. Have a great holiday.

  102. 102
    hnorman5 says:

    gpucci: “… they could make a very good argument for ID, in their own right.” Probably correct. I can’t judge the IC in complex molecular machines but I think there’s two logical points that are relevant here. The contention that a structure is IC is not a concession that a smaller structure within it is not IC. And — even if the smaller structure is not IC, it doesn’t affect the IC of the larger structure.

  103. 103
    Mung says:

    Perhaps a bit OT for this thread, but interesting nonetheless?

    Looking for any coverage of the origin and evolution of the spliceosomes in The Evolution of the Genome Edited by T. Ryan Gregory. I didn’t find any. Amazing.

    But I did find a pie chart on p. 553 that showed the “distribution of the homologs of the predicted human proteins.” [ETA: This has nothing to do with spliceosomes. Different topic.]

    1% had no animal homology.
    Vertebrate only 22%
    Vertebrates and other animals 24%
    Animals and other eukaryotes 32%
    Eukaryote and prokaryote 21%
    Prokaryotes only < 1%

    Is this really the pattern we would expect to see given common ancestry?

  104. 104
    Dionisio says:

    gpuccio @98:

    “Although the structural working of the catalytic site is highly comparable, it is however realized in very different ways in the two contexts.”

    This seems like a very important point.

    Isn’t it?

  105. 105
    Dionisio says:

    @98:

    Although the structural working of the catalytic site is highly comparable, it is however realized in very different ways in the two contexts.

    In group II intron RNA, indeed, almost everything depends on the six domains in the one molecule, which fold into a very complex 3D structure. For example, the main role of scaffold here is implemented by DI, the biggest domain. Moreover, the only protein contribution is provided by the IEP, with its maturase activity.

    On the contrary, in the spliceosome we have five different RNA molecules, only one of which really corresponds to one domain in the group II intron RNA, and each of these five snRNAs is part of a complex with its specific proteins, a lot of them. The global interaction of all these ribonucleoproteins in some way reconstructs the structure of the catalytic site.

    Even if we consider only the final shared catalytic activity, I would definitely say that the two contexts are very different, and that going from the first to the second is no simple matter, and requires a lot of engineering.

    This is very important to consider seriously.

    What’s the official explanation for transitioning from one context to another?

  106. 106
    gpuccio says:

    Arthur Hunt (and all interested):

    Now, another important point I would like to discuss.

    Group II introns are supposed to be at the origin of spliceosomal introns. But also of the retrotransposon component of metazoa genome. IOWs, of most of our genome: introns and a great part of intergenic non coding DNA. That’s an important theory, and I want to discuss it in some detail.

    Moreover, group II introns have been in some way involved in a theory about the evolution of spliceosomal proteins. I will discuss that point later, when I come to point 2 (the proteins).

    Let’s refer again to the Lambowitz and Belfort paper, the first I quoted.

    In brief, group II introns are obviously similar to other retrotransposons, in particular non-LTR retrotransposons (SINEs and LINEs). You can find some details in the paper section:

    “Mobile group II intron-eukaryotic retrotransposon relationships”

    However, the possible derivations of SINEs and LINEs (important intergenic forms of non coding DNA) from bacterial group II introns, while fascinating, are not really relevant for our discussion here, so I will not go into further detail about this aspect.

    Much more interesting, for us, is the idea that eukaryotic spliceosomal introns, those which are spliced by our friend the spliceosome, may derive from group II self-splicing introns.

    The theory goes more or less this way: group II introns were carried on from prokaryotes in the endosymbiont events, and then “invaded” the eukaryotic genome, becoming the spliceosomal introns.

    That is possible, but there is one major problem: group II introns cannot be found in the eukaryotic nuclear genome (only in the organelles), and spliceosomal introns are rather different.

    For example, the conserved splicing signals in 5′ and 3′ are similar, but not the same:

    GUGYC and AY in group II introns

    GU and AG in spliceosomal introns

    and, of course, spliceosomal introns, as far as I know, lack any ribozyme activity and do not encode IEPs.

    The two references given by the paper for this theory are indeed very old (1991, Cavalier-Smith and Palmer), and I could not find more recent support to the theory.

    I am not really convinced, I must say. However, even if spliceosomal introns “evolved” from group II introns, here again some major process of reorganization obviously took place: the fact remains that group II introns are absent from eukaryotic nuclear DNA, that spliceosomal introns cannot self-splice and require the spliceosome, and that obviously genes cannot be successfully transcribed and translated unless introns are spliced from mRNA.

    OK, more in next post, when possible! With the discussion about proteins, at last! 🙂

    In the meantime, my best wishes for Christmas time to all! 🙂

  107. 107
    gpuccio says:

    nkendall:

    Thank you for your very interesting intervention: I love the analogies between biologic information and human language! 🙂

    You could perhaps be interested in this older OP of mine:

    An attempt at computing dFSCI for English language

    https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/

    Have a great holiday! 🙂

  108. 108
    gpuccio says:

    hnorman5:

    I absolutely agree. Thank you for pointing to that. 🙂

  109. 109
    gpuccio says:

    Dionisio:

    “What’s the official explanation for transitioning from one context to another?”

    I don’t think they have one.

    Certainly, not one that tells us “exactly” how that happened!

    Probably, not even vaguely! 🙂

    Have a very beautiful Christmas! 🙂

  110. 110
    gpuccio says:

    Mung:

    Very interesting numbers, indeed. They correspond very well to my data about the vertebrate transition.

    A wonderful Christmas to you, too! 🙂

  111. 111
    Mung says:

    Let me ask a question about group II introns. If you don’t know the answer I can look it up myself, you don’t have to do that for me. 🙂

    Spliceosomal introns occur within protein coding regions as described in the OP. Is that also true of group II self-splicing introns?

    Another way to ask the question is that spliceosomal introns permit alternative splicing. Is the same true of group II self-splicing introns?

    Another thing I’d like to point out is that it would be quite miraculous that if self-splicing introns existed in the nuclear genome that they no longer do so. They were either all magically converted to something else or miraculously removed. All of them.

    Ain’t evolution grand.

  112. 112
    Dionisio says:

    gpuccio @106:

    “Group II introns are supposed to be at the origin of spliceosomal introns. But also of the retrotransposon component of metazoa genome. IOWs, of most of our genome: introns and a great part of intergenic non coding DNA. That’s an important theory, and I want to discuss it in some detail.”

    I look forward to reading more about this here.

    Thanks.

  113. 113
    Dionisio says:

    gpuccio @109:

    I thank God for allowing me to read your serious scientific articles and comments.

    I thank you for all the time an effort you dedicate to your highly documented articles and for being so concerned about explaining difficult topics in very easy to understand terms and style.

    May you along with your family and friends have a blessed Christmas.

  114. 114
    Dionisio says:

    gpuccio @106:

    “…there is one major problem: group II introns cannot be found in the eukaryotic nuclear genome (only in the organelles), and spliceosomal introns are rather different.”

    “…the fact remains that group II introns are absent from eukaryotic nuclear DNA, that spliceosomal introns cannot self-splice and require the spliceosome, and that obviously genes cannot be successfully transcribed and translated unless introns are spliced from mRNA.”

    I would like to read more on this.

  115. 115
  116. 116
    Eric Anderson says:

    gpuccio @106:

    However, even if spliceosomal introns “evolved” from group II introns, here again some major process of reorganization obviously took place: the fact remains that group II introns are absent from eukaryotic nuclear DNA, that spliceosomal introns cannot self-splice and require the spliceosome, and that obviously genes cannot be successfully transcribed and translated unless introns are spliced from mRNA.

    Well said. Thanks for taking time to lay this out in detail. This is very valuable.

    —–

    And if you’ll permit me to tease for a moment, even those “self-splicing” introns aren’t really self-splicing (in the sense of being fully autonomous), are they? 🙂

  117. 117
    gpuccio says:

    Eric Anderson:

    “And if you’ll permit me to tease for a moment, even those “self-splicing” introns aren’t really self-splicing (in the sense of being fully autonomous), are they?”

    To be precise, it seems that self-splicing can occur autonomously only in vitro, and under non physiological conditions.

    In vivo, other factors are needed, probably at least the intervention of the IEC protein, with its maturase activity.

  118. 118
    gpuccio says:

    To all:

    I have found another interesting and recent paper about the “evolution” of group II introns, of spliceosomal introns and of the spliceosome.

    Evolution of group II introns

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424553/pdf/13100_2015_Article_37.pdf

    From the abstract:

    Despite long-standing speculation, there is limited understanding about the actual pathway by which group II introns evolved into eukaryotic introns.

    Finally, we summarize the structural and biochemical parallels between group II introns and the spliceosome, including recent data that strongly support their hypothesized evolutionary relationship.

    Here is the “explanation” for the transition from group II introns to spliceosomal introns and to the spliceosome:

    The pathway for the evolution of spliceosomal introns from group II introns.

    Because virtually all eukaryotic genomes contain introns and spliceosomes, with the few exceptions attributed to losses [184-186], the spliceosome was necessarily present in the last eukaryotic common ancestor (LECA). Thus, evolution of ancestral group II introns to the spliceosome would have occurred prior to the LECA. Evidence from genome comparisons indicates that the LECA contained a multitude of introns [187]. Indeed, it is doubtful that such a complex machinery as the spliceosome would have arisen on account of a few introns.

    Models for the conversion of group II introns to the spliceosome are not well refined, and multiple scenarios are possible [188-191]. At some point prior to the LECA, group II introns likely invaded the nuclear genome and proliferated as mobile DNAs. The invading group II intron(s) could have come from the genome of the alpha-proteobacterium that became the mitochondrial endosymbiont or alternatively could have been transferred from a bacterium to the nuclear genome after establishment of the mitochondrion. Rampant intron propagation would leave many introns interrupting essential genes, which would require the maintenance of splicing to ensure cell viability. Consequently, the cell evolved splicing factors to facilitate and eventually control splicing of the introns. Debilitating mutations in ribozyme sequences would occur easily through point mutations, leading to many copies of splicing-deficient introns in the genome. On the other hand, discarding such defective introns by precise deletions of entire introns would be rare. The cell could have solved this problem by evolving a general splicing machinery that acts in trans, leaving the introns free to lose all their ribozyme structures except for certain boundary sequences. The end result was the transfer of splicing catalysis from individual ribozyme units scattered throughout the genome to a single trans-acting RNP machinery that could act on all intron copies.

    Because the modern spliceosome is ostensibly a elaborate derivative of a mobile group II intron RNP, it follows that at a time point prior to the LECA, the ribozyme structure of group II introns fragmented into the U2, U5, and U6 snRNA components of the spliceosome. In addition, the RT protein expanded in length through domain accretion, with the fusion of an RNase H domain, MPN/JAB1 (nuclease) domain, and possibly other domains that form portions of the modern 280-kDa Prp8 protein [167,192]. Additional protein splicing factors such as Sm and SR proteins were incorporated into the spliceosomal machinery. The U1 and U4 snRNAs and snRNPs were added as new regulatory or facilitating activities, since they do not have equivalents in group II introns.

    Emphasis mine.

    I will not comment that for the moment. I have added emphasis to the points that are more interesting, or simply more incredible. Please, read and judge yourselves.

    I must say however that, although IMO this is as far from an “explanation” as one can imagine, and so much near to the classical darwinian concept of a “just so story”, still it is a good and useful summary of the issue we are discussing.

    One last clarification: I have not yet addressed the important point of the relationships between group II introns and the spliceosome protein Prp8. This is an important point, but I will discuss it in detail in the context of the role of spliceosomal proteins.

  119. 119
    gpuccio says:

    Mung:

    “Spliceosomal introns occur within protein coding regions as described in the OP. Is that also true of group II self-splicing introns?”

    This is not an easy answer. Group II introns are localized essentially in two different sites:

    1) Bacterial genome

    2) Organelles in lower eukaryotes and plants

    Not much is known about these interesting entities.

    In the bacterial genome, it seems that they are mainly localized in less important and less conserved genes, and sometimes in intergenic regions. Remember, introns are however rather rare in prokaryotes.

    In organelles, they are more often linked to housekeeping genes, but they are often more or less degenerate, and often they do not have ORFs.

    “Another way to ask the question is that spliceosomal introns permit alternative splicing. Is the same true of group II self-splicing introns?”

    Alternative splicing is essentially an eukaryotic function. In prokaryotes, transcription and translation are strictly coupled, and alternative splicing does not occur, as a rule.

    I think I may have read something about minimal alternative splicing in prokaryotes, but I am not sure, and I cannot find the reference. However, even if something like that exists, it’s rather the exception.

    “Another thing I’d like to point out is that it would be quite miraculous that if self-splicing introns existed in the nuclear genome that they no longer do so. They were either all magically converted to something else or miraculously removed. All of them.

    Ain’t evolution grand.”

    Please, look at my post #118 for some just so story about that point! 🙂

  120. 120
    Mung says:

    Evolution as problem solving. I love it.

  121. 121
    Eric Anderson says:

    gpuccio @117:

    Thanks for indulging me (I know it isn’t the key point you are focusing on).

    “. . . it seems that self-splicing can occur autonomously only in vitro, and under non physiological conditions.”

    Meaning, not in the real world?

    Hmmmm . . .

    I’m not quite ready to pronounce any conclusions yet, but this is starting to sound suspiciously like those self-replicating molecules we keep hearing about that are supposed to kick off the whole abiogenesis creation story (but which don’t exist).

    I’ll have to keep my eye on these so-called self-splicing introns a bit more . . .

  122. 122
    Mung says:

    Eric, Merry Christmas.

    Whether in vivo or in vitro, both are in the real world. A self-replicating molecule in vitro would still be a major design accomplishment.

    Let’s not hang our Santa hats on that. 🙂

  123. 123
    PaV says:

    Mung:

    One wonders how this “self-splicing” takes place in vitro. Do they add reagents, or proteins? What’s involved?

    IOW, are we dealing with a “directed” process in vivo, which scientists stumble upon in vitro?

  124. 124
    Mung says:

    PaV:

    One wonders how this “self-splicing” takes place in vitro.

    Not me. I believe it takes place in vivo.

    I can understand why gpuccio was trying to avoid going through all the different sorts of introns and the evidence for them and for the mechanisms associated with their splicing. 🙂

    I’m not going to be the one to ask him to start over from scratch, lol!

  125. 125
    PaV says:

    Mung:

    My point was that in vitro requires an ‘intelligent agent’ to do what is done quite naturally in vivo: that is, a “directed” process—one that has a “direction” given to it by some intelligent agent.

  126. 126
    Eric Anderson says:

    Mung @124:

    “Whether in vivo or in vitro, both are in the real world.”

    Fair enough. You know what I mean. Maybe we could say “natural world” instead.

    “Not me. I believe it takes place in vivo.”

    On what basis? Just because they call it self-splicing doesn’t make it so.

    I can certainly believe that if an mRNA strand has the right sequence, is carefully shepherded to the right location, protected from interfering cross reactions, and three-dimensionally positioned such that the splicing can take place, then the relevant molecule could trigger a splicing event.

    Sure, I can buy that. And we could even call it “self” splicing if we wanted to. The risk is that people tend to see these “self” driving processes as though it is all just chemistry doing what it does all by itself — move along folks, nothing to see here. This is incredibly naive and is anathema to our (growing) understanding of what is actually required to engineer an organism.

    So, no, I don’t feel bound by the terminology and the labels biologists put on things. I prefer to press and see if the label actually fits. For example, just because Joyce calls his molecules “self-replicating” doesn’t make them so. And I’m starting to suspect that just because people call certain mRNA elements “self-splicing” might not make them so. In contrast to the former, I haven’t looked into the latter in a lot of detail, so I’m open to being corrected. But so far, my suspicions appear to be on the right track.

    A self-replicating molecule in vitro would still be a major design accomplishment.

    Agreed. I’m still patiently waiting . . . 🙂

    Let’s not hang our Santa hats on that.

    I don’t. But I also don’t feel any compunction to give away the store or cede ground were it need not be ceded. Particularly (in the case of self-replicating molecules) when the whole materialistic creation story is absolutely dependent on the existence of these never-before-seen, no-reason-to-believe-exist, highly-unlikely entities.

    Again, apologies for the side track. gpuccio is bringing up some incredibly important points, with which I am in agreement. This “self” issue just jumped out at me as another interesting issue that we shouldn’t be too quick to ignore.

  127. 127
    gpuccio says:

    To all:

    I am sorry that my short answer to Eric is causing some confusion. I will try to clarify better.

    When we say that group II introns are self-splicing, we mean that it’s the intron RNA itself that catalyzes its splicing from the pre-mRNA. IOWs, the catalytic site and activity are formed by the intron RNA itself, and catalyze their own splicing from the mRNA. If you think that this is an amazing result of clever engineering, I fully agree with you! 🙂

    However, this capacity at self-splicing is obviously connected to the retrotransposon nature of these entities, and to their ability to move and retro-home.

    When we say that group II introns can autonomously self-splice in vitro, we mean that they can do so, to some extent, out of a cellular environment. IOWs, you take the pre-mRNA with the group II intron, you put it in a tube, and it can self-splice. Of course, you always have to provide some basic conditions, pH, ions, temperature, and so on, for the reaction to happen, but no major cellular components, like other proteins, are necessary. Mg2+-ions are always necessary for the intron RNA to fold into the correct tertiary structure and for its catalytic function

    When we say that self-splicing can happen in vitro, but in non physiological conditions, it means that strangely the reaction autonomously happens only in conditions that would not be likely in a living cell, in particular high concentrations of a salt with a monovalent cation. A somewhat high temperature is also necessary (45°).

    In vivo, the reaction needs the help of other components, in particular proteins. While I suppose that other proteins can be involved, the main role seems to belong to the intron IEP protein, IOWs, the protein coded by the intron itself by the ORF located in the DIV domain (remember that transcription and translation are strictly coupled in bacteria, while in eukaryotes that are separated by the nuclear membrane). The specific activity of the IEP protein which stabilizes the intron ribozyme is usually called maturase activity.

    I hope this clarifies some of the issues that have emerged in the discussion. However, if you are interested, and really want to suffer ( 🙂 ), here you can find a lot of details:

    Group II Introns: Structure and Catalytic Versatility of Large Natural Ribozymes

    https://www.researchgate.net/publication/10653386_Group_II_Introns_Structure_and_Catalytic_Versatility_of_Large_Natural_Ribozymes

    I quote a simple passage which summarizes well what I have said here:

    Because autocatalysis depends on quite unphysiological reaction conditions (see below), it was postulated that even introns with an efficient in vitro splicing reaction depend on proteins in vivo (Lambowitz and Perlman, 1990). Furthermore, the actual data of different model organisms show clear evidence for a protein-dependent catalysis in vivo. Proteins interacting with intron RNAs seem to support RNA folding or to stabilize the active conformation, whereas the catalytic potential is clearly located in the RNA itself

  128. 128
    gpuccio says:

    Mung:

    “I can understand why gpuccio was trying to avoid going through all the different sorts of introns and the evidence for them and for the mechanisms associated with their splicing.”

    You bet! 🙂

  129. 129
    gpuccio says:

    Arthur Hunt (and all interested):

    And now, the spliceosome proteins.

    Arthur Hunt, having set some basic points with all those who are following the discussion, and having essentially accepted you point 1, I am going now to address you more directly to discuss point 2.

    Let’s see it again. You said (#56):

    As far as the proteins of the spliceosome are concerned, I guess if totally unrelated proteins in prokaryotic systems can also facilitate the activity of the core of the splicing enzyme, then maybe the uniqueness of proteins that make up these complexes is not so great as you are asserting.

    Now, that is maybe a little cryptic, so I will interpret it a little bit, and of course you are free to clarify if I am misunderstanding your point.

    It seems that you are saying:

    “The role of proteins in the spliceosome is somewhat aspecific, and therefore not so relevant from the informational point of view. Evidence of that can be found in the fact that proteins help the splicing in prokaryotes, and that those proteins are completely different from those of the spliceosome.”

    OK, so I will comment the point in that form, unless you intervene to clarify better.

    But I will try to widen a bit the discussion on this issue, because it is a very important one. So, I will follow more or less the following line of discussion:

    a) I will try to explain why in my OP I have focused my attention on the spliceosome proteins, and not on the RNA catalytic core.

    b) I will discuss the roles of the proteins in the spliceosome.

    c) I will discuss the issue of the differences between prokaryotic proteins involved in splicing, and the spliceosome proteins, and what those differences may imply.

    d) Finally, even if that point was not raised by you, I will debate in some detail the presumed derivation of Prp8, my favourite spliceosomal proteins, from gourp II self-splicing introns.

    That will take some time, I imagine, but at least I have traced a general blueprint of what I want to say. That will probably be of help to me and, I hope, to those who will read my next comments.

  130. 130
    Arthur Hunt says:

    A very Merry Christmas to all. I thought I would leave gpuccio and everyone following this a small gift, an additional pointer to another interesting aspect of this discussion. It is in the form of a few words for Google: try searching for information about the maturation of the Chlamydomonas chloroplast psaA mRNA.

    Enjoy!

  131. 131
    Dionisio says:

    gpuccio @127:

    “…take the pre-mRNA with the group II intron, you put it in a tube, and it can self-splice.”

    That’s really cool!

  132. 132
    Dionisio says:

    Definitely the discussion between gpuccio and the distinguished professor Arthur Hunt has turned very insightful, despite its strange start @25.

    Has distinguished professor Arthur Hunt anything to say on what gpuccio has explained so far?

    Does he agree with everything gpuccio has stated so far?

    Just curious.

  133. 133
    Dionisio says:

    gpuccio @127:

    In vivo, the [group II introns self-splicing] reaction needs the help of other components, in particular proteins. While I suppose that other proteins can be involved, the main role seems to belong to the intron IEP protein, IOWs, the protein coded by the intron itself by the ORF located in the DIV domain (remember that transcription and translation are strictly coupled in bacteria, while in eukaryotes that are separated by the nuclear membrane). The specific activity of the IEP protein which stabilizes the intron ribozyme is usually called maturase activity.

    Quite interesting, isn’t it?

  134. 134
    ET says:

    the maturation of the Chlamydomonas chloroplast psaA mRNA- just something else blind and mindless processes cannot account for…

  135. 135

    First of all … Merry Christmas to all.

    Now my comment:
    I won’t pretend to be able to fully follow this quite technical post and all the follow up comments — very fascinating.

    The very title “a molecular machine that defies any non-design explanation.” shouts a challenge of “evidence … evidence … evidence”

    So here is yet another — of many — instances of evidence for Design, for Intelligent Design given here at UD. Its this sort of evidence that several (looking at you rvb8) contributors here claim is totally lacking in the ID argument.

    Perhaps rvb8 is out for coffee, or otherwise unavailable, but after 100+ comments on this post not a single one from rvb8 refuting this as a piece of valid evidence.

    Hopefully rvb8 is indeed out for coffee and deep in study of what is presented here. Hopefully after being forced into a corner of objectivity and following evidence such as presented here … to a logical, not ideological conclusion, he might at long last sense a sort of light coming on.

    One can only hope!

  136. 136
    gpuccio says:

    Arthur Hunt (and all interested):

    Merry Christmas to you and thank you for your participation here.

    Your “Christmas gift” is very interesting, and helps me understand better some aspects of your previous statements. I will consider it in the following discussion, of course.

    For all who may be curious, it is about some specific and very intriguing aspect of splicing in plant organelles, chloroplasts.

  137. 137
  138. 138
    gpuccio says:

    Arthur Hunt (and all interested):

    So, I will go on with my declared schedule, and include at the appropriate step the new information kindly provided by Arthur Hunt at #130, and which can be important to understand his point of view (I must say that our friend from the other side is using a remarkable, although sometimes a little frustrating, “Ars Maieutica” to clarify his thoughts! 🙂 )

    So, let’s go to the first point, which is not so difficult:

    a) I will try to explain why in my OP I have focused my attention on the spliceosome proteins, and not on the RNA catalytic core.

    One easy answer would be that I have much more familiarity with proteins than with nucleotides. That’s absolutely true. But it is not the main reason.

    The main reason is informational.

    I have specified in my OP the individual lengths if the five snRNAs which are the catalytic part of the spliceosome.

    I have also added about them:

    “They are transcribed from multiple gene copies. While their sequences are not particularly conserved (U6 being the most conserved of all), their secondary structure seems to be very conserved.”

    We have also seen in the discussion that those points are valid also for group II introns, even if type II intron RNAs can be much longer, especially when they include the ORF for the IEP in their DIV domain.

    OK, let’s consider this from a quantitaive informational point of view, IOWs from an ID point of view.

    If we sum the length of all five spliceosomal snRBAs (in humans), we get:

    719 nucleotides

    So, the total maximum information content that can be expressed by those 5 genes, taken together, is:

    4^719 = 1438 bits

    But, of course, this is not the true functional information of the sequences. We know that, with the exception of U6, the sequences are scarcely conserved, while the structures are very conserved. That means that the sequence-structure relationship is very flexible.

    I have no idea of how big the true functional information maybe, that would require detailed studies of the sequence conservation of these genes. Let’s say that it is certainly rather lower that the total possible information content. Let’s imagine that it can be in the range of a few hundred bits, just for the sake of discussion. That’s not unlikely, the U6 gene alone is very conserved, and it could contribute 100 – 200 bits of functional information.

    The point is: that functional information is a big amount from a general point of view, certainly beyond the capacities of RV + NS (see my previous posts on those points). But it is “relatively” small if compared to the huge amount of functional information we can observe in some proteins, and in particular in the proteins that are part of the spliceosome.

    We have seen in the OP that Prp8, alone, exhibits at least 3345 bits of human-conserved information in single celled eukaryotes (4211 in fungi). If you consider that we are dealing with exponential values, that’s a lot more!

    Beware, I am not saying that the RNA catalytic site of the spliceosome (or of group II introns) is not complex: as I have said, it is an extraordinary accomplishment of engineering, from a biochemical point of view. And yet, moderate amounts of functional information are sufficient to encode it (if we can call “moderate” a few hundred bits of information).

    ID has a quantitative approach to functional information: therefore, with all respect for the RNA component, the protein component seems more “interesting” from an ID point of view.

    Another aspect has also been detailed in the discussion stimulated by Arthur Hunt: the basic information for the catalytic site was already present in bacteria, in group II introns. So, the spliceosome is reusing that information, even if, as we have discussed, a major re-engineering is obviously necessary to go from the single RNA molecule ribozyme in group II introns to the fragmented RNA + multiple proteins structure of the catalytic site in the spliceosome. But the information for such a re-engineering is not easy to quantify exactly.

    On the other hand, many of the proteins in the spliceosome are informational novelties, as we have seen, with complex and conserved sequences that practically appear for the first time in the eukaryotic spliceosome. That too makes them extremely interesting for an informational analysis from an ID point of view.

    I understand that Arthur Hunt is probably biased towards RNA, and tends to somewhat under-emphasize proteins. That can be expected, given his specific background. I will come back to that point in the course of the discussion. However, most of the evidence that I have presented in my OP is about proteins, and most of the methodology I have developed deals with proteins, so I will stick to proteins in the rest of the debate.

    Point b) in next post.

  139. 139
    Dionisio says:

    ayearningforpublius @135:

    I see your valid point, but note that gpuccio is very serious in his scientific articles and follow-up commentaries, hence his discussion threads don’t need trolls.

    In this current thread we see a distinguished professor at a university in the US presenting scientific arguments that have had the positive effect of making gpuccio write more on this interesting topic. Interestingly, so far his highly educated interlocutor hasn’t commented back on gpuccio’s scientific arguments.

    At the end the readers benefit from their exchange.

    This thread has had almost ten times more non-commenting visitors than commenting ones in its first four days. That’s not too bad.

  140. 140

    Merry Christmas GP, Merry Christmas Mung, Merry Christmas all…

  141. 141
    Dionisio says:

    gpuccio @138:

    I must say that our friend from the other side is using a remarkable, although sometimes a little frustrating, “Ars Maieutica” to clarify his thoughts!

    That’s it! I couldn’t figure out what was going on, but it definitely looks like a convoluted version of the Socratic method:
    https://en.wikipedia.org/wiki/Socratic_method

    Thanks for clarifying this.

  142. 142
    gpuccio says:

    UB:

    Merry Christmas to you, my friend! 🙂

  143. 143
    Dionisio says:

    gpuccio @138:

    “…many of the proteins in the spliceosome are informational novelties, as we have seen, with complex and conserved sequences that practically appear for the first time in the eukaryotic spliceosome.”

    Would the distinguished professor that posted @25 ever realize that he’s on the losing side of this debate?

  144. 144
    Dionisio says:

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  145. 145
    Dionisio says:

    AH @25
    ……. GP @28
    AH @50
    AH @51
    ……. GP @54
    AH @56 *
    ……. GP @60
    ……. GP @69
    ……. GP @75
    ……. GP @86
    ……. GP @98
    ……. GP @106
    ……. GP @118
    ……. GP @127
    ……. GP @129
    AH @130
    ……. GP @136
    ……. GP @138

    (*) error admitted

    (to be continued…)

  146. 146
    gpuccio says:

    Arthur Hunt (and all interested):

    Now, let’s talk of the proteins. My arguments are already clearly expressed in the OP, so I will try not to repeat them too much.

    Let’s see again Arthur Hunt’s statement:

    As far as the proteins of the spliceosome are concerned, I guess if totally unrelated proteins in prokaryotic systems can also facilitate the activity of the core of the splicing enzyme, then maybe the uniqueness of proteins that make up these complexes is not so great as you are asserting.

    My further interpretation:

    “The role of proteins in the spliceosome is somewhat aspecific, and therefore not so relevant from the informational point of view. Evidence of that can be found in the fact that proteins help the splicing in prokaryotes, and that those proteins are completely different from those of the spliceosome.”

    I think that interpretation remains correct. However, when I wrote that I was thinking that Arthur Hunt was referring mainly to the IEPs, IOWs the proteins encoded by group II introns themselves, by the ORF in DIV, essentially in their rather rare occurrences in bacterial genomes, of which LtrA in Lactococcus lactis is one of the best known examples (see my post #86).

    Instead, according to his suggestion in #130, it seems that he is more interested in the “maturation of the Chlamydomonas chloroplast psaA mRNA”. That was not easy to catch, because that is a very specific issue (and I am greatful to Arthur Hunt for pointing at it), and it is not exactly a prokaryotic system, but rather a system in an eukaryotic single celled organism, involving the chloroplast (which is probably of prokaryotic derivation).

    That complicates a little our discussion, because the two scenarios (IEP proteins like LtrA helping the self splicing of group II introns in bacteria and proteins helping in trans splicing of a specific gene in unicellular algae) are quite different. So I will have to deal with them separately.

    One warning to all who are following this discussion. It is not simple, and it will become even less simple. I will try to be as clear as possible, but if anyone has doubts or questions, please be free to ask or comment.

    As a first, easy step, I will briefly summarize my main argument from the OP:

    a) The spliceosome is a wonderful, and very complex, molecular machine. As clarified earlier, we are now debating specifically the functional complexity linked to the protein part, having already discussed in some detail the RNA catalytic core.

    b) The spliceosome is a rather universal complex in eukaryotes. Rare apparent exceptions are interpreted as cases of loss of information. The universality of the spliceosome is a direct consequence of the universality of spliceosomal introns in eukaryotes. No eukaryotic transcription and translation could work without the spliceosome, which is the only tool which can excise spliceosomal introns.

    c) The spliceosome is essentially eukaryotic: the proteins which make it are, in most cases, a complete eukaryotic novelty. I have given examples of that, but we will discuss that aspect again for Prp8 in this discussion.

    d) Spliceosome proteins are, in most cases, exceptionally conserved in all eukaryotes, from single celled organisms to humans. That point is well demonstrated by measuring the human-conserved information in different single celled eukaryotes, as I have done in Fig. 4. Prp8, again, is probably the most conserved protein in the spliceosome, and its level of conservation (1.8 baa from fungi to humans) rivals with the most conserved proteins in eukaryotes.

    e) A final important point is that the spliceosome certainly has an important role in alternative splicing, a regulation network whose functional importance in eukaryotes is recognized practically by all.

    I will dedicate some time to this last point.

    The ability of the spliceosome to take part in transcription regulation through alternative splicing, and probably other mechanisms, seem to be strictly related to its dynamic nature as a malleable molecular system. I quote from:

    “The Spliceosome: The Ultimate RNA Chaperone and Sculptor”

    http://www.cell.com/trends/bio.....15)00211-X (paywall)

    An emerging concept is that the spliceosome is a remarkably dynamic and flexible molecular machine;

    Progression through the splicing reaction is accompanied by extensive remodeling of the protein composition of the subcomplexes associated with the different snRNA–pre-mRNA structural transitions (Figure 6). For example, catalytic activation is associated with the incorporation of approximately 35 proteins in splicing complexes, while a similar number dissociate from them. Few of the more than 150 proteins identified in purified spliceosomal complexes persist during the whole process.

    More in next post.

  147. 147
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  148. 148
    Dionisio says:

    Serious error found @146:

    (and I am greatful to Arthur Hunt fro pointing at it),
    (and I am grateful to Arthur Hunt for pointing at it),

    The word ‘grateful’ got affected by a deleterious RV where the letter ‘e’ got misplaced

    “fro” instead of “for” ? oops!
    the letters o and r were swapped!

    🙂

  149. 149
    Dionisio says:

    @146 achtung!

    “One warning to all who are following this discussion. It is not simple, and it will become even less simple. I will try to be as clear as possible, but if anyone has doubts or questions, please be free to ask or comment.”

    Ok. Thanks.

  150. 150
    gpuccio says:

    Dionisio:

    If only I could RV (possibly helped by NS made by you) compile my answers to Arthur Hunt!

    That would be a lot of work spared! 🙂

  151. 151
    Dionisio says:

    @146, another ‘major’ error:

    letters ‘k’ and ‘a’ swapped places within the word eukaryotic

    ‘ak’ instead of ‘ka’

    b) The spliceosome is a rather universal complex in eukaryotes. Rare apparent exceptions are interpreted as cases of loss of information. The universality of the spliceosome is a direct consequence of the universality of spliceosomal introns in eukaryotes. No euakryotic transcription and translation could work without the spliceosome, which is the only tool which can excise spliceosomal introns.

    euakryotic eukaryotic

  152. 152
    Dionisio says:

    Yes, I see what you mean @150

    Well, what can I say?

    C’est la vie, mon ami
    🙂

    To poorly educated folks like me, Kentucky was associated with things like https://www.kfc.com/
    and to my neighbors also https://www.kentuckyderby.com/

    But now I may associate it with… ok, let’s not talk about that here. 🙂

  153. 153
    Dionisio says:

    @146
    Non deleterious RV detected:

    The letter ‘u’ was accidentally repeated: buuut

    c) The spliceosome is essentially eukaryotic: the proteins which make it are, in most cases, a complete eukaryotic novelty. I have given examples of that, buuut we will discuss that aspect again for Prp8 in this discussion.

    A semantically-endowed word processor installed in my Surface tablet detects and highlights most ‘typos’ and suggests replacements.

  154. 154
    gpuccio says:

    Dionisio:

    OK, my Natural Selector. Done. 🙂

  155. 155
    Mung says:

    *poof!* is not an explanation?

  156. 156
    Dionisio says:

    Mung,

    Yes, these days that would count as a valid explanation, because anything -except ID- counts.

    🙂

  157. 157
    Dionisio says:

    ant? and

    Prp8, again, is probably the most conserved protein in the spliceosome, ant its level of conservation (1.8 baa from fungi to humans) rivals with the most conserved proteins in eukaryotes.

  158. 158
    Dionisio says:

    After all that gpuccio has explained so well, it seems like professor Arthur Hunt owes us some explanations too.

  159. 159
    PaV says:

    Here’s a thread I posted just over a month ago: Evolution as a Ralph’s Supermarket.

    It’s always the same thing: in the minds of Darwinian thinkers, the presence of proteins, or of other constituent parts, is necessary and sufficient to explain any complex structure found in living cells.

    My comment@27:

    A splicesome has upwards of 170 proteins working together. Imagine just two amino acids necessary for one protein to bind to another. Think of all the ways that 170 proteins can be configured. 7.25 x 10^308 permutations (This has nothing to do with binding sites).

    And somehow, we go from prokaryotes to eukaryotes, and eukaryotes cannot produce proteins without splicesomes.

    Yes, just shake the Ralph’s Supermarket real hard—-and maybe for a hundred trillion years.

    If the objection is made, “Well, the prokaryotes came first, and they had a catalytic splicing capacity, and the “origin” of this catalytic activity is part of the OOL,” then my response would be: “First solve this problem of overcoming this huge number of permutations, and, then you can start worry about OOL–which is a much more difficult problem, one which includes this catalytic spliceosome cunundrum.”

    What I’m saying is this: no matter what gpuccio writes indicating the immense complexity, Arthur Hunt will content himself by saying, “Well, yes, it’s complex, but we find these structures there. They had to come from somewhere. It’s just a matter of time–you know given all the replications that can take place.”

    It’s pointless to point out the obvious to those who discount the obvious.

  160. 160
    gpuccio says:

    PaV:

    I had not seen that you had already discussed the spliceosome! Good! 🙂

  161. 161
    ET says:

    Matzke and Pallen adhere to the “Ralph’s Supermarket” concept of evolution for bacterial flagella:

    From The Origin of Species to the origin of bacterial flagella, via Ralph’s Supermarket

  162. 162
    gpuccio says:

    Arthur Hunt (and all interested):

    I would like to address now the theory, cited by many papers, that group II self-splicing introns would be the origin not only of spliceosomal introns, but also of the spliceosome (and, but that is not so interestoing for us here, of a lot of intergenic non coding DNA, like LINEs and SINEs, and maybe telomerases).

    So, what is the relationship between group II introns and the spliceosome?

    There are two aspects.

    The first has been already discussed here in detail: the RNA catalytic core of the spliceosome (the five snRNSa) is clearly derived from group introns. That cannot be denied. However, I have tried to emphasize that the derivation is not at all simple, because only the strict catalytic site (DV – U6) is really conserved, while the rest is different, fragmented and recostructed in the spliceosome through the contribution of the many spliceosomal proteins that form the RNA-protein complexes or snRNPs.

    OK, I will not come back to this.

    The second point, instead, still need to be discussed. Group II introns are also belieeved to be in some way the “ancestors” of spliceosomal proteins.

    Is that true?

    Essentially not, but we need to understand why such a claim is made, and what it really means.

    Some important points:

    1) The claim is made, really, only for Prp8. IOWs, simplifying, Prp8 would be derived from group II IEP, the proteins encoded by the ORF in DIV. Or from some similar retro-transcriptase protein in prokaryotes.

    2) How is that possible? In my OP, I have clearly stated that Prp8, like other spliceosomal proteins, maybe more than any other, is an eukaryotic protein, that it shows no homology with any eukaryotic protein.

    Am I wrong?

    No, I am not. Blasting Prp8 vs prokaryotes, we get no hits (except, as said in the OP, for 3 false hits which are clear errors in the database).

    But there is more.

    If you look at the already quoted paper:

    Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394904/pdf/nihms673151.pdf

    and look at Fig. 6:

    Comparison of Prp8 to group II intron and related RTs

    you can see that Prp8 is compared to 5 different molecules, with which it is supposed to have structural similarities.

    The first is group II IEP (maturase) LtrA from Lactococcus lactis, of which I have already spoken at #86. Number 2 and 3 are two maturases from plants. the last two are other proteins with RT activity.

    OK before we consider why these proteins are supposed to be possible “ancestors” of Prp8, let’s clarify without any doubt one thing:

    I have blasted exactly the molecules referred in the Figure: yeast Prp8 against the other 5, and the result is: absolutely no hit.

    Indeed, if you are curious, the bitscores and E values are, in order:

    20.0 7.6
    23.1 0.9
    21.6 2.6
    20.8 4.8
    26.6 0.099

    No significant homology at all, with any of the 5 possible “ancestors”.

    Now, I would like to remember her, for comparison, that Ltra, the protein which sghould be the best candidate as an “ancestor” of Prp8, is rather well conserved in bacteria, as I have shown in my post #86: about 400 bits of conserved sequence information.

    But then, why do they say that those proteins are somewhat related?

    The answer can be found in the following papers:

    Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078730/pdf/799.pdf

    and

    Crystal structure of Prp8 reveals active site cavity of the spliceosome

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672837/pdf/emss-50962.pdf

    This papers, correctly, show some reasons to believe that some evolutionary connection could exist between Prp8 and those proteins. But what are those reasons?

    a) Enhanced homology queries have shown the presence of some putative domains in Prp8 which show significant (but low) homology with existing domains. You can find them in Fig. 1 of the first paper. Of those domains, the one that is relevant for the derivation from RT molecules is the RT domain (AAs 950 – 1220 in yeast Prp8). This domains shows, with those enhanced sequence analyses, some homology to other existing RT proteins, both bacterial and eukaryotic. That is confirmed by the second level of data:

    b) Structural data show some structural similarity between the RT putative domain in Prp8 and RT domains in the other RT proteins. Finally:

    c) The second paper shows that the RT and En putative domains of Prp8 form a cavity that helps accommodate the RNS catalytic structure of the spliceosome. This cavity is, again, a structural similarity with the tertiary structure of RNA in group II introns, as shown in Fig. 5 of the paper.

    If we want to simplify further, the evolutionary connection between Prp8 and RT proteins rest mainly on weak sequence similarities, that can be shown only by enhanced algorithms, but not by the basic BLAST analysis, and on structural similarities of some domains of Prp8 with some aspects of group II introns structure.

    Another important point is that those domains of Prp8, especially the putative RT domain, do not retain their supposed original function in the molecule: neither Prp8 not the spliceosome appear to have any reverse transcriptase activity.

    So, what does all that mean, especially form an ID point of view?

    I think it is simple enough.

    Darwinian evolutionists essentially look at those faint sequence similarities, and at structure similarities, to find possible “ancestors” of a molecule.

    That’s fair.

    Are those evidences strong enough for Prp8? I am not so sure. However, some evidence exists.

    So, could the Prp8 molecule really derive, in part, from some older RT molecule, maybe also some IEP, having retained some of its structural features?

    It is possible.

    What does that mean from an ID point of view? IOWs, from the point of view of functional information, and of the functional complexity of the molecule, and of course of the whole spliceosome (which includes, of course, more than 100 other different proteins)? What relation has all this with my discussion in this OP?

    Very little. And the reason is very simple.

    My analysis in the OP is not based on weak homologies that can be seen only with enhanced methods, least of all on structural similarities.

    It is based, as said many times, on the huge quantity of sequence similarity that the Prp8 molecule shows from its appearance (in LECA) to humans: in the order of 3000 – 4000 bits, and extremely high sequence identity.

    As opposed to no sequence homology at all with any prokaryotic sequence when established by the same procedure (basic BLAST).

    Remember, The Latr molecule has no sequence similarity at all with yeast Prp8 at a BLAST analysis: 20 bits, and E value of 7.6. The same molecule retains about 400 bits of information in different bacteria, demonstrating that a lot of sequence conservation is necessary to implement its function.

    The yeast Prp8 and human Prp8 share more than 3000 bits of conserved information. Both have no obvious sequence similarity with Latr.

    Some could object that basic Blast is not sensitive enough to detect weak evolutionary connections.

    Well, but my purpose is not to detect weak evolutionary connections. We are not interested in that, if we are making an informational analysis to detect design.

    What we are interested in are huge amounts of functional information which arises at some point in natural history and is then conserved through long evolutionary times.

    Prp8, and more in general the spliceosome proteins, fully satisfies those requisites.

    Its 3000+ bits of specific sequence information that arise in the transition from prokaryotes to eukaryotes, in LECA, are not present before, and are then conserved for more than one billion years of evolutionary history.

    And they are only a small part of the total informational content of the spliceosome.

    OK, that was certainly rather complex. But wait for the Chlamydomonas chloroplast psaA mRNA part! 🙂

  163. 163
    Mung says:

    I think my brain just suffered a spliceosomal event.

  164. 164
    Arthur Hunt says:

    Hi all,

    Many thanks for your patience. I can see that gpuccio is about done with the many things I have thrown out in this discussion. To help this along, I will try to sum up one tangent so attention may be paid to the main interest here, namely the protein components of the spliceosome.

    My own attention on the RNA component of the spliceosome is entirely appropriate, since, as we have learned in this discussion, it is the core of the spliceosome, the catalytic center of the enzyme. in this discussion, we have learned of three versions of this catalytic RNA. One is a single, self-contained catalytic RNA, the group II intron. Another is the set of RNAs that make up the core of the spliceosome. Yet a third, not yet discussed by gpuccio, is typified by the Chlamydomonas chloroplast psaA intron(s). This third example is a split group II intron, in which two separate RNA molecules bind together to form a catalytic RNA. Without more elaboration, I trust that readers can see the the implications regarding the ways in which group II introns may vary, and why, from the perspective of the RNA, the “distance” between group II introns and the spliceosome is not impossibility far. This may be consistent with the implication seen in the preceding that the information content, as it were, of the RNA component of the spliceosome is not very great, and probably not enough to support, from a purely informational perspective, the hypothesis that the spliceosome is a product of design.

    I will in due time turn to the matter of the proteins that participate in the splicing of group II introns and of introns that are substrates of the spliceosome. I will mention at this time, though, one thing that gpuccio needs to consider. This is that it is not appropriate to rely solely on BLAST, either to understand distant evolutionary relationships or to assess information content. At least in the sense laid out by Dembski many years ago. Some of the subunits of the complex I work on defy the logic being used here. I mention this because it will factor in to my further comments.

    Again, many thanks for your patience, and for your continued attention. And special thanks to gpuccio for tolerating my admittedly annoying manner in moving this discussion along.

  165. 165
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  166. 166
    Dionisio says:

    @162

    What does that mean from an ID point of ciew?
    What does that mean from an ID point of view?

  167. 167
    gpuccio says:

    Arthur Hunt (and all interested):

    Thank you for your comment.

    “I will mention at this time, though, one thing that gpuccio needs to consider. This is that it is not appropriate to rely solely on BLAST, either to understand distant evolutionary relationships or to assess information content. At least in the sense laid out by Dembski many years ago. Some of the subunits of the complex I work on defy the logic being used here. I mention this because it will factor in to my further comments.”

    This seems interesting, and I am looking forward to your further comments. I am very willing to consider your point, but I really need that you make it before! 🙂

    Just as a due clarification, I would remind here that I rely on BLAST and long evolutionary conservation to assess information content at sequence level.

  168. 168
    DATCG says:

    #164 Arthur Hunt

    Thanks for joining discussion.

    “… distant evolutionary relationships or to assess information content.”

    First, lets admit an assumption.
    1) “..distant evolutionary relationships” assumes materialist only doctrine? Based on what specific
    context or mechanism(s)? That rules out Design?

    For sake of discussion, lets say it’s a fact. Some self-splicing Introns evolved over time to a Spliceosome. What I hope to see is by what path and Neo-Darwinian mechanism?

    2) Evolution does not rule out Evolution by Design(Front-Loading or Pre-Adaptation) unless one A Priori rules it out.

    “… rely solely on BLAST… to assess information
    content”
    3) Of course not. It’s one tool. GPuccio has not
    represented it any other way here that I know of. Look forward to other methods, data, or information from you.

    4) “Some subunits of the complex I work on defy the logic being used here.”

    OK, cannot wait for the great reveal. But as there’s more than one tool like BLAST to describe DNA information, there’s more than one way to infer Design.

    From DNA Metadata to coordination and organization of interdepedent systems, life dances to an orchestrated beat. Each unit, subunit a part of a coordinated system. Organized proteins across multiple domains pulled together to form a specific function in many cases, using what was once cast as “junk” DNA to both govern, change and reformulate on the fly at times tied to environmental stimulus. A dynamic system that both reflects on it’s surroundings and acts.

    Not to mention information sensing, controlled release, entrances and blocking, sharing, error correction, and cognitive signal processing. In life at all levels from organism to cells internally and externally.

    Organized, step-by-step processing, coordinated task unfolding at rapid rates, with dynamic reads, writes and error checking.

  169. 169
    DATCG says:

    A bit off-topic, but very curious where Hunt stands on debates taking place over neo-Darwinism or Extended Theory.

    Where btw, ID scientist did attend…

    Modern Synthesis – Extend or Blow it up

    note for readers: see Table 3 for comparisons of
    EES to past standards and Traditional predictions in evolution.

  170. 170
    DATCG says:

    #167 Gpuccio

    “I am very willing to consider your point, but I really need that you make it before!”

    and preferably a specific link or two on the assertion would help as well 🙂 Telling people to google is a bit trollish. Just give me specifics please.

  171. 171
    gpuccio says:

    DATCG:

    Thank you for your interventions. I fully agree with your concepts.

    I am indeed very happy of the discussion here. It’s exactly what I have always hoped for: a respectful discussion between the two sides about biological details and their interpretation.

    So, I am really grateful to Arthur Hunt for stimulating it and taking part.

    Like you, I cannot wait for the great reveal. I am sure it will stimulate further interesting discussion and intellectual confrontation. Which is what I do love.

    I agree with you that “telling people to google is a bit trollish.” But the reference to Chlamydomonas psaA was very specific, and I had no real difficulty in finding what it was about. I am going to discuss it in my next posts, because it is really weird and interesting.

    I really hope that you will stay in the discussion. Your contribution is precious! 🙂

  172. 172
    Dionisio says:

    What’s so weird and interesting about that Chlamydomonas psaA?

    Is it that it has four propellers around itself, thus proving that drones are the natural result of Neo-Darwinian evolution?

    While we anxiously await the big revelation by the distinguished professor Arthur Hunt, it would be interesting to see what gpuccio found about the Chlamydomonas psaA that makes it such a strong case to prove Neo-Darwinism and disprove ID.

  173. 173
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  174. 174
    gpuccio says:

    Dionisio:

    “Is it that it has four propellers around itself, thus proving that drones are the natural result of Neo-Darwinian evolution?”

    More or less… 🙂

    “it would be interesting to see what gpuccio found about the Chlamydomonas psaA that makes it such a strong case to prove Neo-Darwinism and disprove ID.”

    I would not say so. I would rather say that it is a weird system, difficult to understand from any point of view.

    I will be more clear in next post.

  175. 175
    Dionisio says:

    gpuccio,

    Thanks for clarifying that.

    Still, after reading what the distinguished professor Arthur Hunt has written here so far, I keep asking:

    Where’s the beef?

    🙂

  176. 176
    gpuccio says:

    Arthur Hunt (and all interested):

    So, the famous Chlamydomonas psaA.

    A few premises, so that all may follow the discussion (I hope!).

    We have already said that group II self-splicing introns are distributed as follows:

    a) In bacterial genomes (where they are anyway rather rare)

    b) Organelles in lower eukaryotes and plants

    They are, instead, absent in eukaryotic nuclear genomes.

    In my #119, an answer to Mung, I have also specified:

    “In the bacterial genome, it seems that they are mainly localized in less important and less conserved genes, and sometimes in intergenic regions. Remember, introns are however rather rare in prokaryotes.

    In organelles, they are more often linked to housekeeping genes, but they are often more or less degenerate, and often they do not have ORFs.”

    Now we are going to deal with the b) situation: group II introns in a very important gene in an organelle (the chloroplast) of a lower eukaryote. And degenerate too, in a very special way!

    If you are already confused, wait for the rest!

    So, let’s introduce our protagonist:

    Chlamydomonas reinhardtii

    What is it? It’s a single celled green alga, a “simple” form of plant. Here is its Wikipedia page:

    https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii

    For various reasons, it is also a model organism, like C. elegans, Drosophila, and others. IOWs, there is a lot of information and research about it.

    Now, let’s se the gene:

    psaA

    The protein is 751 AAs long, and its complete name is:

    Photosystem I P700 chlorophyll a apoprotein A1 (P12154).

    Its function, according to Uniprot:

    “PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX.”

    IOWs, it is an important part of Photosystem I, a photosyntetic system.

    Quite an important molecule, therefore!

    The protein is, of course, located in the chloroplast, the photosyntetic organelle of plants.

    It can be useful to remember that chloroplasts are thought to be derived from cyanobacteria through an endosymbiotic event.

    Indeed, the psaA protein from the chloroplast of Chlamydomonas_reinhardtii is extremely similar to the same protein in cyanobacteria (best hit: 1337 bits, 1.78 baa, 86% identitis, 91% positives).

    Let’s go to the gene.

    It can be useful to remember that only a few of the chloroplast proteins are encoded by the chloroplast genome. It is supposed that many of the ancestral cyanobacterial genes of the plastid were transferred to the nucleus or were lost. Only approximately 100 proteins are still encoded in the chloroplast genome, while most of the few thousand proteins of the plastid proteome are encoded in the nucleus and then imported to the chloroplast.

    Well, in Chlamidomonas reinhardtii the psaA gene is one of those encoded by the chloroplast genome, but it has a very strange peculiarity: it is split into three separate exons that are dispersed on the chloroplast genome.

    That’s some degeneration!

    The exons are transcribed separately.

    And the introns? There should be two of them, for three exons.

    Well, they are fragmented, too. The three exons, indeed, are flanked by sequences which are parts of the original group II introns.

    So, each exon is transcribed separately from the others, and each transcript includes the flanking “intronic” parts.

    This is strange enough. But even stranger is what happens after that, IOWs the “maturation” of those transcripts to form the final mRNA.

    We will see that in next post. 🙂

  177. 177
    Dionisio says:

    @175 follow up

    For those who aren’t familiar with the question asked @175, this short video may help to understand its contextual meaning:

    https://www.youtube.com/embed/R6_eWWfNB54

  178. 178
    gpuccio says:

    Dionisio:

    Very interesting!

    It’s always important to quote our sources, in science. 🙂

  179. 179
    Dionisio says:

    @176:

    a) In bacterial genomes (where they are anyway rater rare)
    rather?

    They are, instead, absent in euakryotic nuclear genomes.
    eukaryotic?

    Chlamydomonas reinhardtii?
    Huh?
    Who in the world comes up with these names? 🙂

    For various reasons, it is also a model organism, like C. elegans, Drosophila, and others. IOWs, there are is lot of information and research about it.
    there are is ?

  180. 180
    Dionisio says:

    @178:

    “It’s always important to quote our sources, in science.”

    Yes, that’s exactly how your politely dissenting interlocutors usually do here, don’t they? 🙂

  181. 181
    Mung says:

    gpuccio:

    So, I am really grateful to Arthur Hunt for stimulating it and taking part.

    I second that.

  182. 182
    gpuccio says:

    Arthur Hunt (and all interested):

    Just a brief update, to answer at least some questions.

    Organellar group II introns, as said, are defective. Therefore, they require for splicing the intervention of proteins, nuclear encoded proteins.

    IOWs, group II introns in organelles cannot any more effect their own splicing, and so they are spliced by one or more nuclear proteins.

    However, if only a single RNA molecule in the transcript is spliced, this is called cis-splicing. It is similar, in a sense, to what the spliceosome does with spliceosomal introns in the nuclear genome, but the protein components are absolutely different.

    But there is another form of splicing of group II introns in organelles, and that’s exactly what we observe in our psaA gene in Chlamydomonas. A few examples of this mechanism are known, but the Chlamydomonas psaA is the only one that has been studied in some detail.

    The fact is that, as we have seen, psaA is not only degenerate, but also fragmented, and dispersed in the chloroplast genome. Not only the three exons, but also the two group II introns are fragmented, and parts of them flank each of the three exons.

    As each exon is transcribed separately, with its flanking parts, we have at that point three different transcripts. So, the nuclear proteins that accomplish the maturation of this fragmented pre-mRNA have to do two different things:

    a) Reconstruct an appropriate pre-mRNA from the three transcripts, so that the final result contains the three exons and the two reconstructed introns

    b) Splice the two introns, generating the mature mRNA

    Rather amazing, isn’t it?

    This form of splicing is called trans- splicing, because it acts on different transcripts joining them. As said, our psaA is the best known, but not the only, example.

    Add to that that another gene takes part in the reconstruction: it is called tscA, and it is a gene in the chloroplast genome that does not encode for a protein, but for a short RNA sequence.

    The tscA transcript is essential to complete the reconstruction of the introns, but to do that it must be processed by the nuclear proteins that assist in the splicing.

    In a sense, tscA is the last piece of the puzzle, which must be inserted to reconstruct the introns before their splicing.

    I will stop here for the moment. I hope you get the picture.

    However, there are still a few aspects of the matter that are even more amazing. To next post. 🙂

  183. 183
    Dionisio says:

    @176:

    […] each exon is transcribed separately from the others, and each transcript includes the flanking “intronic” parts.

    This is strange enough. But even stranger is what happens after that, IOWs the “maturation” of those transcripts to form the final mRNA.

    Wow! now I see why you said that it is weird and interesting.

  184. 184
    Dionisio says:

    @182:

    the nuclear proteins that accomplish the maturation of this fragmented pre-mRNA have to do two different things:

    a) Reconstruct an appropriate pre-mRNA from the three transcripts, so that the final result contains the three exons and the two reconstructed introns

    b) Splice the two introns, generating the mature mRNA

    Rather amazing, isn’t it?

    Amazing is an understatement.

    The step a) must guarantee the correct sequence of connected transcripts, right?

    How’s that achieved?

    Do the separate transcripts have something that identifies each of them as either ‘first’, ‘second’, or ‘third’?

    Perhaps it’s obvious, but I don’t see it.

    I will stop here for the moment. I hope you get the picture.

    Yeah, right. 🙂

    If this were a ballet choreography, dancers would struggle trying to remember what to do at every moment in synch with the music. What a chaos.
    But the cells figured out how to do it right.

  185. 185
    Dionisio says:

    @182:

    […] there are still a few aspects of the matter that are even more amazing. To next post.

    Wow! That’s quite weird indeed.

  186. 186
    Dionisio says:

    @182:

    Can’t wait to watch the next episode. The plot keeps thickening. 🙂

  187. 187
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  188. 188
    Dionisio says:

    @146:

    “The Spliceosome: The Ultimate RNA Chaperone and Sculptor”

    (paywall)

    Check this out:

    http://europepmc.org/abstract/MED/26682498

    http://europepmc.org/articles/.....pdf=render

  189. 189
    ET says:

    Arthur Hunt:

    This may be consistent with the implication seen in the preceding that the information content, as it were, of the RNA component of the spliceosome is not very great, and probably not enough to support, from a purely informational perspective, the hypothesis that the spliceosome is a product of design.

    That may or may not be true but it still remains that there isn’t any non-telic account for those RNAs’ existence.

    As Dr. Behe once said:

    “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

    So it is for the spliceosome

  190. 190
    Dionisio says:

    Some interesting papers listed @10, @12, @31

    Here’s one:

    Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990488/pdf/nihms806199.pdf

  191. 191
    Dionisio says:

    Some interesting papers listed @10, @12, @31

    Here’s one:

    The nuts and bolts of the endogenous spliceosome
    http://onlinelibrary.wiley.com......1377/epdf

  192. 192
    Dionisio says:

    Juicy!

    Structural biology of the spliceosome

    Structural studies of the endogenous spliceosome – The supraspliceosome

    Lots of yummy cookies in this jar:

    http://www.sciencedirect.com/s.....125/supp/C

  193. 193
    gpuccio says:

    ET:

    As I have said, the RNA component of the spliceosome is amazing in its own right. Especially if we consider that the original functional RNA molecule, the group II self-splicing intron, is fragmented, transformed, coupled to many proteins, reconstructed.

    But, of course, in terms of mere sequence content in the RNA sequence, the functional information is big but not huge. Probably in the order of a few hundreds of bits.

    That could probably be enough to argue for design, but I prefer better margins, and with the protein component I think we have a safer case.

    You may wonder why I stick to the information content of individual molecules, especially proteins. Of course there is a lot of meta-information beyond that, and I would like very much to argue for it, too: the interactions, the irreducible complexity, the regulations, and so on.

    But I stick to protein sequences for two simple reasons: I have a definite way to approximately measure functional information in them, at least in specific cases, and the functional information I find at that level is so abundant that it already allows to make a mind-blogging argument for design.

  194. 194
    DATCG says:

    #171 Gpuccio,

    Agreed, as am I glad for Arthur Hunt’s appearance. The more the merrier.

    My concern is to highlight reference papers Arthur himself approves and uses as guidance. I’ve reviewed briefly(read in part) and read in whole some of the papers offered by others here. Along with my own search on evolutionary scenario for the Spliceosome.

    And while I enjoy any insights given, what good does it do us all if left to our own interpretations? Or, maybe not seeing a paper he would recommend for reading?

    I like details. Without the details, to many assumptions are left standing.

    I desire to read what Arthur thinks is important. What are the relevant document(s) in regards to evolutionary history of the Splieocome?

    I want to know I am reading the same information. So a paper or 2 he recommends is important I think to clarify specifics on such a subject of evolution as there are several papers on the Spliceosome history.

    And yes, look forward to more by Arthur and your discussions 🙂

    Glad to see this develop. I know you put a lot of time into this. As well as Arthur having a busy schedule. So do I, thus a need for specific papers 🙂

    Thanks Gpuccio again and to Arthur for responding.

  195. 195
    DATCG says:

    #111 Mung, Gpuccio 118,119 nice…

    Here’s another paper I reviewed a few days ago. Do not think it’s posted. Published 2010 from BMC…

    Evolution of spliceosomal introns following endosymbiotic gene transfer

    Endosymbiotic Theory… Lynn Margulis pops up:
    Or, SymbioGenesis

  196. 196
    gpuccio says:

    Dionisio:

    Wow! You find a real treasure trove! 🙂

  197. 197
    gpuccio says:

    DATCG at #195:

    Very interesting paper indeed.

    And look at what Dionisio found at #192! 🙂

    All this new information will certainly find some important role in the following discussion.

  198. 198
    gpuccio says:

    Arthur Hunt (and all interested):

    First of all, I want to give some reference about the psaA topic. One of the best and most recent papers is the following:

    A Ribonucleoprotein Supercomplex Involved in trans-Splicing of Organelle Group II Introns

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087748/pdf/zbc23330.pdf

    Open access.

    A few important considerations.

    a) All this issue of organelle splicing and especially trans-splicing is very complex, and many things are still not understood. For trans-splicing, the best model is still psaA. I will state just from the beginning that IMO we still know too little to draw appropriate conclusions. However, I will try just the same to outline the problems, and some proposed “explanations”.

    b) As you can see in the paper I referenced, there is a small group of examples of trans-splicing in chloroplasts (see Table 1), and another group of cases in mitochondrial genes (Table 2). For the moment, I will focus on psaA in chlamydiomonas. But I will make a first important general comment here: this small group of genes seems to show that the cases of trans-splicing are very different one from the other: different genes, different fragmentation, probably different proteins involved. With some similarities, as we will see.

    c) Even if we know a limited number of cases, and most of them only approximately, trans-splicing could be more frequent than presently understood. However, it seems to involve, practically always, important genes, so its role cannot be underemphasized.

    OK, now let’s deal with psaA, and add some important information about it. In next post.

  199. 199
    Dionisio says:

    gpuccio,

    The more we know, more is ahead for us to learn.

    This fascinating topic that you’ve brought up for discussion, starting with an excellent OP that’s followed by a very comprehensive series of insightful comments (mostly in response to professor Arthur Hunt’s inputs), has motivated me to search for additional information that could shed more light on what is known about this amazing biological machinery and its functioning.

    But I have to admit that the available information is becoming so overwhelming by its increasing volume, that sometimes I lose track of the papers. This happens with other biological topics too.

    The Big Data problem they have been talking about for the last several years seems to get worse with the avalanche of research discoveries made in wet and dry labs out there.

    The free Zotero tool may help to alleviate the problem, but discipline is still required to avoid skipping important papers after having been located. Zotero also helps to prevent repetitions. My lack of constant discipline has mace me lose track of interesting papers I had located before. It’s frustrating to realize that my laziness has led me to squander time I had spent searching for information.

    It’s encouraging to see that sometimes you may use some of the papers that have been found. That motivates me to try better next time.

  200. 200
    gpuccio says:

    Arthur Hunt (and all interested):

    The first question is: how complex is the trans-splicing of psaA in Chlamydiomonas?

    Of course, the description I have already given of the process seems to imply great complexity. But what is, in detail, the role of the protein component?

    Unfortunately, even for this deeply studied case, we know probably too little. But something we know.

    The paper I have referenced here, which is of 2016, makes a good summary of what is known, and adds a lot of original information.

    Let’s start with this very good summary of the main premises, which I have in some way already provided:

    In the green alga Chlamydomonas reinhardtii, exceptional examples of split group II introns were described as part of the chloroplast psaA gene that encodes an apoprotein of photosystem I. The psaA gene is split into three dispersed exons, which are flanked by truncated group II intron sequences (14). Whereas the second intron (psaA-i2) is bipartite, the first intron (psaA-i1) is tripartite, and the missing group II intron secondary structure is delivered in trans by the chloroplast-encoded tscA RNA (15). After separate transcription, two group II introns are built up by base pairing, followed by two trans-splicing reactions and, ultimately, formation of the mature psaA mRNA. Splicing of such variant group II introns relies on nucleus-encoded splicing factors to compensate for lack of functional motifs and to retain splicing activity (11, 16). However, it is still unknown and under scientific debate whether these splicing factors function in a spliceosomal-like yet intron-specific manner.

    I will anticipate here that much of the interest in these trans-splicing complexes is that they are thought to be some model for the origine of the spliceosome. In that sense, they are certainly related to our main discussion.

    But how complex is the trans-splicing machine for psaA?

    In previous works, at least 14 proteins were thought to be implied, but only 7 of them have really been identified.

    For C. reinhardtii, seven splicing factors, specific for group II introns, have been described at the molecular level (17,–23). Whereas splicing factor Raa1 (RNA maturation of psaA RNA) is involved in splicing of both reactions, Raa3, Raa4, Raa8, and Rat2 (RNA maturation of psaA tscA RNA) are psaA-i1-specific. Raa2 and Raa7 act specifically on the splicing of psaA-i2.

    We will go back to these proteins later.

    The role of many of these proteins has been assessed because specific mutants showed impairment of photosynthesis.

    It was also supposed that those proteins acted in the form of some high molecular weight complex. However, the referenced paper has for the first time given evidence of that.

    The results presented here define two core-splicing complexes, subcomplexes I and II. We further demonstrate that there is an interaction network of at least 11 and 7 interaction partners in subcomplex I and II, respectively. Several of the uncharacterized proteins are most probably further not yet identified trans-splicing factors.

    As an image is better that a thousand words, let’s look at Fig. 1, which gives in B and D a gross scheme of the two subcomplexes, and in A and C a list of the core components of each of them. Raa1 is a big protein which seems to have an important role in both subcomplexes.

    The paper also confirms the important of the “missing piece”, the tscA gene, in completing the structure of intron 1, and the intricate role of the proteins in the subcomplexes to help the maturation of this small RNA molecule.

    But what do we know of the 7 proteins that have been so far characterized?

    If you look again at Figure 1, the lists in A and C, you can find some important information in the column “description”. For many of them, no functional annotation is available (IOWs, no known domains have been identified in the sequences). A couple of them show some known domain homology (for example, Raa2 has a pseudouridine synthase domain, for some reason that is not shown in Fig. 1, but you can find the information in Fig. 4). However, the most common domain found in them is the OPR sequence, an Octatricopeptide repeat sequence probably implied in RNA binding. Pentatricopeptide repeat sequences are also implied in other cases of trans-splicing.

    The general idea is: these proteins are, at least some of them, rather isolated proteins. For example, the very big Raa1 protein (2103 AAs), if blasted, shows only 4 low homology hits (107 -352 bits), all with green algae organisms.

    IOWs, these are not widely conserved proteins. Not at all. As far as we know, they are rather organism specific proteins, with some low homology to a few existing domains.

    A lot of further details can be found in the paper, but I will not deal with them here.

    So, as the result of all this information, I would like to highlight a few points:

    a) The complexity of the system is apparently very high, and nobody seems to deny that, even if we still miss a lot of information to really understand it as a whole.

    b) One amazing aspect of this system is how specific it seems to be. Indeed, as far as we know, it is specific not only for the organism Chlamidomonas reinhardtii, but also for the psaA gene. But there is more: it is specific for each of the two introns in that gene: indeed, many proteins are involved only in the splicing of one of the two introns.

    c) Finally, this amazing system seems to be made mainly of specific proteins that we find practically only in this organism.

    I hope you are as amazed as I am.

    There is a final important point to illustrate, and I will do that in next post.

  201. 201
    gpuccio says:

    Arthur Hunt (and all interested):

    Another aspect about psaA is related to the following paper:

    On the Complexity of Chloroplast RNA Metabolism: psaA Trans-splicing Can be Bypassed in Chlamydomonas

    https://academic.oup.com/mbe/article/31/10/2697/1013909

    I will try to make it simple.

    In the introduction, this paper gives us an important piece of information:

    This type of trans-splicing occurs in the plastids and mitochondria of many organisms and in a variety of different genes (Glanz and Kuck 2009). For example, psaA is trans-spliced in Chlamydomonas but is an intron-less gene in higher plant plastids, and conversely rps12 is trans-spliced in higher plants but not in Chlamydomonas.

    OK. Let’s remember that.

    Then comes some information that we already know, but it can be useful to refresh it:

    Most of these genes are required specifically for splicing of only one of the two split introns. At least seven genes are essential for trans-splicing of the first intron, some of which are necessary for processing of tscA from a polycistronic precursor (Hahn et al. 1998; Rivier 2000; Balczun et al. 2005; Glanz et al. 2012). Five loci are required for trans-splicing of the second intron (Perron et al. 1999), and two are involved in splicing of both the introns (Merendino et al. 2006).

    Then the paper briefly discusses two possible theories to “explain” the complexity of the trans-splicing system we are discussing (psaA and other similar cases).

    As I have already pointed out, nobody here is doubting that complexity. The system appears to be complex, everyone is rather certain of that.

    But how can we explain that complexity? What is the reason for it?

    I would like to emphasize that the main question, in this discussion in the paper, is not so much “how”, but rather “why”. Why did such a complex system originate? Why is it necessary?

    Of course, they also say something about the “how”, as we will see later.

    This discussion is interesting, because of course everyone of us is probably wondering, at this point: why such a complex system? For one specific task?

    And of course, that kind of discussion, at least in a very general sense, can also be used as a starting guide to debate the spliceosome itself (I will try later to point at the important differences, however).

    So, the authors of the paper give a clear and simple summary of two possible theories about the “why”. I will try to simplify them even further here, but if you want you can read their words directly in the paper, in the two paragraphs that start with:

    “There may be multiple reasons for the remarkable complexity of chloroplast RNA metabolism.”

    Essentially, the two theories are:

    a) The complexity is needed for adaptational or regulatory reasons. We can call this theory the “regulatory” theory. The complexity offers tools to change the working of the system in response to different situations.

    b) The complexity arises simply to compensate for random errors in the genome, in particular the degradation of the original DNA (fragmentation, transformation, loss of function). The authors call this the “spoiled kid hypothesis”, where the spoiled kid is the degenerate DNA of the gene, and the mutations in the nuclear genome which compensate for that degeneracy are called an “evolutionary ratchet”. IOWs, in this theory the complexity that arises to compensate for the degeneracy has one purpose only: to compensate for the degeneracy.

    Theory a) is clear enough. It is usually the theory applied to many complex systems, including the spliceosome, whose many regulatory functions have been well demonstrated. One form of the theory, however, assumes that the spliceosome originated as a ratchet, and then evolved new functions. But of course it is possible that both the compensating function and the regulatory function were developed at the same time.

    In theory b), instead, there is no regulatory function. The system is only a ratchet. It serves nothing else.

    (By the way, I am not responsible for the “ratchet” analogy, it is in the paper, and not only in this one)

    Is everything clear?

    Let’s stop just a moment. To next post.

  202. 202
    Dionisio says:

    @198:

    The plot thickens…

    This discussion is getting better with every comment posted.

    And some of us here are learning much from it.

  203. 203
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  204. 204
    ET says:

    (sarcasm alert with respect to the spliceosome)-

    But it’s all material processes using physical material. There isn’t anything magical going on, just plain ole physics and chemistry.

  205. 205
    ET says:

    (sarcasm alert with respect to the spliceosome)-

    But it’s all material processes using physical material. There isn’t anything magical going on, just plain ole physics and chemistry.

  206. 206
    Dionisio says:

    @200 & @201:

    As usual, very thorough attention to details explained with much pedagogy.

    This discussion could be a valuable chapter if a biology textbook for post docs.

    The complexity of the described issues is so visible that one gets dizzy trying to follow the whole explanation for the first time. Several rereads might be required for the penny to drop.

    It seems like gpuccio has rolled up his sleeves and gotten to work hard on this.

    Many of his readers (myself included) are benefiting from his effort.

    Thanks.

  207. 207
    Dionisio says:

    ET @204 & 205:

    Of course, that’s just pure physics.

    Is there another option?

    🙂

  208. 208
    Dionisio says:

    @200:

    So, as the result of all this information, I would like to highlight a few points:

    a) The complexity of the system is apparently very high, and nobody seems to deny that, even if we still miss a lot of information to really understand it as a whole.

    b) One amazing aspect of this system is how specific it seems to be. Indeed, as far as we know, it is specific not only for the organism Chlamidomonas reinhardtii, but also for the psaA gene. But there is more: it is specific for each of the two introns in that gene: indeed, many proteins are involved only in the splicing of one of the two introns.

    c) Finally, this amazing system seems to be made mainly of specific proteins that we find practically only in this organism.

    I hope you are as amazed as I am.

    That functional complexity is just an illusion.
    We just don’t understand evolution.
    🙂

  209. 209

    Dionisio @ 203: You set the bar very high, my friend.

  210. 210
    gpuccio says:

    Arthur Hunt (and all interested):

    Now, before going to the experimental part of the paper reference at #201, let’s say still something about theory b): the ratchet theory for psaA trans-splicing.

    As we have seen, this theory assumes that mutations at the level of nuclear genome (what they call “suppressor mutations) “compensate” for the alteration in the chloroplast gene (the “spoiled kid”).

    So, in this case, the compensating “suppressor mutations” would be those which generate the many proteins in the nuclear genome which effect the trans-splicing, while the “spoiled kid” is the degenerate and fragmented psaA gene in the chloroplast genome.

    But there is a problem. If the degeneracy of the gene (for example, being fragmented into three separated exons/intron-parts, plus a small RNA coding gene) is such that it prevents completely an important function (photosynthesis), IOWs if the spoiled kid is really and severely spoiled, the organism should be subject to strong negative selection, and there is no evolutionary time to “wait” for the compensating mutations to provide the complex solution.

    In the words of the authors:

    When a plastid mutation severely
    affects RNA metabolism, the theory of constructive neutral evolution (CNE) proposes that suppression may involve a preexisting nucleus-encoded factor which restores adequate gene expression, and allows a step towards “irremediable complexity”

    What does this mean?

    It means that they are proposing a new sub-theory, called CNE. That theory is not really new. We find a good summary of it, more in general, in the abstract of a paper of 2011:

    How a neutral evolutionary ratchet can build cellular complexity

    http://onlinelibrary.wiley.com.....9/abstract

    Complex cellular machines and processes are commonly believed to be products of selection, and it is typically understood to be the job of evolutionary biologists to show how selective advantage can account for each step in their origin and subsequent growth in complexity. Here, we describe how complex machines might instead evolve in the absence of positive selection through a process of “presuppression,” first termed constructive neutral evolution (CNE) more than a decade ago. If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, CNE is a unidirectional evolutionary ratchet leading to complexity, if complexity is equated with the number of components or steps necessary to carry out a cellular process. CNE can explain “functions” that seem to make little sense in terms of cellular economy, like RNA editing or splicing, but it may also contribute to the complexity of machines with clear benefit to the cell, like the ribosome, and to organismal complexity overall. We suggest that CNE-based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.

    To say it simply, in cases like the psaA degeneracy, where survival does not seem likely without some remedy, the remedy must be already there, at the time when the kid becomes spoiled. So, the idea is that neutral evolution provides the new information in advance, so that it is ready to act when the situation required it. That’s probably why they call that neutral evolution “constructive”! 🙂

    So, going back to our psaA, when the chloroplast gene becomes fragmented and degenerate (which, frankly, does not seem an event which should require a lot of time), the 14+ proteins that will effect its trans-splicing are already there, kindly arranged by “constructive” neutral evolution.

    I know what you are thinking… 🙂

    In the words of the authors of the paper referenced at #201:

    A pool of potential preexisting suppressors for chloroplast mutations could be constituted by proteins that have functions in RNAmetabolism and can be co-opted for the new task.

    Did they say “co-opted?”. Yes, they did!

    OK, no problem in that, I suppose. After all, it is a “pool” of potential compensating proteins. Maybe a lot of them, who knows?

    And after all, they only have to recognize the trascripts from four different genomic sites, reconstruct a complex RNA structure from them, and in some way correctly effect the splicing. Where’s the problem?

    And for those who are tired of Behe’s old concept of “irreducible complexity”, we have here a brilliant, new and certainly more fashionable concept:

    Irremediable complexity!

    IOWs, a complexity which should not be necessary, but becomes “irremediable” because of serious, unavoidable events (spoiled kids, which, as each parent knows, can cause a lot of trouble).

    The CNE theory explains how this type of transgenomic suppression mechanism could be part of a “drive toward irremediable complexity”.

    OK, no comment for the moment. We still have to look at the experimental part of the paper:

    On the Complexity of Chloroplast RNA Metabolism: psaA Trans-splicing Can be Bypassed in Chlamydomonas

    In next post.

  211. 211
    gpuccio says:

    Arthur Hunt (and all interested):

    The experimental part of the paper is simple enough and clear enough, and it aims essentially to demonstrate that, at least in the case of psaA, theory b), the ratchet theory, is probably true.

    And I must say that their argument is of some interest.

    Our model organism, Chlamydomonas, is very good for getting mutants.

    So, they took three different mutants, one for each of the three proteins raa1, raa2 and raa3. As expected, each of these mutant was defective at photosynthesis, because of the defective psaA trans-splicing.

    Of course, according to what we have already said, in the raa1 mutant the splcing of both introns was compromised, while in raa2 mutant only intron 2 was involved, and in the raa3 mtant only intron 1.

    Then they inserted into the chloroplast genome of the three mutants an intron-less version of the psaA gene.

    The simple result is that photsynthesis was rescued in all three mutants.

    But there is more: they compared the behaviour of the “rescued” mutants with the Wild Type, and they could not observe any difference.

    The comparison was made not only in standard conditions, but also in some stress conditions: iron deprivation, competitive growth, high temperature, low oxygen. In all these settings, growth and behaviour of the rescued strains and of the WT were not different.

    They conclude, therefore that theory b) must be true: the trans-splicing system, however complex it is, has apparently only the purpose of trans-splicing the degenerate psaA gene. If we provide the organism with an intron-less gene, it is no more necessary.

    Now, this is very interesting, and I don’t want in any way to underemphasize these results, which I have tried to report as simply and clearly as possible.

    I will add, however, a couple of cautionary notes:

    1) Test in the lab of the relative fitness of different populations should be considered with some caution. Of course, in the wild and in long evolutionary times a lot of differences could be revealed which cannot be apparent in a short test under controlled conditions. This is true for all these kinds of tests. IOWs, it is still possible that the trans-splicing system has regulatory functions which could not be observed in the tests made during the experiment.

    2) Let’s remember that we still have a very limited understanding of this system. I would reasonably wait for further information about the proteins involved, the structure, the molecular function, and above all the similarities and differences between different trans-splicing systems in different organisms, before drawing final conclusions about this complex issue.

    That said, I frankly admit that these results, taken as they are, are in favour of theory b) for this specific system.

    Which makes the system itself, as we understand it at present, a really weird object from all points of view.

    Many more things could be said about this aspect, but I will stop here for the moment, and leave some space to a possible discussion.

    In next post, I will rather outline the (few) similarities between this trans-splicing system and our spliceosome, and the (many) differences.

    And maybe add some interesting recent information about the spliceosome itself.

  212. 212
    gpuccio says:

    Arthur Hunt (and all interested):

    Just an add-on to the previous post.

    For those who liked the concept of irremediable complexity, there is more.

    From the Introduction in the same paper:

    The whims of the plastid—the “spoiled kid”—are thus compensated by a liberal nuclear genome. In the long term, this might allow the occurrence and persistence of apparently futile steps of gene
    expression, such as RNA editing or trans-splicing.

    (emphasis mine)

    And from the Discussion:

    Posttranscriptional RNA editing provides another striking example of complex but apparently futile RNA metabolism.

    (emphasis mine)

    As you can see (I repeat myself) nobody here is denying the complexity. But this fascinating type of complexity is now labeled as both irremediable complexity and futile complexity.

    Behe will probably be envious! 🙂

  213. 213
    ET says:

    CNE? That one cracks me up. Molecules just diffuse throughout the cell and if they happen to meet another and join then that’s just wonderful if it makes something useful. It isn’t as if those molecules had something to do on their own or some other molecule to link up with. They just happened to be there and meet up with a mate.

    Larry Moran is a fan of constructive neutral theory. To me it’s just another just-so story.

    Tornado in a junkyard, anyone?

  214. 214
    gpuccio says:

    ET:

    Shall I say it?

    OK:

    CNE is rubbish! 🙂

  215. 215
    Dionisio says:

    “CNE is rubbish!”

    That’s so rude. 🙂

  216. 216
    Dionisio says:

    TWSYF @209:

    gpuccio is who has set the bar too high for his politely dissenting interlocutors.

    I’m just trying to make it easier for the rest of us to keep track of the interesting discussion GP is having with a distinguished professor.

    BTW, gpuccio posted three additional comments that render the info @203 incomplete.

    I’m awaiting the breakthrough revelation that professor Arthur Hunt promised.

  217. 217
    Mung says:

    gpuccio:

    Is everything clear?

    Clear as chloroplaster!

  218. 218
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  219. 219
    Dionisio says:

    TWSYF @209:

    @216 follow-up

    You may want to read the comment @206.

  220. 220
    Dionisio says:

    So CNE includes some kind of co-option too?
    Hey, why not?
    At least it sounds important.
    🙂

  221. 221
    Dionisio says:

    Irremediable complexity?

    It sounds important, doesn’t it?

    🙂

    How about complex functionally specified informational complexity?

  222. 222
    DATCG says:

    Chuckles 🙂 OK, that was funny. Thanks for the continued reviews Gpuccio and digging on your part!

    Irremediable Complexity was briefly addressed by Michael Behe in 2011…

    Brief Review of Irremediable Complexity and CNE by Behe

    Note: its from 2011. I’m sure more experimental work has been done since to “support the feasibility of the model.”

    The authors think the evolution of such a complex is well beyond the powers of positive natural selection: “Even Darwin might be reluctant to advance a claim that eukaryotic spliceosomal introns remove themselves more efficiently or accurately from mRNAs than did their self-splicing group II antecedents, or that they achieved this by ‘numerous, successive, slight modifications’ each driven by selection to this end.”1

    Well, I can certainly agree with them about the unlikelihood of Darwinian processes putting together something as complex as the spliceosome. However, leaving aside the few RNAs involved in the splicesome, I think their hypothesis of CNE as the cause for the interaction of hundreds of proteins — or even a handful — is quite implausible. (An essay skeptical of large claims for CNE, written from a Darwinian-selectionist viewpoint, has appeared recently-3 along with a response from the authors-4).

    see references 3 and 4 above at the linked article

    The authors’ rationale for how a protein drifts into becoming part of a larger complex is illustrated by Figure 1 of their recent paper (similar to the single figure in their Science essay). A hypothetical “Protein A” is imagined to be working just fine on its own, when hypothetical “Protein B” serendipitously mutates to bind to it. This interaction, postulate the authors, is neutral, neither helping nor harming the ability of Protein A to do its job. Over the generations Protein A eventually suffers a mutation which would have decreased or eliminated its activity. However, because of the fact that Protein B is bound to it, the mutation does not harm the activity of Protein A.

    This is still envisioned to be a neutral interaction by the authors, and organisms containing the Protein A-Protein B complex drift to fixation in the population. Then other mutations come along, co-adapting the structures of Protein A and Protein B to each other. At this point the AB complex is necessary for the activity of Protein A.

    Repeat this process several hundred more times with other proteins, and you’ve(voila) built up a protein aggregate with complexity of the order of the spliceosome.

    (voila) emphasis mine

    Or at least so the story goes. Is it plausible? As as neo-Darinian tale? Maybe. But with more details I hope.

    I’ll leave the rest of the review for readers to pursue.

  223. 223
    gpuccio says:

    DATCG:

    Thank you for the link! 🙂

    I did not know that Behe had already touched tose points, and so brilliantly, otherwise I would certainly have quoted him!

    Luckily, you have provided the reference.

    I am really happy to be, once again, in perfect accord with what Behe says. 🙂

  224. 224
    DATCG says:

    GPuccio, the article by Behe. You might appreciate the lead line. 😉

    An intriguing “hypothesis” paper entitled “How a neutral evolutionary ratchet can build cellular complexity”1, where the authors speculate about a possible solution to a possible problem, recently appeared in the journal IUBMB Life. It is an expanded version of a short essay called “Irremediable Complexity?”2 published last year in Science.

  225. 225
    gpuccio says:

    DATCG:

    Yes, the interesting part is that, as I have tried to emphasize, nobody denies the complexity.

    And nobody denies that the complexity works, that it is indeed functional.

    So, according to these people, we have:

    Irremediable futile functional complexity

    The concept of the century! 🙂

  226. 226
    Dionisio says:

    DATCG and gpuccio,

    Let’s not rush to conclusions before reading the breakthrough revelation that professor Arthur Hunt promised.

    Let’s be patient.

    🙂

  227. 227
    Dionisio says:

    No matter how persuasive the CNE might be, I still prefer Cinderella’s fairytale, because it makes more sense from a rational perspective: a pumpkin was converted into an elegant carriage, mice became beautiful horses, a grasshopper was hired as the cochero.
    🙂

    Is CNE in the “third way” arsenal?

  228. 228
    Dionisio says:

    Irremediable complexity ?

    See the 112 papers citing the featured paper:

    https://www.researchgate.net/publication/47755596_Irremediable_Complexity

  229. 229
    Dionisio says:

    See the papers referenced in this paper:

    … However, the very different mechanism of the RNA editing systems in existence, and their very limited distribution within specific groups of organisms indicate that they are more likely derived traits that evolved later in evolution [65,66]. The sheer complexity of the kRNA editing process, with no obvious selective advantage, led to the proposal that insertion/deletion editing arose via a constructive neutral evolution (CNE) pathway [67]. Indeed, RNA editing in trypanosomes is always mentioned in support of CNE as an example of how seemingly non-advantageous, complex processes can arise [68,69]. …

    PLOS NEGLECT TROP D
    Laura E. Kirby, Donna Koslowsky
    DOI: 10.1371/journal.pntd.0005989

    https://www.researchgate.net/publication/320295574_Mitochondrial_dual-coding_genes_in_Trypanosome_brucei

  230. 230
    DATCG says:

    Gpuccio,

    Pardon the pun, but an Intronic Interlude while awaiting Arthur’s next comment?

    What of Introns? Once deemed as “junk” DNA. I’d looked at them in past specifically for potential signs of function and design. Documentation on new functions of Introns is growing. Another angle, but still coordinated with careful splicing and targeting by the Spliceosome.

    Not to distract from this post.

    Looking forward to Arthur’s follow up. But maybe in future, if not you, someone here @UD could keep track on Intron’s functions and possible dual role relationships? Maybe that’s stretching it a bit 😉 But something’s missing.

    We’re getting the splice events for mRNA, but also producing ciRNAs or other noncoded RNAs.

    From alternative splicing to Circular Long Noncoded RNAs – ciRNAs. Some reside in the nucleus, others in cytoplasm.

    Is there added constraint on Spliceosome as a result of Intron functionality? As in wrong splice, wrong dice. How much room for a mistake is there?

    Circular RNAs are more stable than linear. I suspect more will be found.

    For anyone who wants something to read, General overview of current progress…

    Introns: The Functional Benefits of Introns in Genomes(from 2015)

    In the present review, we first introduce some studies showing what molecular characteristics of introns cannot be explained by a simple random mutational process that real junk DNAs may have undergone. Subsequently, we summarize the functional characteristics of introns that have been studied providing clues about the adaptive significance of introns in genomes.

    more…

    Taken together, first introns among all introns within genes have special functional characteristics, indicating that the existence of introns within genes is highly unlikely to be the product of a random process.

    Agreed… Addressable subspace must be tightly controlled, otherwise it’s all downhill and access is lost. Creating a cascading roll of errors until ending in catastrophic event, or removed by error correction.

  231. 231
    gpuccio says:

    Arthur Hunt (and all interested):

    The interest for group II introns trans-splicing (or even cis-splicing) in organelles is in part connected to the idea that these scenario could be considered as a model of the evolution of the spliceosome.

    That idea is more or less as follows:

    a) Group II introns in bacterial genomes are usually self-splicing. They are relatively autonomous retrotransposon entities, and they use their intrinsic ribozyme activity to self-splice and retro-home.

    However, even in this simplest scenario the intervention of a protein is necessary, but it is the IEP, a protein encoded directly by the intron itself.

    b) When group II introns are found in eukaryotic organelles, however, they are usually degenerate, and lack the ORF for the IEP.

    As a consequence of that, apparently, they need the intervention of other proteins, proteins encoded in the nuclear genome of the eukaryote, to be spliced.

    c) Such splicing can happen both in cis (the proteins act on one transcript) or in trans (the proteins act on different transcripts, that need to be reconstructed. The second scenario (trans-splicing) is necessary when the original gene has been fragmented, and the individual parts are transcribed separately. Of course, trans-splicing is more complex than cis-splicing, and it seems to involve more complex multi-protein structures. psaA, that we have discussed in detail, is the best model for this kind of scenario.

    d) Finally, the eukaryotic nuclear genome lacks group II introns, but is repleted with spliceosomal introns. The splicing of these introns requires a very complex structure, our major spliceosome (except for some rarer froms of introns, which are spliced by the moinor spliceosome).

    e) So, the idea would be that trans-splicing, with its discreetly complex multiprotein structures, could be considered an indication of how the spliceosome itself evolved, especially if we accept that spliceosomal introns evolved from group II introns when they invaded the nuclear genome of eukaryotes.

    Now, I will try to show what are the similarities between the two scenarios (trans-splicing and spliceosomal splicing), and then what are the differences.

    Similarities:

    1) The main common feature is that the intron is spliced by some complex multi-protein structure, and that the proteins are encoded by the nuclear genome.

    2) The second common feature is that the catalytic activity of the splicing is essentially implemented by the RNA component, which retains a similar structure, even if constructed in different ways.

    I would like to specify that this point is more obvious for the self-splicing of group II introns and spliceosomal splicing. I have not really found details on how the catalysis takes place in trans-splicing, but I imagine that the RNA component may have an important role there too.

    OK, that’s all about similarities, IMO. Now let’s go to the:

    Differences:

    1) Specificity vs universality.

    Trans-splicing, as we have seen, is very specific. The multiprotein structure that effects the reconstruction and splicing of psaA seems to act only on that gene. Moreover, as we have seen, different proteins are neede for each of the two introns.

    On the other hand, the spliceosome is highly universal. It is very similar in all eukaryotes, and all spliceosomal introns are spliced by the same spliceosome (even if with the great flexibility allowed by the basic structure).

    2) Difference in function:

    Trans-splicing does two different things: it reconstructs the fragmented gene, even participating in the maturation of its parts, like the tscA RNA; and then it effects the splicing of the two introns.

    The spliceosome does only the splicing, but with all the additional complexity linked to the differences in intron length, sequence and structure, and to alternative splicing and other regulatory processes.

    Moreover, group II introns are deeply different from spliceosomal introns, even if they could be derived from them. Gorup II introns are rather variants of a similar structure, while spliceosomal introns vary a lot in length, splicing sites, added functions, and so on. Spliceosomal introns also lack any catalytic and retrotransposon activity. That’s why the catalytic splicing is “demanded” to the 5 snRNAs in the spliceosome.

    Finally, if we believe to the meaning of the results presented in post #211, the trans-splicing system seems to serve essentially for splicing, and could not have additional regulatory functions. The additional regulatory functions of the spliceosome-spliceosomal introns system, instead, are beyond any doubt.

    3) Difference in conservation:

    Both the trans splicing complex and the spliceosome are essentially eukaryotic structures.

    However, while the psa trans-splicing complex is made of proteins that could well be defined as “taxonomically restricted” to that organism, the proteins which make up the spliceosome are, as we have seen, extremely conserved in all eukaryotes.

    To illustrate this point, I will present here two blasts from two proteins, both of them from Chlamydiosomam reinhardtii:

    a) Raa1 is probably the main structural protein in the trans-splicing process. I have blasted it against all known sequences in the non redundant protein database of NCBI (practically all know proteins). Here is the result:

    Protein Raa1 from Chlamydiosomam reinhardtii (Q5K4K9)

    Length: 2103 AAs

    Blasted against the whole protein database:

    Only 4 hits:

    Volvox carteri f. nagariensis (colonial green alga)

    487 bits 318 identities

    Gonium pectorale (colonial green alga)

    352 bits 272 identities

    Monoraphidium neglectum (single-celled green alga)

    171 bits 175 identities

    Gonium pectorale (colonial green alga)

    152 bits 208 identities

    That’s all. A really taxonomically restricted protein.

    b) Of course, Chlamydiosomam reinhardtii is not only the proud owner of the most studied trans-splicing complex. It also owns a spliceosome, like all eukaryotes.

    So, I have blasted the Prp8 protein, which is the main structural protein in the U5 subunit of the spliceosome, vs the most “distant” eukaryotic group: vertebrates. Here are the results:

    Protein Prp8 from Chlamydiosomam reinhardtii (A8HPL0)

    Length: 2346 AAs

    Blasted against vertebrates:

    First 100 hits:

    Best hit: Patagioenas fasciata monilis (bird)

    4040 bits 1889 identities

    Lowest hit (among the first 100): Clupea harengus (bony fish)

    4013 bits 1878 identities

    A truly universal protein. More than 4000 bits of conservation between green algae and vertebrates. Remember, about 1 billion years.

    And the amazing thing is the consistency of conservation: only 27 bits of difference between the best and worst of the first 100 hits in vertebrates!

    With more than 80% identity, this sequence remains practically the same in all contexts!

    So, these are IMO the main similarities and differences between the two scenarios: trans-splicing and spliceosomal splicing. Everyone can make up his mind about the possible meaning of trans-splicing as a “model” for spliceosome evolution.

    As for me, I would simply say that they are two very different systems with some similarities. Each of them is highly complex, even if the spliceosome is certainly much more complex.

    Moreover, the complexity of the splicesome can be approximately and reliably measured through the high conservation of its protein components for extremely long evolutionary times.

    The complexity of the trans-splicing system, instead, although intuitively obvious, cannot be really assessed, for two important reasons:

    – we know too little of the detailed structure and biochemical function

    – the proteins are taxonomically restricted, and therefore we can infer nothing about their functional information from conservation.

  232. 232
    gpuccio says:

    DATCG:

    Fascinating issues indeed. I fully agree with you.

    I hope we can touch some of them in this discussion, if some time is left! 🙂

  233. 233
    DATCG says:

    #231 Gpuccio nice summary.

    e) So, the idea would be that trans-splicing, with its discreetly complex multiprotein structures, could be considered an indication of how the spliceosome itself evolved, especially if we accept that spliceosomal introns evolved from group II introns when they invaded the nuclear genome of eukaryotes.

    I’m not so sure about the “invasion” story, but willing to listen.

    Wadda ya know, they reference Koonin. Does he ever sleep?
    The Intron Invasion! Published 2010

    Group II introns have not been found in the nuclear genomes of eukaryotes, but their hypothesized descendants, spliceosomal introns and retrotransposons, are highly abundant in eukaryotes, together comprising more than half of the human genome.

    I look forward to Arthur’s rejoinder 🙂

  234. 234
    Mung says:

    gpuccio: I am really happy to be, once again, in perfect accord with what Behe says.

    You should be. You are just a Behe sock-puppet.

  235. 235
    gpuccio says:

    Mung:

    “You are just a Behe sock-puppet.”

    It’s still an honour! 🙂

  236. 236
    ET says:

    Arthur Hunt is very knowledgeable with respect to biology. That said he, like all evolutionists, doesn’t have any idea how blind and mindless processes could have produced the spliceosome. As I eluded to earlier all evolutionists for whatever reason think that if something can be described in physical terms, ie physics and chemistry, then clearly materialistic processes produced it. So they always revert to that- “Look we can observe it happening and it is in accordance with physics and chemistry. Case closed.”

    That is their entire argument.

  237. 237

    Michael Behe is a true hero of our era. Love the guy.

    ET @ 236: Excellent points.

  238. 238
    Dionisio says:

    ET @236:

    Computer software programs operate on pure physical processes -electronic circuits- therefore they must have originated from physical processes. Is that right?

  239. 239
    Dionisio says:

    DATCG @230:

    The authors of the paper you referenced could be uneducated pro-ID Korean folks who don’t understand evolution. 🙂
    Let’s not rely on pro-ID sources to get information from. 🙂

  240. 240
    ET says:

    Dionsio@ 238- Of course computer software programs originated from physical processes cuz we originated from physical processes. See? That was easy-peasy. 😎

    Seriously THAT is the argument. 🙄

  241. 241
    Dionisio says:

    ET @240:

    Exactly. You’ve got it right. 🙂
    Now we’re on the same page on this topic. 🙂

    Poor gpuccio keeps having that weird “functional complexity” illusion and has come up with a convoluted algorithm to quantify it at the protein level. 🙂

    Maybe the breakthrough revelation promised by professor Arthur Hunt will finally persuade our friend to change his mind on the subject? 🙂

    PS. BTW, does anybody have a clue when we are going to see professor A. Hunt’s next comment posted here? Could that still happen this year? 🙂

  242. 242
    gpuccio says:

    Arthur Hunt (and all interested):

    Just to demonstrate that we never know enough.

    A recent paper, signaled by Dionisio at #192, seems to revolutionize, in some measure, what we know of the spliceosome:

    Structural studies of the endogenous spliceosome – The supraspliceosome

    http://www.sciencedirect.com/s.....via%3Dihub

    Paywalled.

    Here is the abstract:

    Pre-mRNA splicing is executed in mammalian cell nuclei within a huge (21 MDa) and highly dynamic molecular machine – the supraspliceosome – that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Detailed structural analysis of this huge and complex structure requires a stepwise approach using hybrid methods. Structural studies of the supraspliceosome by room temperature electron tomography, cryo-electron tomography, and scanning transmission electron microscope mass measurements revealed that it is composed of four native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. It also elucidated the arrangement of the native spliceosomes within the intact supraspliceosome. Native spliceosomes and supraspliceosomes contain all five spliceosomal U snRNPs together with other splicing factors, and are active in splicing. The structure of the native spliceosome, at a resolution of 20 Å, was determined by cryo-electron microscopy, and a unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in silico studies. The supraspliceosome also harbor components for all pre-mRNA processing activities. Thus the supraspliceosome – the endogenous spliceosome – is a stand-alone complete macromolecular machine capable of performing splicing, alternative splicing, and encompass all nuclear pre-mRNA processing activities that the pre-mRNA has to undergo before it can exit from the nucleus to the cytoplasm to encode for protein. Further high-resolution cryo-electron microscopy studies of the endogenous spliceosome are required to decipher the regulation of alternative splicing, and elucidate the network of processing activities within it.

    I will try to sum up the main facts and models detailed in this paper. We should take them with some caution, but they are certainly extremely interesting.

    a) What we know about the gradual assembly of the spliceosome comes from in vitro studies.

    b) The authors of this paper have used new techniques to study the spliceosome in its natural context: in the nucleus of cells.

    c) The results are rather amazing. In vivo, the spliceosome would work in a mega configuration, made of four individual spliceosomes, connected by a pre-mRNA.

    d) The authors call this structure “supraspliceosome”, and each individual spliceosomal unit “native spliceosome”.

    e) The supraspliceosome has a molecular weight of 21 MDa, while each native spliceosome is 4.8 MDa.

    f) Differently from what is known from in vitro assembly, each unit of the supraspliceosome (native spliceosome) contains all the five U ribonucleoproteins at all times.

    g) The supraspliceosome is assembled before the splicing.

    h) Each supraspliceosome includes one complete pre-mRNA, which can be of whatever length or number of introns. Even short pre-mRNAs (like two exons and one intron) are enough to assemble the supraspliceosome.

    i) The supraspliceosome seems to splice 4 introns at a time, and after that the pre-mRNA is thought to undergo a process of rolling.

    The supraspliceosome is a stand-alone macromolecular machine (Fig. 13), composed of four native spliceosomes [29, 30, 37] that are connected by a single pre-mRNA molecule [40], capable of performing splicing of its pre-mRNA [37] – independent of its length or number of introns [6, 31].

    The supraspliceosome is a multiprocessor machine that can simultaneously splice four introns – not necessarily in a consecutive manner. This configuration enables examination, prior to introns excision, if correct splice junctions will be combined, and allows rearrangement of splice junction combinations to select the appropriate ones, thus ensuring the fidelity of splicing and alternative splicing.
    The supraspliceosome model predicts that each transcript will be assembled in a tetrameric supraspliceosome. Splicing of a multi-intronic pre-mRNA can be facilitated by the translocation of the pre-mRNA through the complex in a ‘rolling model’ fashion. After processing of four introns the RNA roles in to place a new subset of introns for processing.

    j) The supraspliceosome has important and complex regulatory functions:

    The supraspliceosome provides a unique and general machine that encompasses the extensive network of interactions and offers coordination and regulation of the different splicing events that a multiintronic pre-mRNA has to undergo. It regulates alternative splicing [39, 40], and harbors a quality control mechanism (reviewed in Ref [31, 41]), as well as all the additional processing activities, such as 5’-end and 3’-end processing, and RNA editing [35, 43]. Furthermore, intronic pre-microRNAs were found in supraspliceosomes and their processing occurs there [44, 45]. Also, a sub-fraction of SNORDs assembled in noncanonical RNPs were found in supraspliceosomes likely playing a role in alternative splicing [46]. Thus, supraspliceosomes harbor components of all pre-mRNA processing activities, thus representing the nuclear pre-mRNA processing machine.

    Very interesting, isn’t it? 🙂

  243. 243
    Dionisio says:

    When isolated from mammalian cell nuclei, all nuclear pre-mRNAs are packaged in multi-subunit large ribonucleoprotein complexes—supraspliceosomes—composed of four native spliceosomes interconnected by the pre-mRNA.

    Supraspliceosomes contain all five spliceosomal U snRNPs, together with other splicing factors, and are functional in splicing.

    Supraspliceosomes studied thus far represent the steady-state population of nuclear pre-mRNAs that were isolated at different stages of the splicing reaction.

    To analyze specific splicing complexes, here, we affinity purified Pseudomonas aeruginosa phage 7 (PP7)-tagged splicing complexes assembled in vivo on Adenovirus Major Late (AdML) transcripts at specific functional stages, and characterized them using molecular techniques including mass spectrometry.

    First, we show that these affinity purified splicing complexes assembled on PP7-tagged AdML mRNA or on PP7-tagged AdML pre-mRNA are assembled in supraspliceosomes.

    Second, similar to the general population of supraspliceosomes, these defined supraspliceosomes populations are assembled with all five U snRNPs at all splicing stages.

    This study shows that dynamic changes in base-pairing interactions of U snRNA:U snRNA and U snRNA:pre-mRNA that occur in vivo during the splicing reaction do not require changes in U snRNP composition of the supraspliceosome.

    Furthermore, there is no need to reassemble a native spliceosome for the splicing of each intron, and rearrangements of the interactions will suffice.

    Supraspliceosomes at Defined Functional States Portray the Pre-Assembled Nature of the Pre-mRNA Processing Machine in the Cell Nucleus

    Hani Kotzer-Nevo 1?, Flavia de Lima Alves 2?, Juri Rappsilber 2,3?, Joseph Sperling 4? and Ruth Sperling 1,* ?

    Int. J. Mol. Sci. 2014, 15(7), 11637-11664;
    doi:10.3390/ijms150711637

    http://www.mdpi.com/1422-0067/15/7/11637/pdf
    http://www.mdpi.com/1422-0067/15/7/11637/htm
    http://www.mdpi.com/1422-0067/15/7/11637

  244. 244
    Dionisio says:

    The Supraspliceosome — A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus

    Author links open overlay panel Kinneret Shefer a, Joseph Sperling a, Ruth Sperling b

    https://doi.org/10.1016/j.csbj.2014.09.008

    Computational and Structural Biotechnology Journal

    Volume 11, Issue 19, September 2014, Pages 113-122

    https://www.sciencedirect.com/science/article/pii/S2001037014000348

    https://www.sciencedirect.com/science/article/pii/S2001037014000348/pdfft?md5=21d9c3c06c61fa29987e17e840819804&pid=1-s2.0-S2001037014000348-main.pdf

    https://pdfs.semanticscholar.org/f461/418c3e6be7f3b809adb84ab5cede7d1c9007.pdf

  245. 245
    Dionisio says:

    The same authors of the 2017 paper referenced by gpuccio @242 coauthored the 2014 papers referenced @243 & @244.

    The newer paper may contain new information obtained in the 3 years after the older papers were published.

  246. 246
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56

    (to be continued…)

  247. 247
    DATCG says:

    #242 Gpuccio
    Very interesting 🙂
    Thanks for giving a review of whats behind the wall.

    #239 Dionisio, sad days when scientist must worry their careers are in jeopardy for daring to question Darwinism and/or conjecture of finding Design. Take religion out of it. Simply recognizing Design is grounds for firing, run out of office, locked out, entire careers over. The Orwellian Thought Minders seek to punish, not just oppress free thought. So much for “free thinkers.” What’s so radical about seeing design? In this instance, the 1st Intron? It’s astonishing to dismiss it out of hand without serious consideration. It immediately reminded me of hardware/software storage requirements for media, search and information exchange. Can there be some criticisms elsewhere? Sure there can. But most storage and retrieval methods require formation of “marks” and/or “introns” for dynamic access, including headers, pointers and significant indexing. All interspersed through out the “randomly” distributed Metadata. There are different requirements based upon load distribution and purpose of systems. Thus differences across prokaryotes and eukaryotes for splicing and/or storage/retrieval access methods.

    #245 Diniosio, thanks, will review! Was hoping to read the latest before running into paywall, but these will get me up to speed.

  248. 248
    ET says:

    The one thing we have overlooked is the fact that both splicing and editing require knowledge– meaning they just don’t happen. There has to be knowledge of what to splice and edit- on how to splice and edit- etc

  249. 249
    Dionisio says:

    ET @248:

    Exactly. What, how, when, why?

  250. 250
    ET says:

    Dionsio- It’s amazing what evolutionists have to ignore in order to remain loyal to the blind watchmaker. If ever there was a concept based on ignorance it is evolution by means of blind and mindless processes

  251. 251
    Dionisio says:

    Connecting the dots: chromatin and alternative splicing in EMT
    Jessica A. Warns, James R. Davie and Archana Dhasarathy
    Biochem Cell Biol. 2016 Feb; 94(1): 12–25.
    doi: 10.1139/bcb-2015-0053
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704998/pdf/nihms708121.pdf

  252. 252
    Dionisio says:

    ET @250:

    I understand their condition, because I’ve been there, done that.

    Unfortunately, as we grow older, we lose our sense of wonder. We stop paying attention to details. Eventually we don’t care about the contextual meaning of words. Our condition degenerates to the point that we don’t understand the meaning of our experiences because we don’t care about it. Then, we don’t care about factual evidences and we don’t pursue truth. It’s a miserable condition that could be described as “anyway, whatever”.

    No amount of academic education or intellectual capacity can free one from such a pathetic condition.

    What is amazing is that I’m not there doing that anymore.

    Now I enjoy watching my little grandchildren being fascinated with little things. I pray that they don’t lose that beautiful sense of wonder.

    I would like to teach them to test everything and hold what is good. But that doesn’t mean to try everything. How can they test without trying? They’ll need wisdom. Where can they get it from? That’s what I want to show them.

  253. 253
    gpuccio says:

    Dionisio (and all interested):

    Very interesting paper at #251.

    Of course, all regulatory processes with the “alternative” qualification must be supra-regulated by epigenetic changes.

    Indeed, if something can be done in one way or in some other, alternative way, there must be a reason fro that choice. Of course it could also be a merely random choice, but in that case we could scarcely expect working systems at all.

    So, epigenetics is supposed to supra-regulate transcription, alternative splicing, and many other regulatory networks.

    We could probably add alternative polyadenilation of mRNA precursors, which seems to be Arthur Hunt’s very interesting main field of research.

    This is a recent review:

    Alternative polyadenylation of mRNA precursors

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483950/

    Abstract
    Alternative polyadenylation (APA) is an RNA-processing mechanism that generates distinct 3? termini on mRNAs and other RNA polymerase II transcripts. It is widespread across all eukaryotic species and is recognized as a major mechanism of gene regulation. APA exhibits tissue specificity and is important for cell proliferation and differentiation. In this Review, we discuss the roles of APA in diverse cellular processes, including mRNA metabolism, protein diversification and protein localization, and more generally in gene regulation. We also discuss the molecular mechanisms underlying APA, such as variation in the concentration of core processing factors and RNA-binding proteins, as well as transcription-based regulation.

    And this is probably the most recent paper published by our kind contributor about that:

    Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502444/

    ABSTRACT
    Stresses from various environmental challenges continually confront plants, and their responses are important for growth and survival. One molecular response to such challenges involves the alternative polyadenylation of mRNA. In plants, it is unclear how stress affects the production and fate of alternative mRNA isoforms. Using a genome-scale approach, we show that in Arabidopsis thaliana, hypoxia leads to increases in the number of mRNA isoforms with polyadenylated 3? ends that map to 5?-untranslated regions (UTRs), introns, and protein-coding regions. RNAs with 3? ends within protein-coding regions and introns were less stable than mRNAs that end at 3?-UTR poly(A) sites. Additionally, these RNA isoforms were underrepresented in polysomes isolated from control and hypoxic plants. By contrast, mRNA isoforms with 3? ends that lie within annotated 5?-UTRs were overrepresented in polysomes and were as stable as canonical mRNA isoforms. These results indicate that the generation of noncanonical mRNA isoforms is an important feature of the abiotic stress response. The finding that several noncanonical mRNA isoforms are relatively unstable suggests that the production of non-stop and intronic mRNA isoforms may represent a form of negative regulation in plants, providing a conceptual link with mechanisms that generate these isoforms (such as alternative polyadenylation) and RNA surveillance.

    As I said, we never know enough! 🙂

    But, in the end, the final question always remains:

    Quis custodiet ipsos custodes? (Giovenale)

    Who Watches the Watchmen? (Alan Moore)

    IOWs, what supraregulates epigenetics? 🙂

  254. 254
    gpuccio says:

    ET at #248 (and all interested):

    “The one thing we have overlooked is the fact that both splicing and editing require knowledge– meaning they just don’t happen. There has to be knowledge of what to splice and edit- on how to splice and edit- etc”

    Great point.

    For example, while I was discussing the psaA trans-splicing here, I have wondered many times about the folowing:

    How can any system, evolved or not, keep trace of where the different parts are written? Or at least of what the different parts are?

    Because that seems a basic requirement to recognize them and to reconstruct the fragmented gene.

    Now, in this case we have 4 parts: the three exons with their flanking fragments of the intron, and the tscA gene. They are probably even degenerate: the tscA RNA certainly needs processing before joining the rest.

    That reminds me a little of hard disk fragmentation, in a sense! You can write a file fragmenting it in many parts. But you certainly need some record of where the parts are, and of what they are.

    Now, the point is that the fragmentation and degeneration of the components of the psaA gene are usually attributed to “rearrangements of organelle genomes”. IOWs, they should be just unlucky events randomly caused by other DNA rearrangements.

    One argument in favour of the random origin of the fragmentation could be the simple fact that in similar organisms the same gene is not fragmented.

    But if the fragmentation is due to some deleterious random event, why should there be any trace of it? Of the nature and location of the fragments?

    Maybe the location is not important, after all. Trans-splicing occurs on pre-mRNAs, and the location of the gene could not be important.

    But certainly, the RNA fragments must be recognized, and there must be some trace of how to process and reunite them.

    As the gene is a fundamental one, it seems that the rescuing information should have existed before the fragmentation event, or just have been created immediately after the event itself.

    Indeed, the fragmentation events cannot realistically be imagined as gradual. It probably rather happened suddenly, as the result of some major DNA rearrangement.

    And the organism cannot reasonably avoid strong negative selection, if the gene does not work.

    I think that’s the reason why neo-darwinists recur to the bizarre idea of Constructive Neutral Evolution to make some sense of it: the information was certainly there before the event, kindly provided by random neutral events! 🙂

    But, if you read carefully the description of what CNE should be, for example here:

    http://onlinelibrary.wiley.com.....9/abstract

    If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely.

    As you can see, the idea seems to be that “mutations”, maybe not too severe, can be balanced by some existing structure, and that the complexity is built “gradually”.

    But there is nothing gradual in the fragmentation of a gene in 4 different parts!

    How can any pre-existing structure be “ready” to assist some gene if it is randomly fragmented?

    The idea itself is really beyond my wildest imagination!

  255. 255
    Dionisio says:

    gpuccio @253:

    So, epigenetics is supposed to supra-regulate transcription, alternative splicing, and many other regulatory networks.

    We could probably add alternative polyadenilation of mRNA precursors, which seems to be Arthur Hunt’s very interesting main field of research.

    The plot thickens…

    As I said, we never know enough!

    But, in the end, the final question always remains:

    Quis custodiet ipsos custodes? (Giovenale)

    Who Watches the Watchmen? (Alan Moore)

    IOWs, what supraregulates epigenetics?

    Does this relate (somehow) to your concept of biological “procedures”?

  256. 256
    Dionisio says:

    Do we have to wait until next year to read a new comment from professor Arthur Hunt?

  257. 257
    gpuccio says:

    Dionisio:

    “Does this relate (somehow) to your concept of biological “procedures”?”

    Yes, definitely!

    “Do we have to wait until next year to read a new comment from professor Arthur Hunt?”

    Don’t be impatient. Next year is not so far away! 🙂

  258. 258
    Dionisio says:

    gpuccio,

    That’s right, this year is practically over.

    Let’s wait and see…

  259. 259
    Dionisio says:

    gpuccio @254:

    “And the organism cannot reasonably avoid strong negative selection, is the gene does not work.”

    is the gene does not work.
    if the gene does not work?

    is – if?

    How can any pre-existing structure be “ready” to assist some gene if it is randomly fragmented?

    Well, that’s a good question.

    But maybe the structure somehow evolved to be flexible enough to adapt to different situations, including random fragmentations of genes? Can you think of another option?
    🙂

  260. 260
    gpuccio says:

    Dionisio:

    Don’t be fastidious!

    After all any gene could be disrupted.

    The rescue mechanism seems to be intron specific, so we only need a specific rescue for each possible intron fragment.

    And, as a few proteins are needed for each intron, we just have to multiply that for… 5? 10?

    But there’s no problem at all. We can rely on a “pool” of RNA binding proteins, ready for all situations.

    How many?

    Thousands? Millions? Billions?

    Who knows?

  261. 261
    Dionisio says:

    gpuccio,

    Yes, that’s a valid explanation within the neo-Darwinian “anyway, whatever (somehow)” paradigm.

    🙂

  262. 262
    Dionisio says:

    We haven’t heard from professor Arthur Hunt since last year.

    🙂

  263. 263
    gpuccio says:

    Arthur Hunt (and all interested):

    While we wait for some possible new intervention by Arthur Hunt, I would like, just for the sake of completeness, to propose a few reflections about the points he has already made, in the measure that I can understand them.

    I will start with what he said at post #51:

    I will add one thing to stir the pot. I think that the fact that the spliceosome is at its core a catalytic RNA calls into question assertions about the irreducible complexity of the complex. For reasons I hope are obvious.

    Not so obvious maybe.

    At #54. I have already made some clarifications about the irreducible complexity of the spliceosome:

    “As you can see, I am not denying in any way that splicing can be performed by simpler and different structures. I also explicitly quote here self-splicing introns as an example of a different way to achieve splicing.

    My point is that the whole system which implements splicing for eukaryotic spliceosomal introns is a new and different entity, and that it is irreducibly complex.

    I have also specified that I don’t mean by that that all the components of the system are indispensable to achieve the function. But it is difficult to deny that some important irreducible core must be present to implement all the subtle and necessary aspects of eukaryotic splicing in most of eukaryotic genes.”

    Now, for greater clarity, I would like to add the following concept:

    The possible irreducible complexity must be evaluated in reference to the true general function in the spliceosome complex.

    Of course the simple catalytic activity can be implemented by the RNA core, as we can see in group II self-splicing introns. But the role of the spliceosome is to effect the splicing in all the different spliceosomal introns that are found in the eukaryotic nuclear genome, and to do that in accord with the regulatory networks implied in alternative splicing.

    To do that, it certainly needs a robust protein structure, which may not imply all of the 150+ proteins as an irreducible core, but certainly implies a good number of them, which are as far as we know absolutely necessary to achieve the spliceosomal function as described.

    So, if we define correctly its important function, the spliceosome is IMO highly ireducibly complex.

    Arthur Hunt also says (at v#56):

    As far as the proteins of the spliceosome are concerned, I guess if totally unrelated proteins in prokaryotic systems can also facilitate the activity of the core of the splicing enzyme, then maybe the uniqueness of proteins that make up these complexes is not so great as you are asserting.

    I am not sure of what he means here by “uniqueness”.

    The “totally unrelated proteins in prokaryotic systems” that “can also facilitate the activity of the core of the splicing enzyme” should be either the individual IEPs that stabilize the catalytic RNA in group II introns in prokaryotes, or the nuclear proteins that assist in cis or trans splicing of degenerate goup II introns in plant organelles.

    It seems that Arthur Hunt’s reasoning, here, is more or less the following (my interpretation, of course):

    “The catalytic RNA core needs protein assistance in different scenarios. As different, and completely unrelated, proteins can assist the catalysis in different situations, then we can say that assisting the catalysis is a rather easy function to implement, even with very different proteins. Therefore, those proteins cannot have such a high functional specificity as you seem to believe.”

    That the proteins are very different there can be no doubt. We have seen in detail that the proteins that assist catalysis in psaA trans-splicing, for example, are totally unrelated to spliceosomal proteins.

    Indeed, they are mainly totally unrelated to anything else, as we have seen.

    But what does that mean?

    Again, the two functions that we are observing are very different, even if they both are related to the catalytic splicing of introns.

    In the case of psaA, the function is extremely specific for one, and only one, situation: a very important gene that is fragmented, introns that are fragmented, some needful information that must be reconstructed and appropriately spliced. It is really amazing that a whole system of many proteins is necessary to accomplish one such specific task, but that is what we observe (at least with the information we have at present).

    Taxonomically restricted and complex proteins implement the task, maybe only that task.

    But the spliceosome does something very different. It is an universal and flexible machine, which incorporates the RNA catalytic core so that it can be applied to all spliceosomal introns, and possibly in such a way that all regulatory networks linked to alternative splicing may be implemented too.

    It is universal cellular machine, like the ribosome.

    Is it so surprising that the proteins in the spliceosome are so many, and that they are completely unrelated to the proteins in psaA trans-splicing? The functions are really different, so the proteins that implement them are dramatically different. That’s exactly what we should expect, in terms of functional information.

    But there is more. In the case of psaA trans-splicing, even if nobody really doubts of the complexity in the system, there are two problems which at present prevent us from quantifying realistically the functional information implied:

    1) The molecular mechanism is still poorly understood

    2) The proteins are not conserved in other organisms, indeed they do not exist in other organisms, and so it is impossible to use evolutionary conservation as a measure of functional complexity.

    IOWs, we are rather sure that Raa1, for example, must be complex in its function (how can we doubt that for a protein of 2000+ AAs), but we cannot really measure, even approximately, that functional complexity.

    But in the case of the spliceosome, things are very different. Proteins are universal and extremely conserved. For very long evolutionary periods.

    We have seen that for Prp8 we can assess a functional information of the order of 3000 – 4000 bits. Even Chamydomonas reinhardtii Prp8 has about 4000 bits of homology with humans.

    That is, I would say, an undeniable evidence of its huge functional information and specificity, IOWs of how “unique” this protein is.

    Of course, Arthur Hunt also says, in post #164:

    I will in due time turn to the matter of the proteins that participate in the splicing of group II introns and of introns that are substrates of the spliceosome. I will mention at this time, though, one thing that gpuccio needs to consider. This is that it is not appropriate to rely solely on BLAST, either to understand distant evolutionary relationships or to assess information content. At least in the sense laid out by Dembski many years ago. Some of the subunits of the complex I work on defy the logic being used here. I mention this because it will factor in to my further comments.

    As I have said, I use BLAST to assess functional information in proteins conserved for long evolutionary periods. The only assumption here is that such a conservation can only be explained by strong functional restraints, and therefore by a strong effect of negative, purifying selection. That is, as far as I can understand, in perfect accord with the basics of neo-darwinian theory.

    “To understand distant evolutionary relationships” and “to assess information content” are two very different tasks.

    In the first, one can be interested in higher sensitivity to detect very low similarities. Tools like Psi-blast can be appropriate for that. From the NCBI site:

    “PSI-BLAST provides a means of detecting distant relationships between proteins”

    But for an ID analysis, we are not interested in distant relationships, or in low similarities. We are interested in strong sequence conservation, which can be evidence for undeniable functional constraint.

    In that sense, ID tools must privilege specificity, not sensitivity. We need to reduce or eliminate false positives, and for that we will tolerate false negatives.

    That’s why Blast is an appropriate tool. When we find a very high homology between proteins by Blast, especially if in the range of hundreds or thousands of bits, we can be certain that such an homology is absolutely real, and cannot be explained by chance. And if that homology has survived hundreds of million years of evolutionary time, negative selection is the only possible explanation.

    I am not sure of the meaning of the Dembski reference.

    Finally, I am really interested in the “subunits of the complex” Arthur Hunt works on, to understand why and how they “defy the logic being used here”.

    But for that, I suppose that I really need his help! 🙂

  264. 264
    Origenes says:

    GPuccio,

    It seems to me that Arthur Hunt misinterpreted the following sentence from the OP:

    GPuccio: So, the spliceosome is certainly highly irreducibly complex, even if we may not be able to clearly identify the essential nucleus of molecules which is absolutely necessary to the minimal function.

    If I understand you correctly, you meant “the essential nucleus of molecules” in a very abstract way. You were not talking about the physical heart / core of the spliceosome. You are talking about parts which are essential for the system to function, wherever they are.
    I think Arthur Hunt read: GPuccio doesn’t know what molecules are at the heart of the spliceosome (but I do) and he says that irreducible complexity depends on these molecules, or something … whatever he means.
    If I am correct that would explain:

    A. Hunt: You did not mention the single most important thing about the spliceosome and splicing.

    Translation: you don’t know what is at the nucleus (heart) of the spliceosome, so you didn’t mention it.

    Hunt: Of course, I was referring to the fact that the spliceosome is a ribozyme. At the heart of the splicesosome sits what is essentially a self-splicing intron.

    Translation: You could not “clearly identify the essential nucleus of molecules”, right? Well, I did it for you: a self-splicing intron.

    Hunt: I think that the fact that the spliceosome is at its core a catalytic RNA calls into question assertions about the irreducible complexity of the complex. For reasons I hope are obvious.

    Translation: Irreducibility was somehow connected to identifying the essential nucleus, right? Well now that you know that it is a self-splicing intron, well, … this “calls into question assertions about the irreducible complexity of the complex. For reasons I hope are obvious.”.

    Uh … maybe obvious if you misinterpret the OP.

    – – – –
    happy new year all

  265. 265
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242
    …….……. GP @253 **
    …….……. GP @254 **
    …….……. GP @263

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56
    (**) not addressed to professor A. Hunt directly

    (to be continued…)

  266. 266
    gpuccio says:

    Origenes:

    “If I understand you correctly, you meant “the essential nucleus of molecules” in a very abstract way. You were not talking about the physical heart / core of the spliceosome. You are talking about parts which are essential for the system to function, wherever they are.”

    Yes, you understand me very correctly. 🙂

    Your exegesis of Arthur Hunt’s statements is very interesting, but of course I cannot speak for him. 🙂

    Happy new year to you.

  267. 267
    Origenes says:

    GPuccio,

    Perhaps you have experienced otherwise, but I have learned that materialists, without exception, always “succeed” in misunderstanding my arguments.

  268. 268
    gpuccio says:

    Arthur Hunt (and all interested):

    Some further thoughts about Irreducible Complexity.

    I have already clarified that my idea is that some irreducibly complex core of proteins is necessary for the spliceosomal function to take place. Probably, that core does not include all the 150+ proteins associated with the spliceosome, but it certainly includes a good number of them.

    But we have, in our discussion here, an interesting and rather clear experimental demonstration of the irreducible complexity of another, simpler structure: the protein complex which effects the trans-splicing of psaA in Chlamydiomonas reinhardtii.

    Now, of course that structure is completely different from the spliceosome, and different is also its function, as I have discussed. But there is no doubt that it has been considered, by many, as an example of how a structure like the spliceosome can arise and work. So, a demonstration that the trans-splicing complex is irreducibly complex can be considered, in some way, as a strong suggestion that the spliceosome, which is certainly much more complex, is irreducibly complex too.

    But what is the experimental demonstration that the trans-splicing protein structure is irreducibly complex?

    Well, we can find it in the paper I have quoted:

    On the Complexity of Chloroplast RNA Metabolism: psaA Trans-splicing Can be Bypassed in Chlamydomonas

    https://academic.oup.com/mbe/article/31/10/2697/1013909

    We know, from older papers, that at least 14 nucleus-encoded proteins have been associated, through mutant analysis, to the trans-splicing.

    Well, the 2014 paper uses, for the demonstration that trans-splicing can be bypassed by transformation with an intrnless gene, three different mutants: Raa1, Raa2, Raa3.

    Each of those three mutants derives from mutations in three different nuclear proteins. And each of the mutant is defective in photosynthesis, because of an ineffective trans-splicing of the psaA gene. Which is exactly the reason why they are used in the experiment.

    So, we have a clear and experimental demonstration that the trans-splicing mechanism includes an irreducibly complex core of at least three different proteins (probably many more), whose mutation affects the trans-splicing in three different ways.

    Each of those three proteins is necessary for the function. The loss of any one of those three proteins causes the loss of function.

    That is irreducible complexity, I suppose.

  269. 269
    Dionisio says:

    gpuccio,

    Off topic:

    Last summer you wrote a very insightful comment on the abstract of a paper that was not for public access.

    It seems like the given paper is now open access.
    Somebody posted it in the same thread where you had written your comment:
    https://uncommondescent.com/evolution/self-organization-new-james-shapiro-paper-on-the-read-write-genome/#comment-647217

  270. 270
    Dionisio says:

    @268:

    So, we have a clear and experimental demonstration that the trans-splicing mechanism includes an irreducibly complex core of at least three different proteins (probably many more), whose mutation affects the trans-splicing in three different ways.

    Each of those three proteins is necessary for the function. The loss of any one of those three proteins causes the loss of function.

    That is irreducible complexity, I suppose.

    Maybe not… 🙂

    A: Can a rectangular portable table stand alone on a tiled floor on three legs on the corners?
    B: of course! haven’t seen it?
    A: but then no heavy objects can be placed near the corner that has no leg, right?
    B: perhaps…
    A: then the table can stand but is not fully functional and lacks stability
    B: well, but it stands, right?
    A: can it stand alone on just two legs?
    B: yes, attach the legless side of the table to a wall
    A: huh?
    B: you see? the four legs aren’t necessary… even three legs aren’t required
    A: but…
    B: no irreducible complexity!
    A: ok, whatever…

  271. 271
    Dionisio says:

    Any news from professor Hunt yet?

    🙂

  272. 272
    Dionisio says:

    @268:

    […] some irreducibly complex core of proteins is necessary for the spliceosomal function to take place. Probably, that core does not include all the 150+ proteins associated with the spliceosome, but it certainly includes a good number of them.

    That’s related to the OP.
    However, curiously professor Hunt’s comments brought up a topic that led to this interesting analysis conclusion:

    But we have, in our discussion here, an interesting and rather clear experimental demonstration of the irreducible complexity of another, simpler structure: the protein complex which effects the trans-splicing of psaA in Chlamydiomonas reinhardtii.

  273. 273
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242
    …….……. GP @253 **
    …….……. GP @254 **
    …….……. GP @263
    …….……. GP @268

    AH is the distinguished professor Arthur Hunt

    GP is the author of the excellent OP that started this discussion thread

    (*) first publicly admitted mistake @56
    (**) not addressed to professor A. Hunt directly

    (to be continued…)

  274. 274
    gpuccio says:

    Dionisio:

    Random thoughts while reading the Shapiro paper.

    I like how “third way” theorizers, like Shapiro, use words. Here is an example, just from the beginning of the paper:

    The following sections present examples of these generic processes repeatedly achieving evolutionary innovations. These cases exemplify broader implications of biological agency (i.e. direct biochemical and biomechanical activity) in generating evolutionary variation:

    “Broader implications of biological agency”??? What would that mean?

    Let’s go on. Maybe we can understand better.

    Point 1.a is simple enough and clear enough. Horizontal transfer, symbiogenesis, hybridization. IOWs, information remixing. OK.

    Point 1.b is already on the mystical side:

    “cells have agency in generating organisms with new genome configurations” ?!

    “the genome functions as a read–write (RW) storage system in evolution” ?

    “The RW genome is subject to a range of generic inscriptions” !!! (is this a generic inscription?)

    and so on. I am a little bit lost here.

    But let’s go on. Clarifications will certainly come.

    Point 1.c. Ah, here we come to “natural genetic engineering” (NGE). The meat, as you would say.

    But we don’t learn much. The rather perplexing conclusion seems to be that:

    By altering the regulatory context, one kind of genome-modification activity can stimulate other kinds in a positive feedback loop that amplifies evolutionary innovation.

    Sounds good, doesn’t it? Again, we will probably see real examples in the rest of the paper.

    Point 1.d seems an attempt to use the above information (which we still do not have) as “an empirical molecular–cellular basis for saltationist views of the evolutionary process, similar to those proposed by certain early evolutionists” (with references that range from 1894 to 2013).

    OK, this is just the premise.

    Section 2 is again about HGT, and again it is simple and clear: HGT is common, important, still working. OK, correct. Nothing really new.

    Section 3 is about symbiogenetic events. Nothing new here again, even if NGE is marginally called into action, without explanations:

    Eukaryotic diversification thus resulted from biochemical NGE functions executing deletions, transfers and rearrangements of mitochondrial DNA.

    Section 4 is about hybridizations and whole genome duplications. Information shuffling again. No special problems, but no special novelties.

    Section 5, of course, is “the meat”:

    Amplification of mobile DNA accompanies increased organismal complexity and provides information-rich cassettes for adaptive innovations

    First, an important recognition of the role of mobile elements (ME):

    All organisms contain repetitive DNA elements capable of transposing to novel genome locations [153]. Both transposition purely at the DNA level and retrotransposition through RNA intermediates tend to increase the copy number of a particular element, and MEs are collectively referred to as dispersed repetitive DNA.

    Reaching levels of non coding DNA praise that would certainly be criticized by traditional neo darwinists, and are probably more compatible with our ID forum:

    The class of mobile repetitive DNA has typically been considered functionally distinct from the relatively fixed, low copy DNA encoding the vast majority of organismal proteins. Hence, it was significant when the initial draft human genome sequence revealed that at least 44% of our genomes consisted of MEs [154]. (Today, our fraction of repetitive DNA is estimated to be as high as 67% [155].) In fact, the repetitive, so-called ‘non-coding’ content of the genome scales more closely with organismal complexity defined by the number of distinct cell types than does the protein-coding content, which plateaus in organisms of about a dozen different cell types [156]. In other words, MEs and other ‘non-coding’ sequences are especially prevalent in genomes of the most highly evolved organisms.

    With reference 156 being, among others, the often execrated Mattick!

    The roles of mobile elements are many and important (I could not agree more!):

    Focusing our attention on mammals, where the most in-depth genomic analysis has been performed, we can discern at least three major evolutionary roles for MEs [157]:

    (1)?MEs provide distributed signals, such as binding site for structural proteins and replication factors, to format the genome as a physically organized self-replicating sequence database [158–160];

    (2)?Although characterized by some as non-functional ‘junk DNA’ [161,162], MEs provide cis-regulatory signals to rewire transcriptional networks determining multiple higher-level traits, including key mammalian innovations on both uterine and placental sides of the maternal–fetal interface in viviparous reproduction [163–166];

    (3)?MEs provide the majority of conserved sequences comprising taxonomically specific ‘long non-coding lncRNAs’ [167–169], a class of molecule that we increasingly recognize as modulating epigenetic control [170] and regulating complex traits like stem cell pluripotency [171–174], internal organ and nervous system development [175–177], and innate and adaptive immunity [178,179].

    As said, I agree. Many times I have stated that ME are the most likely design tool, and that a lot of evidence supports their role in guided intelligent variation.

    Of course, Shapiro does not say anything about how ME should be able to do all that they apparently do. Magic, again?

    Section 6 is more a “conclusions” section. Here we learn that:

    1) “These examples show us that core biological capacities for self-modification in response to ecological challenge have been integral to the history of life on earth.”

    IOWs, life has been constantly designed! 🙂

    2) “That conclusion should not surprise us”

    Well, maybe just a little…

    And the reason for that is:

    3) “because extant organisms are descendants of multiple evolutionary episodes. ”

    Wow! That’s an explanation indeed! I repent of my surprise.

    4) “Considering potential interactions between dynamic ecological conditions and the biological engines of cell and genome variation raises important questions about control and specificity in evolutionary innovation.”

    OK. Important questions are always welcome.

    5) “The years to come likely hold surprising lessons about how cell fusions, genome doublings, and natural genetic engineering may operate non-randomly to enhance the probabilities of evolutionary success.”

    Standard “conclusion of conclusions”, as everybody who has ever published a paper well knows! 🙂

    Maybe a little more word-refined than the usual: “further research is needed to clarify better many aspects of what we discussed here”. But that’s exactly what we expect from “third way” theorizers, as already said. 🙂

    I don’t see in the paper much more than was in the abstract. Therefore, I am in no need to modify what I had already written at comment #2 here:

    https://uncommondescent.com/evolution/self-organization-new-james-shapiro-paper-on-the-read-write-genome/#comment-647217

    in answer to J-Mac. His comment at #1 remains perfectly valid:

    “Seems obvious Shapiro has not problem to butter his bread on both sides…”

  275. 275
    Dionisio says:

    gpuccio,

    Interesting ‘random thoughts’ on Shapiro’s paper.
    You have dissected the paper and exposed its main contents.
    I think I see your point clearly.
    Thanks.

    I seems to me like the third way folks admit correctly that the neo-Darwinian theory doesn’t explain everything coherently. But then they try to explain things in a convoluted way that elms to get lost in confusing statements that don’t seem to make sense, as you noted.

    PS. IOWs, life has been constantly desinged!
    designed?

  276. 276
  277. 277
    gpuccio says:

    Dionisio:

    From:

    Living Organisms Author Their Read-Write Genomes in Evolution

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745447/pdf/biology-06-00042.pdf

    The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

    Emphasis mine.

    In what sense “non random”?

    From section 7, where all the answers should be:

    From these, and many other lines of molecular biology research, it has become abundantly clear that every genome is a densely formatted molecular database, syntactically organized to respond appropriately to the dynamic conditions of cellular life.

    OK, it is “syntactically organized”.

    7.4:

    By virtue of their abundance and the capacity to move throughout the genome, mobile DNA
    elements have specific properties necessary for rewiring and innovating transcriptional regulatory
    networks in evolution.

    Emphasis mine.

    “Necessary”, certainly! But “sufficient”?

    The following sections quote many interesting examples of how mobile elements are implied in both the regulation of regulatory elements and the synthesis on non coding RNAs implied in regulation.

    A 2015 study of human embryonic stem cells (hESCs) identified fully 99.8% of the candidate human-specific transcription factor-binding sites within human-specific retrotransposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS

    A 2017 analysis of 259 mouse embryonic cells at different stages from zygote to blastocyst reports enrichment of mobile DNA in expressed promoters and stage-specific utilization of different classes of mobile elements

    The placental tissue necessary for prenatal embryonic development depends on endogenous retroviruses for syncytial trophoblast development, as well as transcriptional programming. The essential “syncytin” proteins that fuse the cell membranes and provide an immune-protective barrier in the placenta are actually endogenous retroviral Env (envelope) proteins that are expressed from different ERV families in each mammalian order

    A 2015 article reports the utilization of evolutionarily ancient MER130 SINEs to form an integrated enhancer network for embryonic development of mouse dorsal neocortex

    A recent study in human cells identified 962 MER41 family primate-specific endogenous retroviral elements as binding sites for IFN-triggered transcription factors

    In Vesper bats, for example, over 61% of taxon-specific microRNAs can be traced back to mobile elements, largely from bat-specific DNA transposons [549]. Mobile DNA-derived microRNAs arise from lineage-specific transposition events [550,551] that can occur in bursts of genome innovation

    A 2012 analysis reported that 97% of human lncRNAs are primate-specific and found mobile DNA element sequences in 83% of 9241 human lncRNAs, where they constituted 42% of total lncRNA sequence

    So, there can be no doubts that mobile elements are important for genome design and redesign. That rings a bell, doesn’t it?

    No, wait a moment! Shapiro of course does not believe in design. At most, he believes in Natural Genetic Engineering!

    IOWs, design without a designer, engineering without an engineer.

    Which works… how?

    In all these (multiple) papers originated by Shapiro in a very short span of time, I have not found one single idea about explaining how mobile elements can do all that they do. Or why their activity is “non random”.

    “Non random” can mean two things: designed, or caused by specific laws of nature.

    What are the laws of nature that explain the “non random” activity of mobile elements?

    I can find no mention of them in Shapiro’s papers.

    Maybe because of course they do not exist. 🙂

    One last question: how can Shapiro originate so many different (OK, maybe not so different) papers at the same time? As one friend said here, does he even sleep?

    OK, probably they were simply originated by Natural Paper Writing, after all! 🙂

  278. 278
    gpuccio says:

    Dionisio:

    This paper that you referenced at #13 of the other thread:

    On causal roles and selected effects: our genome is mostly junk.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718017/pdf/12915_2017_Article_460.pdf

    is a very good summary of the worst conservative neo-darwinian views turned very bad philosophy! Everything is there, from redefinition of function in neo-darwinian terms to the infamous Constructive Neutral Evolution!

    Thank you for the link: it’s very useful to have all the bad stuff together, in its most recent formulation. 🙂

  279. 279
    Dionisio says:

    @277:

    Natural Genetic Engineering!

    IOWs, design without a designer, engineering without an engineer.

    Which works… how?

    Well, we should know by now: co-option! 🙂

    What are the laws of nature that explain the “non random” activity of mobile elements?

    Well, we should know by now: quantum physics! 🙂

  280. 280
    Dionisio says:

    @278:

    the worst conservative neo-darwinian views turned very bad philosophy! Everything is there, from redefinition of function in neo-darwinian terms to the infamous Constructive Neutral Evolution!

    A real treasure trove (of plain nonsense)! 🙂

  281. 281
    Dionisio says:

    gpuccio,

    Did you look at the last two links provided by toza in that same thread?
    https://uncommondescent.com/evolution/self-organization-new-james-shapiro-paper-on-the-read-write-genome/#comment-647217

    They seem to criticize Dr. Shapiro pretty harshly.

    Perhaps that’s the price to pay for buttering his bread on both sides? 🙂

  282. 282
    ET says:

    gpuccio- It is my gut feeling that Dr James Shapiro was coerced into “natural genetic engineering that evolved via blind and mindless processes”. Jerry Coyne probably had an office right down the hall from his and he couldn’t allow a colleague to give away anything.

  283. 283
    Dionisio says:

    ET @282,
    Interesting comment about the possible reasons behind Dr. Shapiro’s buttering his bread on both sides. 🙂
    Thanks.

  284. 284
    Dionisio says:

    ET @282,

    Your comment seems to thicken the plot. 🙂

  285. 285
    gpuccio says:

    Dionisio:

    The Panda’s Thumb piece is not even an article. It is just a political piece against “anti-science”.

    In a very general sense, I agree. I am not anti-science at all. Frankly, I am somewhat annoyed when true anti-science arguments emerge in this blog (and sometimes they do), but I simply stay silent.

    Science is an important part of human cognition, and there is no reason to be against it, in any way.

    Scientism is a bad philosophy that tries to give to science the role of exclusive truth repository. As a bad philosophy of science, I deeply dislike scientism, and I believe that it is a truly anti-science view of reality, because it betrays the foundations themselves of good science.

    Science itself, of course, can be wrong. That’s its precious privilege. When it is wrong, scientific arguments only can make it right.

    In the case of neo-darwinism, I am convinced that a deep cognitive bias has been working for decades, making biological science in our era strongly prejudiced in favour of a wrong and deeply bad scientific paradigm. That is a shame for science itself, and should be antagonized by all true lovers of scientific thought. That’s what I try to do here, in my personal way.

    For the rest, I have no problems at all with science, including of course biology. And I am not interested in political fights about it, because again I believe that science should always be well above those planes.

  286. 286
    gpuccio says:

    Dionisio:

    The EES site seems a good repository of general “third way” arguments. But where is it that they criticize Shapiro? They should be on a similar page with him, apparently!

  287. 287
    gpuccio says:

    Dionisio, ET:

    The amazing thing with all these third way fans is that they seem not to realize that:

    a) The neo-darwinian model, as we all agree, cannot certainly explain functional complexity in biology by RV + NS

    (for details, see my OPs and following discussions here):

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

    https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/

    but

    b) If they try to put away, or even simply minimize, the role of NS, as those third way freaks seem so eager to do, they are left literally with nothing: no explanations at all, of anything. The probabilistic barriers that NS certainly cannot overcome become then absolute barriers, that they don’t try to climb in any way, not even just going through the motions. So, design remains the only, solitary king of biological explanations.

    Are these third way guys our friends or our enemies?

    I really don’t know.

    And, frankly, I don’t like not to know.

    In the end, I probably prefer some honest and clear and consistent enemy, like Lewontin, or Dawkins, or Coyne! 🙂

  288. 288

    GP,

    Maybe they provide a necessary stepping stone for those of our enemies that weren’t really our enemies after all.

    It may turn out that blindness is harder to sell when you can open your eyes.

  289. 289
    Dionisio says:

    gpuccio @285:

    Agree completely.

    I like science, specially biology, which is becoming the queen of science, heavily relying on other branches of science: mathematics, physics, chemistry. Modern biology is closely associated with information technology, cybernetics, control systems.

    The fact that the big data problem in biology is turning more serious than in physics confirms the enormous complexity of the biological systems and testifies about the beauty of modern biology.

    Unfortunately, many folks out there prefer to waste time on political fights, instead of engaging in polite scientific discussion, like you do here.

  290. 290
    Dionisio says:

    gpuccio @286:

    Apparently after a quick look I rushed to the wrong conclusion and incorrectly placed the two websites in the same category. Thanks for the correction.

  291. 291
    Dionisio says:

    gpuccio @287:

    If they try to put away, or even simply minimize, the role of NS, as those third way freaks seem so eager to do, they are left literally with nothing: no explanations at all, of anything. The probabilistic barriers that NS certainly cannot overcome become then absolute barriers, that they don’t try to climb in any way, not even just going through the motions. So, design remains the only, solitary king of biological explanations.

    Are these third way guys our friends or our enemies?

    I really don’t know.

    And, frankly, I don’t like not to know.

    They seem to be alone in the middle of the battlefield, hence they are strongly criticized by both contending sides.

    The neo-Darwinian folks go beyond criticism and practically call the third way folks ‘defectors’ and ‘traitors’ in their own terms. That’s not polite at all.

    Perhaps that’s the price the third way folks have to pay for buttering their bread on both sides? 🙂

  292. 292
    Dionisio says:

    Upright BiPed @288:

    All they do is claim ‘natural’ design, ‘natural’ engineering, but their former colleagues in the neo-Darwinian party don’t forgive them for having used such forbidden words as ‘design’ even if it’s sugarcoated with the adjective ‘natural’ in front.

    They third way folks crossed the demarcation line and now are being shot at by the neo-Darwinian border patrols.

    They either recant their newly adopted ideas and go back to where they were before or change the term ‘natural’ in front of ‘design’ to ‘intelligent’ and join the ID group.

    There’s no other side in the battlefield.

  293. 293
    gpuccio says:

    Dionisio:

    “There’s no other side in the battlefield.”

    That’s absolutely correct: no other game in town.

    The fight is between RV + NS and design. Nothing else makes any sense.

    So, as long as the third way people go on stating that RV + NS can’t do it, they are really arguing in favour of design. Even if they don’t like it! 🙂

  294. 294
    gpuccio says:

    Arthur Hunt (and all interested):

    Here is a very recent update on the molecular functions of the spliceosome:

    The Spliceosome: A Protein-Directed Metalloribozyme

    http://www.sciencedirect.com/s.....via%3Dihub

    Regarding irreducible complexity, the authors find a very interesting sub-core of the spliceosome which remains remarkably constant throughout the whole spliceosomal cycle:

    A rigid core of the spliceosome
    Despite its dynamic changes during each splicing cycle, the spliceosome—from the Bact to the ILS complex—contains a rigid core of about 20 discrete components [35,36,42–47] (Fig. 2a). These components include the entire U6 snRNA, the bulk of U5 snRNA, a portion of U2 snRNA, and at least 17 proteins. The location and the overall conformation of these components remain nearly indistinguishable among the structurally characterized yeast Bact[42,43], C [44,45], C* [46,47], and ILS [35,36] complexes. Consequently, all RNA components of the splicing active site—ISL of U6 snRNA, loop I of U5 snRNA, and helix I of the U2/U6 duplex—remain largely unchanged in all spliceosomal complexes throughout the splicing reaction (Fig. 2b). The rigid protein components include the bulk of the central spliceosomal protein Prp8 (Spp42 in S. pombe), Snu114 (Cwf10 in S. pombe) and the heptameric Sm complex of the U5 snRNP, Cef1 (Cdc5 in S. pombe), and Syf2 of the NTC, and six components of the NTR including Prp45, Prp46 (Cwf1 in S. pombe), Cwc2 (Cwf2 in S. pombe), Ecm2 (Cwf5 in S. pombe), Bud31 (Cwf14 in S. pombe), and Cwc15 (Cwf15 in S. pombe) (Fig. 2a). These proteins are organized around the three snRNA elements, stabilizing their rigid conformation, and remain largely static in the Bact, C, C?, and ILS complexes

    Emphasis mine.

  295. 295
    gpuccio says:

    Arthur Hunt (and all interested):

    From the same paper quoted at #294, a very interesting conclusion, absolutely pertinent to our discussion:

    As previously suggested [3], the splicing active site of the spliceosome is strikingly similar to that of the group II self-splicing intron [35,36]. These similarities include the position and coordination of the two catalytic metal ions, the fine features of metal-coordinating nucleotides, and the catalytic triplex [3,35,36]. Similar to pre-mRNA splicing, the group IIB self-splicing intron also has an intron lariat intermediate [76]. These preliminary analyses strongly argue for a common ancestry between the spliceosome and the group II introns [77–79]. However, despite these similarities, the overall structure and operational principles of the spliceosome are markedly different from those of the group II introns [35,36]. The overall structure of the U2, U5, or U6 snRNA does not have a mimicry in the group II introns. The placement and conformation of the RNA elements in the spliceosome are determined in large part by surrounding protein components. Unlike the group II introns [79], the splicing active site of the spliceosome is accommodated by a positively charged catalytic cavity on the surface of Prp8 and supported by a number of splicing factors throughout the two steps of transesterification [35,36]. The assembled spliceosome refers to at least seven distinct states, whose inter-conversion is driven by conserved ATPases/helicases [9,10]. In summary, the catalytic activity of the spliceosome, but not of the group II intron, is directed by the protein components.

    The spliceosome is a central RNP enzyme in all eukaryotic cells. The unique structural features of the spliceosome also sharply contrast those of the other central RNP enzyme—the ribosome. Compared with the spliceosome, the ribosome is considerably more stable with a large subunit and a small subunit, both of which are amenable to crystallization and structural investigation [80–82]. RNA elements account for more than half of the total molecular mass in the bacterial or mammalian ribosome, but less than 10% in the human spliceosome. For this and all other reasons discussed previously, the spliceosome is a unique protein-directed metalloribozyme.

    Emphasis mine.

  296. 296
    gpuccio says:

    Arthur Hunt (and all interested):

    This is interesting and pertinent too:

    Intron specificity in pre-mRNA splicing.

    https://link.springer.com/article/10.1007%2Fs00294-017-0802-8

    Paywall.

    Abstract

    The occurrence of spliceosomal introns in eukaryotic genomes is highly diverse and ranges from few introns in an organism to multiple introns per gene. Introns vary with respect to their lengths, strengths of splicing signals, and position in resident genes. Higher intronic density and diversity in genetically complex organisms relies on increased efficiency and accuracy of spliceosomes for pre-mRNA splicing. Since intron diversity is critical for functions in RNA stability, regulation of gene expression and alternative splicing, RNA-binding proteins, spliceosomal regulatory factors and post-translational modifications of splicing factors ought to make the splicing process intron-specific. We recently reported function and regulation of a ubiquitin fold harboring splicing regulator, Sde2, which following activation by ubiquitin-specific proteases facilitates excision of selected introns from a subset of multi-intronic genes in Schizosaccharomyces pombe (Thakran et al. EMBO J, https://doi.org/10.15252/embj.201796751, 2017). By reviewing our findings with understandings of intron functions and regulated splicing processes, we propose possible functions and mechanism of intron-specific pre-mRNA splicing and suggest that this process is crucial to highlight importance of introns in eukaryotic genomes.

  297. 297
    gpuccio says:

    Arthur Hunt (and all interested):

    But neo-darwinists, as we very well know, are not easily discouraged! 🙂

    Here is, for example, a very recent just-so story about the evolution of our spliceosome, with some interesting connotations, even in the abstract:

    Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709842/

    Abstract

    The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences.

    Emphasis mine.

    No comment! 🙂

  298. 298
    Dionisio says:

    @294, 295:

    Journal of Molecular Biology
    Volume 429, Issue 17,
    18 August 2017, Pages 2640-2653

    Very interesting paper.
    Timely catch!

  299. 299
    Dionisio says:

    @297:

    Wow! Another interesting paper! Nice catch! Fishing season is on! 🙂

  300. 300
    Dionisio says:

    Any news from professor Arthur Hunt yet?

  301. 301
  302. 302
  303. 303
    Dionisio says:

    Upright BiPed @301:

    GP at 295.
    “Boom”

    🙂 🙂 🙂

  304. 304
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242
    …….……. GP @253 **
    …….……. GP @254 **
    …….……. GP @263
    …….……. GP @268
    …….……. GP @294
    …….……. GP @295
    …….……. GP @296
    …….……. GP @297

    AH is the distinguished professor Arthur Hunt
    GP is the author of the excellent OP that started this discussion thread
    (*) first publicly admitted mistake @56
    (**) not addressed to professor A. Hunt directly
    (to be continued…)

  305. 305
    Dionisio says:

    Professor Arthur Hunt posted his last comment in this discussion @164 last December 26, 2017.
    Since then gpuccio has addressed to him 17 comments with very insightful explanations.
    Perhaps professor Hunt is getting ready to respond to gpuccio?
    We look forward to reading his next comments.

  306. 306
    Dionisio says:

    @294:

    “The rigid protein components include the bulk of the central spliceosomal protein Prp8”

    Did we read about this protein Prp8 somewhere else in this thread?

    🙂

  307. 307
    Dionisio says:

    @295:

    “…the overall structure and operational principles of the spliceosome are markedly different from those of the group II introns…”

    “…the catalytic activity of the spliceosome, but not of the group II intron, is directed by the protein components.”

    🙂

  308. 308
    Dionisio says:

    @295:

    “The placement and conformation of the RNA elements in the spliceosome are determined in large part by surrounding protein components.”

    🙂

  309. 309
    Dionisio says:

    @295:

    “RNA elements account for more than half of the total molecular mass in the bacterial or mammalian ribosome, but less than 10% in the human spliceosome.”

    🙂

  310. 310
    Dionisio says:

    @295:

    “the spliceosome is a unique protein-directed metalloribozyme.”

    🙂

  311. 311
    Dionisio says:

    gpuccio,

    In the OP figure #2 Prp24 is shown in the center.

    Prp3, Prp31, Prp4 are listed under U4/U6 snRNP.

    Prp8, Prp6, Prp28 are listed under U5 snRNP.

    Then you wrote:

    The Prp8 protein.

    I will add a few words about this proteins, which is probably the most amazing component of the spliceosome, and well represents its essential features.

    This protein has many amazing charactertistics

    How did you single out Prp8?
    Did you look at the other Prp* proteins mentioned above too?

    Thanks.

  312. 312
    Dionisio says:

    OP brief summary:

    So, the subject of this OP is spliceosomal splicing, which is restricted to eukaryotes.

    So, the spliceosome. A few important points about it:

    It is an amazing molecular machine. Even more, it is an amazing molecular cycle, involving many different stages each of which is an amazing molecular machine.

    1. The spliceosome is a molecular machine which appears in eukaryotes.

    2. The spliceosome is a molecular machine which is universally present in eukaryotes.

    3. The spliceosome is a molecular machine whose information is extremely conserved throughout eukaryotes, up to humans.

    4. The spliceosome is a wonderful example of irreducibly complexity.

    The Splicing code.

    The Prp8 protein.

    a) It is, as far as I can say, the longest protein in the whole spliceosomal system, and a very long protein indeed: 2335 AAs.

    b) It is completely absent in prokaryotes.

    c) It is extremely conserved in eukaryotes, probably the most conserved protein in the whole spliceosomal complex

    d) It is a protein which is extremely important for the function of the spliceosome.

  313. 313
    gpuccio says:

    Dionisio:

    “How did you single out Prp8?”

    I sorted out Prp8 essentially because it was the longest protein, it had no sequence homologues in prokaryotes and it was extremely conserved in eukaryotes.

    Yes, I looked at most other proteins in my list too, and I could see that, while those features were common to most of them, Prp8 was certainly the one which best exhibited them.

    While I went on deepening my understanding of the details of the spliceosome, I also realized that there were a lot of structural and functional reasons to consider Prp8 as the key protein in the spliceosome.

    So, this is IMO a very good demonstration that following the tracks of functional information by the methodology I use is a very good and effective way to detect extremely objective functional features! 🙂

  314. 314
    Dionisio says:

    @313:

    That makes sense. Thanks.

  315. 315
    Dionisio says:

    lncRNA involved in alternate splicing?

    LncRNAs can also regulate intron splicing of the sense transcripts by masking splicing sites through its complementary sequences.

    For example, alternative splicing competitor lncRNA (ASCO-lncRNA) can hijack nuclear speckle RNA-binding protein (NSR) to alter splicing patterns of transcripts in response to auxin in Arabidopsis […]

    Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.).
    Wang CY1, Liu SR1, Zhang XY1, Ma YJ1, Hu CG1, Zhang JZ1
    Sci Rep. 2017 Feb 24;7:43226.
    doi: 10.1038/srep43226.

    The known -not the unknown- clearly points to complex functionally specified informational complexity

  316. 316
    Dionisio says:

    @315 correction:

    lncRNA involved in intron splicing?

  317. 317
    gpuccio says:

    Dionisio (and all interested):

    Again about Prp8 and its really extraordinary sequence conservation.

    I have compared Prp8 with another well known protein, the beta chain of hemoglobin (HBB). This is a small globular protein (147 AAs in humans) with a very important function. However, its sequence-function relationship is not extremely strict, and the protein is known to undergo some important neutral variation in long evolutionary times.

    So, I have taken HBB and Prp8 and compared their evolutionary history by blasting the two proteins in Danio rerio (a bony fish) and in humans, and computing the KaKs for both couples of proteins.

    Comparing a bony fish with humans gives us an evolutionary time of something less than 400 million years, the assumed time of the fish-tetrapods split, which is a good time frame to evaluate KaKs.

    Here are the results. First, the blasts:

    HBB (human vs Danio Rerio, 147 AAs):

    172 bits
    76 identities (51%)
    106 positives (71%)
    bits per aminoacid: 1.170068

    Prp8 (human vs Danio Rerio, 2335 AAs):

    4786 bits
    2286 identities (98%)
    2319 positives (98%)
    bits per aminoacid: 2.049679

    Now, look at the big difference between these two proteins.

    HBB is certainly conserved, but in about 390 million years its sequence retains “only” 51% identities, while Prp8 retains 98% of its sequence.

    The difference in bitscore is tremendous (4786 vs 172), but of course it is also due to the difference in length.

    But if we use the bits per aminoacid metrics, which corrects for length, the difference is still amazing:

    2.049679 vs 1.170068

    IOWs the functional specificity, or density, is double in Prp8 if compared to HBB!

    Now let’s go to the KaKs ratio.

    I will remind here, for the convenience of all, that Ka is the number of nonsynonymous substitutions per non-synonymous site (IOWs, those substitutions which change the encoded aminoacid), while Ks is the number of synonymous substitutions per synonymous site (IOWs, those substitutions which do not change the encoded aminoacid), in the same period.

    Here is the simple Wikipedia page:

    https://en.wikipedia.org/wiki/Ka/Ks_ratio

    from which I quote:

    “The Ka/Ks ratio is used to infer the direction and magnitude of natural selection acting on protein coding genes. A ratio greater than 1 implies positive or Darwinian selection (driving change); less than 1 implies purifying or stabilizing selection (acting against change); and a ratio of exactly 1 indicates neutral (i.e. no) selection”

    and

    “The Ka/Ks ratio is a more powerful test of the neutral model of evolution than many others available in population genetics as it requires fewer assumptions.”

    So, just to simplify:

    Forget the values above 1 (they are very rarely seen).

    Values near to 1 indicate neutral variation in the whole sequence (non synonymous mutations happen at the same rate as synonymous mutations)

    Values significantly lower than 1 indicate negative (purifying) selection: non synonymous mutations are antagonized by negative selection.

    In proteins where the sequence is conserved, we expect values lower than 1.

    To compute the KaKs I have used the R package seqinR, and the function kaks.

    So, let’s see:

    HBB (Danio rerio vs human):

    Ka = 0.3799238
    Ks = 1.399608
    Ka/Ks = 0.2714501

    This value is well below 1, so we can say that HBB has been under negative (purifying) selection in the last 390 million years.

    But let’s go to Prp8:

    Prp8 (Danio rerio vs human):

    Ka = 0.0139506
    Ks = 1.482462
    Ka/Ks = 0.009410427

    Two important points:

    a) The rate of synonymous substitutions (Ks) is absolutely comparable in the two proteins:

    HBB vs Prp8
    1.399608 vs 1.482462

    This means that the rate of neutral variation is rather constant. This is, as I have said many times, the best proof of molecular common descent.

    b) The rate of non synonymous substitutions (Ka), instead, is strikingly different. In both proteins, indeed, it is lower than the Ks, but in Prp8 it is much lower (almost 30 times lower!):

    HBB vs Prp8
    0.3799238 vs 0.0139506

    As a consequence, the Ka/Ks ratio is almost 30 times lower in Prp8:

    HBB vs Prp8
    0.2714501 vs 0.009410427

    IOWs, both proteins are under purifying selection, but the purifying selection, as measured by the low Ka/Ks, is almost 30 times stronger in Prp8!

    So, there can be no doubts about the functional specificity of the Prp8 sequence!

  318. 318
    Dionisio says:

    gpuccio,

    Interesting analysis. Thanks.

    What common molecule did the proteins HBB and Prp8 come from?

  319. 319
    gpuccio says:

    Dionisio:

    “What common molecule did the proteins HBB and Prp8 come from?”

    No common molecule, as far as I can see.

    They belong to different protein superfamilies, and they have nothing in common.

    If we blast one against the other (the human forms), the bitscore is 16.9, with an E value of 2.0.

    I would like to clarify one thing.

    When I say that we have strong evidence of molecular common descent, I mean that the protein homologues derive physically through common descent.

    IOWs, Human Prp8 derives with physical continuity for the Prp8 of the common ancestor of fish and tetrapods, to remain with my previous example.

    That is the only way we can explain the value of the Ks between the two proteins: neutral variation has acted on the protein, in each of the two lineages, after the split, in a way that is grossly proportional to time.

    Remember the values of Ka, Ks and Ka/Ks between human Prp8 and Fish Prp8 (390 million years split):

    Prp8 (Danio rerio vs human):

    Ka = 0.0139506
    Ks = 1.482462
    Ka/Ks = 0.009410427

    Now, if we compute the same values between human Prp8 and mouse Prp8 (less than 100 million years split) we have:

    Prp8 (Mouse vs human):

    Ka = 0.000870346
    Ks = 0.4489751
    Ka/Ks = 0.001938517

    Here, again, the Ka/Ks ratio is extremely low, because the Ka is greatly lower than the Ks.

    Hower, both Ka and Ks are much lower than the values we found in Danio rerio.

    Ka: 0.000870346 vs 0.0139506

    Ks: 0.4489751 vs 1.482462

    And if we look in particular to the two Ks values, which are influenced only by neutral variation, the ratio (fish-human / mouse/human) is:

    3.30188

    This corresponds rather well (considering the many approximations in evolutionary times and intrinsic variance of biological systems) to the ratio between the two approximate split times:

    390 / 80 = 4.875

    The important point is that such gross proportionality is retained throughout all groups of organisms and all time spans.

    For example, if we compute the Ks for human and chimp Prp8, the result is:

    Ks (chimp – humans): 0.01565742

    Again, the ratio:

    fish-human Ks / chimp-human Ks

    1.482462/0.01565742 = 65

    is comparable to the ratio between the approximate split times:

    390 / 6 = 94.68112

    There is always this correspondence, extremely significant even is not precise, between evolutionary times and Ks values, in each pairwise confrontation.

    I am aware of no possible explanation for that pattern, other than neutral variation acting on homologues that are physically transmitted throughout evolutionary times.

    That’s what I call molecular common descent.

    But when a new protein superfamily appears, there is no reason to believe that it derives from some other sequence ancestor. It could, if the engineering starts from some existing protein sequence, but if the engineering is so relevant that no sequence or structure similarity remains detectable (as it is the case for different superfamilies), we can have no proof of that derivation.

    Of course, a new sequence could also be engineered from non coding sequences, and therefore have no derivation from other protein sequences at all.

    For Prp8, we have seen that there are no sequence homologies in prokaryotes, but many believe that there are vague structure similarities with reverse transcriptases, and that therefore the molecule could distantly derive from some such sequence.

    As I have said, that is possible (but certainly not certain), but it is not interesting at all from the point of view of functional complexity, because the working sequence of Prp8 has nothing in common with reverse transcriptases except for vague structure similarities, and Prp8 is definitely not a reverse transcriptase.

    The huge functional sequence that is conserved almost entirely from the first eukaryotes to humans has practically nothing in common with the sequence of reverse transcriptases, and is a true sequence novelty that appears in eukaryotes.

  320. 320
  321. 321
    gpuccio says:

    es58:

    This is, I suppose, one example of the “metabolism first” approach.

    These guys are hopeless, but at least they have understood that metabolism is a severe necessity for any form of life, which is certainly true. So they try the impossible to pursue that way.

    The tone of the “non scientific” article, however, is really funny:

    “Scientists think about 3.8 billion years ago, a cocktail of organic compounds managed to come together in some way to create the first life. We know it was primitive and dumb, but still — it was life!”

    This is, instead, the more serious abstract of the paper itself, for those who could be interested:

    Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle

    Abstract

    The development of metabolic approaches towards understanding the origins of life, which have focused mainly on the citric acid (TCA) cycle, have languished—primarily due to a lack of experimentally demonstrable and sustainable cycle(s) of reactions. We show here the existence of a protometabolic analog of the TCA involving two linked cycles, which convert glyoxylate into CO2 and produce aspartic acid in the presence of ammonia. The reactions proceed from either pyruvate, oxaloacetate or malonate in the presence of glyoxylate as the carbon source and hydrogen peroxide as the oxidant under neutral aqueous conditions and at mild temperatures. The reaction pathway demonstrates turnover under controlled conditions. These results indicate that simpler versions of metabolic cycles could have emerged under potential prebiotic conditions, laying the foundation for the appearance of more sophisticated metabolic pathways once control by (polymeric) catalysts became available.

  322. 322
    Dionisio says:

    gpuccio,

    My question @318 was dumb, but you graciously still managed to answer it @319 with a very clarifying (as usual) explanation and with sufficient technical details (also as usual) that even I can understand it.

    Thanks.

  323. 323
    DATCG says:

    Enjoying reading this series!

    Introns, the Spliceosome, all the other guidance mechanmisms in place for splicing are fascinating in regards to information processing, decision trees or branching.

    Was going to post previously in relation to Direct Access Methods – known as Random Access Method in past.

    What is Rule of Random Access Method?

    It is Not Random.

    It’s directed. Highly regulated addressable assets for storage and retrieval.

    Great stuff at 295-… on down 🙂

    I suspect Introns are excellent case for Design principles.

    Found a bit more on paper you highlighted at #296…
    http://emboj.embopress.org/content/37/1/89

    It’s at Research Gate as well.

    Found this PDF by these authors here:

    Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing>

    From the abstract:

    These findings suggest that ubiquitin-like processing of Sde2 into a short-lived activated form may function as a checkpoint to ensure proper splicing of certain pre-mRNAs in fission yeast.

    Activated for guided, specific splicing.

    Mutations could cause inefficiency or failure?

    “Sde2-C is an intron-specific pre-mRNA splicing factor”

    LysSde2-C is a unique pre-mRNA splicing regulator
    LysSde2-C appears to function differently from other pre-mRNA splicing regulators of the spliceosome. LysSde2-C promotes efficient excision of selected introns from selected transcripts in S. pombe, but it is not required for general pre-mRNA splicing. LysSde2-C thereby becomes a critical control factor for the expression of selected proteins, a majority of which function at the chromatin.

    Therefore, growth defects or drug sensitivities of (Delta)sde2 strain could not be attributed to splicing defects of individual genes. The lack of any obvious common feature in Sde2 target pre-mRNAs leads us to postulate that some RNA secondary structures could make their splicing Sde2 dependent.

    Importantly, Sde2-specific proteases play a key regulatory role in pre-mRNA splicing by processing the inactive Sde2 precursor to generate the active spliceosomal LysSde2-C, as Sde2UBL is inhibitory for its incorporation into the spliceosome.

    Fascinating regulatory functions. Wish I had more time to join in and catch up.

  324. 324
    DATCG says:

    Look forward to reading Hunt’s opinions on all of your postings Gpuccio. And where he migh have agreements or disagreements.

  325. 325
    gpuccio says:

    DATG:

    Thank you for your inputs. I will look at them with great interest! 🙂

    You are always welcome to the discussion. 🙂

  326. 326
    DATCG says:

    before I forget, was going to post the other day on “Fragmented” and narrative of fragmented genes, etc., as
    degradation of original DNA.

    Maybe, certainly it makes since from a bottom-up, series of random mutations and unguided happenstance…

    from your previous post on “spoiled kid hypothesis…” and “evolutionary ratchet”

    b) The complexity arises simply to compensate for random errors in the genome, in particular the degradation of the original DNA (fragmentation, transformation, loss of function). The authors call this the “spoiled kid hypothesis”, where the spoiled kid is the degenerate DNA of the gene, and the mutations in the nuclear genome which compensate for that degeneracy are called an “evolutionary ratchet”. IOWs, in this theory the complexity that arises to compensate for the degeneracy has one purpose only: to compensate for the degeneracy.

    What if instead of assumptions of blind process and degeneracy, we ask why this might be intentionally dispersed in relation to information as a definitional, rules based allocation of resources? For specific placement and retrieval purposes?

    Another words, what might we be missing in terms of specific processing needs and organizational structure, as well as coordination? Design often times has trade offs, but with specific intent of cost/benefit analysis. What may look chaotic, degenerate, may be a different use for exceptions.

    Just thinking outside the box.

  327. 327
    Dionisio says:

    DATCG @323:

    That’s interesting what you’ve found.
    I look forward to reading gpuccio’s comments on your posts.

  328. 328
    Dionisio says:

    DATCG @324:

    I’m looking forward to reading professor Hunt’s future comments on the pile of comments gpuccio has addressed to him.

    The distinguished professor is probably very busy with his many academic activities, but let’s hope he’ll find some time to come back and present his counterarguments to the detailed explanations gpuccio wrote in this thread.

  329. 329
    Dionisio says:

    DATCG @326:

    Maybe, certainly it makes since from a bottom-up

    sense?

  330. 330
    gpuccio says:

    DATCG:

    The “Direct Access Method” idea is very interesting. I have thought many times that this complex issue of introns, fragmentation of information, and so on strongly reminds information access problems in hardware and software.

    In comment 254 I wrote:

    “That reminds me a little of hard disk fragmentation, in a sense! You can write a file fragmenting it in many parts. But you certainly need some record of where the parts are, and of what they are.”

    The whole issue of spliceosomal introns in eukaryotes is a deep mystery. I think we still miss some important aspects of the whole matter.

    Interestingly, as you very correctly suggest, while the spliceosome itself is a rather universal and flexible machine/system, a lot of extra components add to its function, making it specific for particular introns or group of introns, maybe providing also further support to regulation through alternative splicing. The Sde2 system, described in the paper you linked, is a very good example of that.

    It’s particularly fascinating that such a mechanism (the Sde2 involvement in the spliceosome for the specific splicing of certain pre-mRNAs) is connected to the ubiquitin-specific proteases system, a regulation network which involves practically all cellular systems.

    Another interesting aspect is that the proteins involved (Sde2, UBP5, UBP15), while universally present in eukaryotes, change a lot in the course of natural history. In that sense, they are very different from Prp8 and other spliceosomal proteins.

    UBP15, for example, a 981 AAs long protein in humans, has very low homology scores in saccharomices species, the best hit being just 391 bits.

    This low conservation in regulatory proteins is, IMO, almost always a sign of functional differentiation, rather than low functional specificity (like in the case of HBB).

    So we apparently have a scenario of a rather conserved spliceosome which acts a an universal machine, whose behaviour in different cases and in different species is finely regulated by lots of accessory factors, probably very specific for the different scenarios and the different species, and therefore much less conserved and highly differentiated.

  331. 331
    Dionisio says:

    DATCG @326:

    “What if instead of assumptions of blind process and degeneracy, we ask why this might be intentionally dispersed in relation to information as a definitional, rules based allocation of resources? For specific placement and retrieval purposes?”

    intriguing concept… hmm…

    the plot thickens…

    🙂

  332. 332
    Dionisio says:

    @330:

    “The whole issue of spliceosomal introns in eukaryotes is a deep mystery. I think we still miss some important aspects of the whole matter.”

  333. 333
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:

    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242
    …….……. GP @253 **
    …….……. GP @254 **
    …….……. GP @263
    …….……. GP @268
    …….……. GP @294
    …….……. GP @295
    …….……. GP @296
    …….……. GP @297
    …….……. GP @313 **
    …….……. GP @317 **
    …….……. GP @319 **
    …….……. GP @330 **

    AH is the distinguished professor Arthur Hunt
    GP is the author of the excellent OP that started this discussion thread
    (*) first publicly admitted mistake @56
    (**) related to the main discussion, but not addressed to professor A. Hunt directly
    (to be continued…)

  334. 334
    Dionisio says:

    gpuccio @330:
    RE: DATCG @323

    reminds of modularity, systems drivers for specific devices, OOP/OOD object classes, etc.

    are you saying that those concepts in Computer Science were defined long before the universities were created?

    🙂

  335. 335
    gpuccio says:

    Dionisio:

    “are you saying that those concepts in Computer Science were defined long before the universities were created?”

    So it seems! 🙂

  336. 336
    Dionisio says:

    gpuccio @330:

    “So we apparently have a scenario of a rather conserved spliceosome which acts a an universal machine, whose behaviour in different cases and in different species is finely regulated by lots of accessory factors, probably very specific for the different scenarios and the different species, and therefore much less conserved and highly differentiated.”

    OK, this is a very delicate issue you’ve raised here.
    Let me explain:
    My former boss, the director of software development for y employer, came up with a killer idea that catapulted the product they developed to the top of the line in its niche industry. His idea, which was wisely based on his knowledge and experience in the given engineering design field, but also -very importantly- based on his numerous consultations with other engineers in the field.
    What was his idea? Well, basically what you just described in the mouthful statement quoted above. That’s basically it. That was the game changer at that time.

    But now you tell me that his brilliant idea was thought of long before him?

    Next time I talk to him I’ll mention this… I’ll let you know his reaction.

    After looking at the amazing biological systems, computer-based systems out there look like Lego Duplo for toddlers.

    🙂

  337. 337
    Dionisio says:

    gpuccio @330:

    “It’s particularly fascinating that such a mechanism (the Sde2 involvement in the spliceosome for the specific splicing of certain pre-mRNAs) is connected to the ubiquitin-specific proteases system, a regulation network which involves practically all cellular systems.”

    a recent ubiquitin-related paper is referenced here:

    https://uncommondescent.com/evolution/rethinking-biology-what-role-does-physical-structure-play-in-the-development-of-cells/#comment-647913

  338. 338
    gpuccio says:

    Dionisio:

    Very interesting paper.

    With 500-1000 E3 ligases which provide the necessary specificity, the ubiquitin system could well be one of the most complex regulatory systems in biology! 🙂

  339. 339
    Dionisio says:

    Discussion between AH and GP
    Index of posted comments:
    AH @25
    …….……. GP @28
    AH @50
    AH @51
    …….……. GP @54
    AH @56 *
    …….……. GP @60
    …….……. GP @69
    …….……. GP @75
    …….……. GP @86
    …….……. GP @98
    …….……. GP @106
    …….……. GP @118 **
    …….……. GP @119 **
    …….……. GP @127
    …….……. GP @129
    AH @130
    …….……. GP @136
    …….……. GP @138
    …….……. GP @146
    …….……. GP @162
    AH @164
    …….……. GP @167
    …….……. GP @176
    …….……. GP @182
    …….……. GP @198
    …….……. GP @200
    …….……. GP @201
    …….……. GP @210
    …….……. GP @211
    …….……. GP @212
    …….……. GP @231
    …….……. GP @242
    …….……. GP @253 **
    …….……. GP @254 **
    …….……. GP @263
    …….……. GP @268
    …….……. GP @294
    …….……. GP @295
    …….……. GP @296
    …….……. GP @297
    …….……. GP @313 **
    …….……. GP @317 **
    …….……. GP @319 **
    …….……. GP @330 **
    AH is the distinguished professor Arthur Hunt
    GP is the author of the excellent OP that started this discussion thread
    (*) first publicly admitted mistake @56
    (**) related to the main discussion, but not addressed to professor A. Hunt directly
    (to be continued…)

  340. 340
    Dionisio says:

    Any news from professor Arthur Hunt yet?

    🙂

  341. 341
    Dionisio says:

    Was this the last time we heard from the professor?

    164 December 26, 2017 at 8:10 pm

    That’s a few days short of 3 weeks ago. Not that long yet. We still can wait…

    But maybe in the meantime, we could start refreshing our memory on some terminology of what used to be considered the Royal Game before computers took over it.

    How to Checkmate in Chess

    The purpose of the game is to checkmate the opponent’s king. This happens when the king is put into check and cannot get out of check. There are only three ways a king can get out of check: move out of the way (though he cannot castle!), block the check with another piece, or capture the piece threatening the king. If a king cannot escape checkmate then the game is over. Customarily the king is not captured or removed from the board, the game is simply declared over.

    How to Draw a Chess Game

    Occasionally chess games do not end with a winner, but with a draw. There are 5 reasons why a chess game may end in a draw:
    The position reaches a stalemate where it is one player’s turn to move, but his king is NOT in check and yet he does not have another legal move
    The players may simply agree to a draw and stop playing
    There are not enough pieces on the board to force a checkmate (example: a king and a bishop vs.a king)
    A player declares a draw if the same exact position is repeated three times (though not necessarily three times in a row)
    Fifty consecutive moves have been played where neither player has moved a pawn or captured a piece

    Text quoted from
    https://www.chess.com/learn-how-to-play-chess

    I think we’re seeing an obvious checkmate in this case, but that’s just my uneducated opinion. What do y’all think it is?

    BTW, was Paolo Boi (c. 1575) the greatest chess player from Sicily ?

    🙂

  342. 342
    gpuccio says:

    Dionisio:

    I don’t know why Arthur Hunt has not provided his announced argument. However, as you say, we still can wait.

    I like intellectual confrontation, and in a sense it can be compared to a fight, or to a chess game. But there is one important difference. In intellectual confrontation, it’s not really important who wins or loses. In a sense, nobody wins or loses.

    What is really important is the discussion itself, the ideas that surface, the sincere approach to truth. That is true, IMO, for any serious discussion, and in a particular way for scientific discussions.

    So, when good ideas are expressed, and truth remains the true aim of the discussion, maybe even of the fight, I do believe that everyone wins.

    I hope that in this discussion a few good ideas have emerged. 🙂

    In the meantime, I would say that many interesting aspects of the spliceosome, and of some related structures, have been touched in some detail. That’s good.

    My personal impression is that, in the end, the strong premise which is the title itself of the OP has been convincingly argued for:

    The spliceosome is a molecular machine that defies any non-design explanation.

    But, of course, that’s just my opinion.

    And, as you said, we still can wait… 🙂

  343. 343
    gpuccio says:

    Dionisio:

    “BTW, was Paolo Boi (c. 1575) the greatest chess player from Sicily ?”

    You definitely know more about Sicily than I do! 🙂

  344. 344
    Dionisio says:

    gpuccio @342,

    Agree.

    What matters at the end of a serious discussion is how much additional light has been shed on the big picture. That’s why a prerequisite for serious discussions is that all discussants are interested in finding the truth about the discussed topic. I don’t think that condition is always met.

    In this particular thread I think several interesting related issues have been presented in your excellent OP and in the many follow up comments you and other folks have posted. Thus some of us -specially I- have learned very interesting things.

    Biology is turning more fantastic every day. I don’t know how far it can get at this pace, but it’s definitely fascinating, at least to me.

    I appreciate the effort you make and the time you take to research so thoroughly the topics you explain so well here.

  345. 345
    Dionisio says:

    @343:

    There were other famous Italian chess players before the world championships started, but they were not from your neighborhood. I think they were from Napoli (or is it Naple?).

    Something I still don’t know is how well they cook in the restaurants by the littoral in Palermo.
    The only way to find that out is going there personally.
    I might start planning a trip there after professor Hunt posts his next comment here.
    🙂

  346. 346
    Dionisio says:

    gpuccio,

    Someone said that chess used to be a Royal Game before the computers took over it. Now the mystery behind it is practically gone.

  347. 347
    Dionisio says:

    gpuccio @342:

    My personal impression is that, in the end, the strong premise which is the title itself of the OP has been convincingly argued for:

    The spliceosome is a molecular machine that defies any non-design explanation.

    Actually, I think it has been strengthened. At least until professor Hunt presents his strong counterargument. Then things might change.

    Let’s wait and see…

    🙂

  348. 348
  349. 349
    Dionisio says:

    es58,

    Life—as we know it, anyway—requires water, common chemicals like oxygen and carbon dioxide that scientists think could be forming on Europa’s icy shell, and an energy source (on Earth, that’s usually the sun, but on Europa it could be geological processes).

    Newsweek
    Life in the Solar System Likely Exists and is More Common Than We Think
    By Meghan Bartels On 1/14/18 at 7:10 AM

    is that all? then poof! really?

    I prefer Disney’s Cinderella’s fairytale, because it makes more sense:
    a pumpkin converted to an elegant carriage, mice turned into beautiful horses, and a grasshopper hired as the official “cochero”.
    🙂

    BTW, this thread is about the spliceosome, which is an amazing machinery, according to gpuccio’s OP and follow-up comments.

    Some of us are looking forward with much anticipation to reading professor Hunt’s next comment, where he supposedly should present the breakthrough counterargument that will finally punch a hole in gpuccio’s presentation.

  350. 350
    DATCG says:

    #330 Gpuccio,

    Yes 🙂 More I hope to add later. Not enough time tonight.

    Came across a video and thought you guys might enjoy. Particularly first line by narrator.

    Hope to see Hunt respond to your series of post Gpuccio.

    Structure of a Spliceosome: Molecular Framework for Understanding Pre-mRNA Splicing…

    https://www.youtube.com/watch?v=JnBf3tq_aXY

    I remember Harvard geneticist George Church pointing out to ID scientist and enthusiast to research the Ribosome.

    A series of quotes from Harvard geneticist George Church…

    Stephen Meyer’s new book Darwin’s Doubt represents an opportunity for bridge-building, rather than dismissive polarization — bridges across cultural divides in great need of professional, respectful dialog — and bridges to span evolutionary gaps.

    Yes, good dialogue, debate, discuss, gain insights.

    As a scientific discipline, many people have casually dismissed Intelligent Design without carefully defining what they mean by intelligence or what they mean by design. Science and math have long histories of proving things, and not just accepting intuition — Fermat’s last theorem was not proven until it was proven. And I think we’re in a similar space with intelligent design.

    The ribosome, both looking at the past and at the future, is a very significant structure — it’s the most complicated thing that is present in all organisms. Craig(Venter) does comparative genomics, and you find that almost the only thing that’s in common across all organisms is the ribosome. And it’s recognizable; it’s highly conserved. So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that’s what I would focus on; how did the ribosome come to be?

    Those are nice sentiments and welcome. And addition of Hunt’s comments here are most welcome. Bridge building is good. Sharpening of each side and insights through debate is healthy and wise, certainly for learning.

    I wonder what Church thinks about the Spliceosome 🙂

    Why did he encourage ID to focus on ribosome? What does he see in it as Design worthy defense?

    Similar to Splceosome? 🙂

    ps Thankful for Edit function, I’ve corrected several spelling mistakes in post-edit process.

  351. 351
    gpuccio says:

    DATCG:

    Very good thoughts! Very good video too.

    Church seems to be a very interesting personality. The idea of building bridges is the only real solution to the stupid polarization of ideological scientism vs ID. Unfortunately, not many people seem really interested in building those bridges, on both sides, even if of course with different responsibilities.

    The ribosome is of course another wonderful molecular machine. More ancient, of course, and that makes probably the discussion more difficult.

    Here is a rather funny “just so story” from Wikipedia about its “evolution”:

    “The ribosome may have first originated in an RNA world, appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when amino acids began to appear.[47] Studies suggest that ancient ribosomes constructed solely of rRNA could have developed the ability to synthesize peptide bonds.[48][49][50] In addition, evidence strongly points to ancient ribosomes as self-replicating complexes, where the rRNA in the ribosomes had informational, structural, and catalytic purposes because it could have coded for tRNAs and proteins needed for ribosomal self-replication.[51] Hypothetical cellular organisms with self-replicating RNA but without DNA are called ribocytes (or ribocells).[52][53]

    As amino acids gradually appeared in the RNA world under prebiotic conditions,[54][55] their interactions with catalytic RNA would increase both the range and efficiency of function of catalytic RNA molecules.[47] Thus, the driving force for the evolution of the ribosome from an ancient self-replicating machine into its current form as a translational machine may have been the selective pressure to incorporate proteins into the ribosome’s self-replicating mechanisms, so as to increase its capacity for self-replication.”

    Just for fun. No comment! 🙂

  352. 352
    gpuccio says:

    DATCG:

    “ps Thankful for Edit function, I’ve corrected several spelling mistakes in post-edit process.”

    The ribosome would agree!

    Quality control by the ribosome following peptide bond formation

    Abstract

    The overall fidelity of protein synthesis has been thought to rely on the combined accuracy of two basic processes: the aminoacylation of transfer RNAs with their cognate amino acid by the aminoacyl-tRNA synthetases, and the selection of cognate aminoacyl-tRNAs by the ribosome in cooperation with the GTPase elongation factor EF-Tu. These two processes, which together ensure the specific acceptance of a correctly charged cognate tRNA into the aminoacyl (A) site, operate before peptide bond formation. Here we report the identification of an additional mechanism that contributes to high fidelity protein synthesis after peptidyl transfer, using a well-defined in vitro bacterial translation system. In this retrospective quality control step, the incorporation of an amino acid from a non-cognate tRNA into the growing polypeptide chain leads to a general loss of specificity in the A site of the ribosome, and thus to a propagation of errors that results in abortive termination of protein synthesis.

  353. 353
    Dionisio says:

    DATCG @350:

    Very interesting video indeed.

    Thanks.

    https://www.youtube.com/embed/JnBf3tq_aXY

  354. 354
    DATCG says:

    #352 and Gpuccio knocks it out of the paaark! 😉 Great paper, thanks!

    #351 well said! Like Church, Venter’s work. Sadly, wonder what kind of heat Church takes simply for offering an olive branch? What is awful is scientist losing positions in the past, even recently.

    What is fascinating after all these years is the “appearance of design” is not going away. It’s growing stronger in terms of language appropriation.

    The paper you reference on Quality Control systems for Protein Synthesis is a case in point.

    In their conclusion…

    Conclusions

    Quality control mechanisms are key throughout the cell in ensuring the faithful replication of the genome and its expression into functional components. Like DNA replication, the quality control system that we describe here for protein synthesis depends on recognition of error following chemical incorporation of the building block into the growing polymer. However, unlike DNA replication, where extension of the growing strand is completed after hydrolytic action of the polymerase removes the misincorporated nucleotides, the quality control described here results in termination of protein synthesis.

    In light of the competition experiments described earlier, we argue that the post-peptidyl transfer process described here might contribute close to an order of magnitude to fidelity in vivo under standard conditions. Moreover, under conditions of starvation, where amino acids become limiting in the cell and miscoding events are increasingly likely, we suggest that this surveillance system could play an even more substantial role in specifying the fidelity of translation. We note that the experiments here were conducted on very early stage RNCs (almost initiation complexes) and that premature release might play a distinct role during the elongation phase of translation. Nevertheless, the effects we have measured in this study are striking. To give some perspective, while false termination at a sense codon normally occurs with a frequency of less than once per 100,000 codons (measured here and in ref 30) in fully matched complexes, in one of the doubly mismatched complexes, false termination occurs half the time. These dramatic changes in the biochemical activity of the ribosome are triggered by single mismatches positioned in the P and E sites of the small ribosomal subunit, highlighting the existence of another intricate molecular system within the ribosome that precisely dictates perfection in the transmission of the genetic code.

    When Design appropriate words are only words you can use to describe overall system behavior at this level, the game is over so-to-speak.

    How else would you describe the system in place? Other than Quality Control? That’s precisely what it is. A highly regulated QC system. That error checks, is triggered to action and termination if required of production.

    QC can have several different levels in engineering or coded systems.

    Simplifying:
    1) non-threatening – function remains,
    2) partial error – degradation – but allowable
    3) danger – abort switch activated – production stopped

    In order to recognize these different levels, error checking mechanisms must match triggers – be cognizant – monitor the processing at different check points, up until final post processing procedures. Proceed or Terminate.

    Error checking cannot happen randomly.

    To early in a process, misses errors entirely. To late, may not miss it, but damage done cannot be rectified in time.

    Quality Control is time dependent. Imagine at these speeds of production and size.

    Different situational outcomes are required for each type of error triggered. Code check depends on narrowed targets or milestones in any phase or post-production stage. Whether it’s materials processing or programmed routines.

    Because even error checks need specific routine calls to complete decision outcome and alert other processes to restart or continue, exit, etc.

    So what about RNA Modification? In the Spliceosome. Is there Post-processing there too? 🙂

  355. 355
    DATCG says:

    Correction last line #354, on RNA modification, post-transcription process.

  356. 356
    DATCG says:

    and…

    Error checking, Quality Control through out. From pre-mRNA onward before being fully processed and passed through Nuclear Pore Complexes on way to cytoplasm.

  357. 357
    gpuccio says:

    DATCG:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912188/

    Moreover, while I have focused my attention especially on Prp8, there are many other important protagonists in the spliceosome. Brr2 is certainly a very good example:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224448/

    By the way, if we look at these two very big proteins in humans:

    Prp8: 2335 AAs

    Brr2: 2136 AAs

    which have such a fundamental role in the U5 subunit of the spliceosome, at the core of the spliceosome itself, and which so strongly interact one with the other, we could be tempted to believe that they are in some way also sequence related, betraying some similar functional information and derivation.

    Well, they are not.

    If we blast human Prp8 vs human Brr2, here is what we get:

    Just three minimal and non-significant homologies:

    Score: 22.7 bits. Total score: 64.3 bits

    E-values: 0.74, 2.4, 2.7

    IOWs, we have two completely different, independent functional sequences, which strictly cooperate to make the spliceosome work.

    Is that irreducible complexity? You bet!

    And is Brr2 highly conserved from single celled eukaryotes to humans? You bet! In the range of 2700 bits! (see Fig. 4 in the OP).

    And has Brr2 some sequence homology in prokaryotes? Yes, but rather low: 311 bits in archaea.

    And is Brr2 highly functionally constrained? You bet!

    ExAC values are 8.00 standard deviations for missense mutations, and 1.00 for probability of Loss of Function. Almost like Prp8!

  358. 358
    Dionisio says:

    DATCG @354-356

    Very interesting commentary. Thanks.
    Also, nice work provoking gpuccio to write more on that interesting topic here.
    🙂

  359. 359
    Dionisio says:

    Any news on professor Arthur Hunt yet?

    🙂

  360. 360
    DATCG says:

    #357 Gpuccio,

    Thanks! will review those papers.

    #354 correction, “error checking cannot happen randomly”
    is intended to be in regards to specific location(s).

    Typically checkpoints happen at key intervals, not randomly. At known areas of transmission, data manipulation and translation. Before and after.

    I’m typing to fast without doing my on checking 🙂

    Or course error checking at location points can be random, in fact encouraged for reasons of efficiency.

    As I’ve done many times based on a set of instruction sets to limit numbers, but maintain overall quality control.

    So constraints of error checking or recognition triggers can fluctuate as required. For example hardening a site for anti-virus.

    The amount of checks may increase along with information triggers. And key component checks may expand, increasing larger load and longer run times.

  361. 361
    DATCG says:

    Gpuccio,

    In searching error processing, noticed you’d originally posted video I shared. LOL, so yes, it’s a good one!

    I’d read through your post, but not watched video. My apologies!

  362. 362
    DATCG says:

    Gpuccio, on 1st paper linked…

    “Because regulation of this process determines the timing and location that a particular protein isoform is produced, changes of alternative splicing patterns have the potential to modulate many cellular activities. Consequently, pre-mRNA splicing must occur with a high degree of specificity and fidelity to ensure the appropriate expression of functional mRNAs.”

    Timing and location matter. How does a hardware system of blunders, mutations finalize correct timing and location before meltdown? Without built-in communication sensors and systems?

    Even if one assumes no error processing?

    Which opens you to a runaway RNA train. I’d like to know how these issues are overcome by mutational events and “junk” dna.

  363. 363
    Dionisio says:

    gpuccio @357:

    we have two completely different, independent functional sequences, which strictly cooperate to make the spliceosome work.

    Is that irreducible complexity? You bet!

    Well, at least until professor Arthur Hunt comes back here and punches a hole in that ID concept.

    BTW, don’t the neo-Darwinian / modern synthesis / extended synthesis folks have someone else who could debate gpuccio here?

    Is professor Arthur Hunt their only ammunition?

    Are they really that weak?

    🙂

  364. 364
    Dionisio says:

    Ok, if professor Hunt can’t come back, then what about the distinguished Canadian biochemistry professor at the U of T?

    I promise not to ask any dishonest questions with tricky words.

    gpuccio doesn’t need help to defend his solid presentation.

    Actually, gpuccio’s presentation doesn’t need to be defended. The neo-Darwinian folks lack arguments anyway.

    Well, let’s wait and see.

    🙂

  365. 365
    Dionisio says:

    DATCG is doing a nice work keeping the serious discussion going.

  366. 366
    gpuccio says:

    Dionisio:

    “Is professor Arthur Hunt their only ammunition?”

    Of course, we cannot force people to take part in the discussion. We can only thank them if they do that! 🙂

  367. 367
    gpuccio says:

    Dionisio:

    “DATCG is doing a nice work keeping the serious discussion going.”

    Yes. 🙂

  368. 368
    Dionisio says:

    Exactly a month ago, December 21, 2017, gpuccio started this discussion thread with an excellent OP.

    The first comment was posted right away. That very first day, less than 10 hours after the thread had started, the distinguished professor Arthur Hunt posted a challenging comment @25. Does this mean that UD posts are being closely watched by some academics out there? Maybe. 🙂

    The last time we heard from the distinguished professor was in his comment posted @164 December 26, 2017.

    We still look forward to reading his expected counterargument.

    In the meantime gpuccio’s OP title remains valid and unchallenged.

  369. 369
  370. 370
    gpuccio says:

    Dionisio:

    I would simply say that Hox genes, and more in general TFs, are a good example of how partially conserved genes can retain some essential functions over a wide spectrum of organisms, and at the same time gain new and specific functions through changes in sequence, or in regulatory elements.

    That confirms the idea, which I have many times expressed, that proteins are much more complex than we usually think. While final effector proteins may use their functional information in a rather compact way, to implement some very specific biochemical function, regulatory proteins, like TFs, or more in general master regulators, are much more flexible, and they are used as functional modules with multiple, often apparently unrelated roles.

    That’s why their natural history often exhibits a frustrating mixture of sequence conservation and divergence, which seems to correspond to a similarly frustrating mixure of conserved and divergent functions.

    The complexity, and functional fine tuning, of the whole scenario is simply amazing.

  371. 371
    Dionisio says:

    gpuccio,

    Excellent statement to summarily conclude your comment @370:

    “The complexity, and functional fine tuning, of the whole scenario is simply amazing.”

    Thanks.

  372. 372
    Dionisio says:

    The occurrence of spliceosomal introns in eukaryotic genomes is highly diverse and ranges from few introns in an organism to multiple introns per gene. Introns vary with respect to their lengths, strengths of splicing signals, and position in resident genes. Higher intronic density and diversity in genetically complex organisms relies on increased efficiency and accuracy of spliceosomes for pre-mRNA splicing. Since intron diversity is critical for functions in RNA stability, regulation of gene expression and alternative splicing, RNA-binding proteins, spliceosomal regulatory factors and post-translational modifications of splicing factors ought to make the splicing process intron-specific. We recently reported function and regulation of a ubiquitin fold harboring splicing regulator, Sde2, which following activation by ubiquitin-specific proteases facilitates excision of selected introns from a subset of multi-intronic genes in Schizosaccharomyces pombe (Thakran et al. EMBO J, https://doi.org/10.15252/embj.201796751, 2017). By reviewing our findings with understandings of intron functions and regulated splicing processes, we propose possible functions and mechanism of intron-specific pre-mRNA splicing and suggest that this process is crucial to highlight importance of introns in eukaryotic genomes.

    Mishra, Shravan Kumar & Thakran, Poonam. (2018). Intron specificity in pre-mRNA splicing. Current Genetics. . 10.1007/s00294-017-0802-8.

    https://link.springer.com/article/10.1007%2Fs00294-017-0802-8

  373. 373
    Dionisio says:

    Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability

    http://www.sciencedirect.com/s.....6517304963

  374. 374
    DATCG says:

    Dionisio @373
    thanks for paper on more Intron functions.

    This goes back to my @230 post on Intron Functions, “… suspect more will be found.”

    Looking for functional design elements in Intronic regions can be rewarded.

    Design elements can simply be a switch, an enhancer or silencer, etc.

    From paper you posted…

    Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage.

    Paper’s “Highlights…”

    – Introns prevent R-loop and DNA damage accumulation on highly expressed yeast genes

    – Insertion of an intron in an R-loop-prone gene attenuates R-loop formation

    – Spliceosome-dependent mRNP assembly, but not splicing, prevents R-loop formation

    – The role of introns in R-loop prevention has been conserved from yeasts to human

  375. 375
    Dionisio says:

    DATCG,

    Your comments are very appreciated.

    BTW, tomorrow it will be one month since the last time professor Arthur Hunt posted a comment in this thread, where he started a discussion with gpuccio the very first day gpuccio’s OP appeared.
    We don’t know why the professor hasn’t come back to defend his previous comments, which seemed intended to punch a hole in gpuccio’s ID presentation.
    The professor’s conspicuous absence could make one suspect he ran out of valid arguments and decided to quit, after seeing that his comments couldn’t make even a shallow dent in gpuccio’s presentation, not even a scratch.
    Perhaps it would have been better to publicly recognize the strength of gpuccio’s presentation and rejoice in the light that was shed on the discussed topic for everybody’s benefit.

  376. 376
    DATCG says:

    Dionisio,

    Maybe, but I doubt Hunt thinks he lacks valid arguments. In his comments he’s confident and comfortable with his statements.

    I’m am waiting for his expansion on his ideas and evidence from #164. And hopeful he responds to Gpuccio’s detailed rebuttals and information.

    I’ve gathered and read different papers on historical evolutionary pathways to the spliceosome. Much of what is said is vague and lacks detail. So I’m hoping he can shed more light on the subject.

    Where does he disagree in detail with Gpuccio on evolution of the Spliceosome? And Irreducible Complexity?

    Quoting a paper Gpuccio referenced in comment #295…
    RNA elements account for more than half of the total molecular mass in the bacterial or mammalian ribosome, but less than 10% in the human spliceosome. For this and all other reasons discussed previously, the spliceosome is a unique protein-directed metalloribozyme.”

    1) RNA elements account for half of total molecular mass in bacterial or mammalian ribosome

    2) RNA elements account for less than 10% in human spliceosome.

    3) The spliceosome is cited as a “unique” Protein-Directed metalloribozme(you highlighted at #310).

    Is the spliceosome “unique” according to authors of that paper? Does Hunt disagree with paper’s conclusion?
    If so, why?

    I hope he can add more specific detail where he disagrees with Gpuccio’s responses and and and expand on his own offerings in #164.

    At least Hunt’s recognizing ID’s hypothesis of Design and challenging Irreducible Complexity on it’s own merit instead of dismissing with ridicule. He’s engaged and I’d like
    to see more engagement like this.

    Precisely the kind of dialogue needing to take place if science is to progress. This is healthy for scientific pursuits in molecular genetics.

    I think Design provides a more natural heuristic thought process of research and discovery. Based upon a systems approach.

    Where as unguided thought processes gave us “junk” DNA and limited thinking.

    I hope Hunt responds. Lets enjoy robust disagreement and discussion. Gpuccio has done his part. Awaiting Hunt’s comments.

    Or, for that matter, if Hunt does not respond, any other neo-Darwinist supporter that supports Hunt’s conclusions.

  377. 377
    Dionisio says:

    DATCG,

    Agree. Thanks.

  378. 378
    gpuccio says:

    DATCG:

    I hope he can add more specific detail where he disagrees with Gpuccio’s responses and and and expand on his own offerings in #164.

    At least Hunt’s recognizing ID’s hypothesis of Design and challenging Irreducible Complexity on it’s own merit instead of dismissing with ridicule. He’s engaged and I’d like to see more engagement like this.

    Precisely the kind of dialogue needing to take place if science is to progress. This is healthy for scientific pursuits in molecular genetics.

    I absolutely agree with you! 🙂

  379. 379
    Dionisio says:

    DATCG,
    Encouraging timely news!

    gpuccio has invited a distinguished scientist, who just recently coauthored a very interesting paper in a very prestigious peer-reviewed journal, to join the serious discussion that the distinguished professor Arthur Hunt started with gpuccio here but unfortunately hasn’t continued since a month ago today.

    Here’s the link to gpuccio’s invitation:

    https://uncommondescent.com/intellectual-freedom/re-seversky-a-lot-of-this-reads-like-complaining-because-science-isnt-coming-up-with-observations-and-theories-that-you-like/#comment-650106

    This would be like the replacement of the starting pitcher in baseball. 🙂

  380. 380
    Dionisio says:

    DATCG @376:

    “I doubt Hunt thinks he lacks valid arguments. In his comments he’s confident and comfortable with his statements.”

    Then what else can explain his conspicuous absence from here for a whole month?
    We don’t know. We hope it’s all well with him.

    But it seems like he quit after the temperature in the discussion went up when gpuccio posted his solid responses.

    At least that’s the impression left. But that could be a misperception.

    Obviously, appearances can be deceiving.

    Let’s wait and see…

  381. 381
    DATCG says:

    Gpuccio, Dionisio I see you’ve made Bob aware of this post.
    Good, maybe he will join in 🙂

    Dionisio, re: reasons for Hunt’s not posting since Dec 26th?

    Not sure, there may be another reason. I’ll wait to see if he post or not. Hopefully he will continue. Could be he’s extremely busy. I’ll give him that benefit for now. He may be preparing a longer commentary in response to Gpuccio as well.

    We shall see.

  382. 382
    gpuccio says:

    DATCG and Dionisio:

    I really think that he must do as he thinks better, there is no obligation to post here. And of course maybe he is only too busy.

    The only problem for me is… I am a very curious person!

    So, I go on wondering what are the subunits of the complex he is studying that defy the logic used here! 🙂

    OK, I must probably work on my character flaws… 🙂

  383. 383
    Dionisio says:

    gpuccio,

    curiosity is bothering me too

  384. 384
    Dionisio says:

    gpuccio,

    Apparently another kind of curiosity is bothering other people out there too…

    https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-650304

    Would you mind to comment on some of the proteins mentioned in the referenced paper?

    Thanks.

  385. 385
  386. 386
    DATCG says:

    Dionisio, will give it a look. Has Bob commented on it?

  387. 387
    gpuccio says:

    Dionisio:

    Very interesting review about cytokinesis. I will try to look deeper into it. 🙂

  388. 388
    Dionisio says:

    Ok, let’s try to keep the readers entertained while waiting for professor Hunt (or a substitute?) to come back and try to say something about the avalanche of solid arguments gpuccio has posted hee in this thread.

    Off topic-

    Lite “nerdy” fun starting @300 here:

    https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-650409

  389. 389
    Dionisio says:

    gpuccio, DATCG,

    The link posted @385 points to posts @289-291 in the linked thread.

    Just the abstracts are available. Do they give a hint of the current situation in the neo-Darwinian party?

  390. 390
    Dionisio says:

    DATCG @386,

    Bob? Do you mean Bob O’H, the scientist associated with Norwegian and German institutions, who just coauthored (along with other 114 scientists) an interesting paper in the peer-review Science journal?
    Is he interested in this heavy-duty kind of science discussion gpuccio leads here?

  391. 391
    Dionisio says:

    gpuccio @387:

    “Very interesting review about cytokinesis.”

    Yes, the link @384 points to post #279 in another thread, where an interesting paper on cytokinesis is referenced.

    I thought your interesting comments on involved proteins is always very appreciated here.

    Thanks.

  392. 392
    Dionisio says:

    DATCG, you’re welcome to look @391 and comment too.

    However, by now I think I have entangled the links so badly that it’s hard to figure out what to look at.

    Sorry. 🙂

  393. 393
    gpuccio says:

    Dionisio:

    I am reading the paper linked at #385. I will come back about it. 🙂

  394. 394
    Dionisio says:

    gpuccio,

    Thank you.

    I’m interested in reading your comments on both, the cytokinesis proteins linked @384 and the one linked @385 about the state of affairs in the modern synthesis/neo-Darwinian theory. If I have to chose one between the two, I prefer the former (cytokinesis).

    But either way you decide to go, take your time, no rush. As long as you can tell us something sooner than a month from now, you’ll do much better than other folks who have taken longer to reappear in this thread. 🙂

  395. 395
    Dionisio says:

    gpuccio,

    Just heard of the ‘replisome’?

    Any comments on those proteins?

    https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-650529

    Thanks.

  396. 396
  397. 397
    gpuccio says:

    Dionisio at #396:

    You bet! The evidence for the role of transposable elements as design tools that shape functional information in genomes is constantly growing. 🙂

  398. 398
    Dionisio says:

    Ok, now I see why that paper rang a bell to my ear.
    Thanks

  399. 399
    Dionisio says:

    gpuccio,

    Have you seen this paper?
    It’s not new.
    Notice some familiar terminology used in the paper.

    https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-650617

  400. 400
    Dionisio says:

    Sorry, I’ve been dumping many paper references here.
    Just wanted to share it.

  401. 401
    gpuccio says:

    Dionisio:

    About the paper at #399.

    Yes, interesting terminology and definitely an attempt to approach evolution from the point of view of functional information.

    But, apart from that, a real disappointment in the end: just a summary of neo-darwinist stereotypes without any real meaning.

    That’s what happens when you exclude in advance the only true explanation: design.

  402. 402
    DATCG says:

    Well, well, nothing from Arthur Hunt. Just a fly by, a mention to use google, a mention to look at certain aspects of splicing and evolution.

    But no defense or even offense.

    I will state my opinion now why he has not posted. If I’m wrong, please Arthur Hunt let us know.

    My thought is he has not commented again in fear of giving any legitimacy to Gpuccio’s well researched post and follow-up.

    There’s a few ways Darwinist, neo-Darwinist, unguided macro-evolutionist rebut Design.

    1) They insult and try to malign it
    2) They bluff with large amounts of papers
    3) They reference vague material on the subject of macro-evolutionary paths of ancient, unknown ancestors
    4) They refuse to engage at all or out of fear do not do so
    5) They engage legitimately on the subject
    6) They engage the person and subject on scientific
    publication, but refuse to allow the person the same
    privilege as happened to Dr. Michael Behe

    #5 I think Hunt began with a good discussion, legitimate
    insights and opposition to Gpuccio that make for good
    debate on the topic

    #4 But, at this late date, with no rebuttal or answers to Gpuccio’s detailed commentary I suspect Arthur Hunt
    may have received heat for being here at all. And
    dropped out due to fear of fellow scientist and zealots on the other side of the debate.

    They simply do not want a real discussion and debate take
    place on facts, observances, science and data.

    If so, that is sad. Because science does not progress without robust disagreement, discussion and debate.

    Insights are gained by instructive disagreements.

    So many here abuse Design Theorist and Scientist by saying
    they are not published or science is not discussed here.

    But we all know that is not true.

    The truth is when science is discussed, none of these false accusers show up to discuss on a good post like this one by Gpuccio. They make excuses.

    It’s hypocrisy.

    I was truly hoping to gain some insight, even if critical of Design by Hunt.

    Maybe he will return one day and share his views. Maybe he was afraid to take it on, or worse was told not to do so. We may never know.

    But by not commenting and not challenging Gpuccio, he leads himself open to criticism. Fairly so.

  403. 403
    gpuccio says:

    DATCG:

    Thank you for your comments. In general, I can agree with what you say. But of course I must remain neutral about Arthur Hunt specifically, not knowing the true reasons for his “disappearance”.

    I must say that I have thought some of the things that you have thought, but I want to remain open-minded, and I try not to judge when I am not sure of what truly happened.

    As you have already seen, having been the first to comment on my new OP, I try to go on with my approach to biological design. The interest and support of those who, like you, share some of my views are the best encouragement that I can receive. 🙂

  404. 404
    Dionisio says:

    Alternative Splicing of Transcription Factors
    Imbriano, Carol & Molinari, Susanna. (2018).
    Genes in Muscle Physiology and Pathology. Genes. 9. 107. 10.3390/genes9020107.
    http://www.mdpi.com/2073-4425/9/2/107/pdf

  405. 405
    Dionisio says:

    Pre-mRNA splicing is a dynamic, multi-step process that is catalyzed by the RNA: protein complex called the spliceosome. The spliceosome contains a core set of RNAs and proteins that are conserved in all organisms that perform splicing. In higher organisms, PPIH directly interacts with the core protein PRPF4 and both integrate into the pre-catalytic spliceosome as part of the tri-snRNP sub-complex. As a first step to understand the protein interactions that dictate PPIH and PRPF4 function, we expressed and purified soluble forms of each protein and formed a complex between them. We found two sites of interaction between PPIH and the N-terminus of PRPF4, an unexpected result. The N-terminus of PRPF4 is an intrinsically disordered region, and does not adopt secondary structure in the presence of PPIH. In the absence of an atomic-resolution structure, we used mutational analysis to identify point mutations that uncouple these two binding sites, and find that mutations in both sites are necessary to break up the complex. A discussion of how this bipartite interaction between PPIH and PRPF4 may modulate spliceosomal function is included.

    Rajiv, Caroline & RaElle Jackson, S & Cocklin, Simon & Z Eisenmesser, Elan & Davis, Tara. (2017). The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding. Biochemical Journal. 474. BCJ20170366. 10.1042/BCJ20170366.

  406. 406
    Dionisio says:

    To interrogate genes essential for cell growth, proliferation and survival in human cells, we carried out a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 screen in a B-cell lymphoma line using a custom extended-knockout (EKO) library of 278,754 single-guide RNAs (sgRNAs) that targeted 19,084 RefSeq genes, 20,852 alternatively spliced exons, and 3,872 hypothetical genes. A new statistical analysis tool called robust analytics and normalization for knockout screens (RANKS) identified 2,280 essential genes, 234 of which were unique. Individual essential genes were validated experimentally and linked to ribosome biogenesis and stress responses. Essential genes exhibited a bimodal distribution across 10 different cell lines, consistent with a continuous variation in essentiality as a function of cell type. Genes essential in more lines had more severe fitness defects and encoded the evolutionarily conserved structural cores of protein complexes, whereas genes essential in fewer lines formed context-specific modules and encoded subunits at the periphery of essential complexes. The essentiality of individual protein residues across the proteome correlated with evolutionary conservation, structural burial, modular domains, and protein interaction interfaces. Many alternatively spliced exons in essential genes were dispensable and were enriched for disordered regions. Fitness defects were observed for 44 newly evolved hypothetical reading frames. These results illuminate the contextual nature and evolution of essential gene functions in human cells.

    A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.
    Bertomeu T#1, Coulombe-Huntington J#1, Chatr-Aryamontri A#1, Bourdages KG1, Coyaud E2, Raught B2, Xia Y3, Tyers M
    Mol Cell Biol. 2017 Dec 13;38(1). pii: e00302-17.
    doi: 10.1128/MCB.00302-17

  407. 407
    DATCG says:

    A new paper discussing Introns and Alternative Splicing, Introns roles and some new revelations…

    Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

    Discussion

    We identify an enrichment of m6A deposition near the 5? SJs(Splice Junctions) of nascent RNA transcripts, and we show that early m6A deposition is associated with distinct RNA processing kinetics.

    Most importantly, we compare the processing of individual m6A-positive transcripts versus their m6A-negative counterparts, demonstrating that m6A directly controls splicing kinetics irrespectively of the underlying transcript sequence.

    Our findings suggest that m6A serves as a labeling signal that could be recognized by m6A reader proteins to destine methylated transcripts for specific splicing kinetics.

    This is in agreement with a study describing m6A methylation as a mark for selective nuclear processing, providing evidence for an m6A-dependent mRNA metabolism (Roundtree et al., 2017).

    Our findings furthermore reveal that intronic m6A peaks are enriched in introns involved in alternative splicing.

    The m6A demethylase FTO binds mostly to introns and mediate removal of m6A. Knockout of FTO causes alternative splicing events with a preference for exon skipping, suggesting that demethylation of mRNA transcripts promotes exon inclusion under normal conditions (Bartosovic et al., 2017).

    Taken together, these findings suggest that intronic m6A marks that are not targeted or not yet removed by FTO mediate exon skipping, while introns involved in constitutive splicing show no enrichment in the m6A signal and most probably are targets of FTO (Bartosovic et al., 2017).

    In mRNAs, m6A is enriched in the consensus DRACH motif; however, not all DRACH motifs are methylated, indicating that the presence of the sequence motif alone is not enough to drive m6A deposition. FTO CLIP data show no significant enrichment of the DRACH motif (Bartosovic et al., 2017), leading us to hypothesize that early intronic m6A deposition is mostly in non-DRACH sequences where FTO can detect and eventually remove the m6A marks.

    Recently, the m6A reader YTHDC1 was shown to recruit SRSF3 while competing away SRSF10. YTHDC1 binds m6A sites and promote exon inclusion (Xiao et al., 2016). In the absence of YTHDC1 and SRSF3, SRSF10 has the availability to bind to free m6A sites independently, promoting exon skipping. SRSF3 knockdown in U2OS cells has also been shown to cause exon-skipping events (Ajiro et al., 2016). Using de novo motif analysis, we identify three additional motifs sharing a SAG core reminiscent of the SRSF binding site consensus, suggesting that m6A could be involved in recruiting splicing factors to control SE and alternative splicing.

    The lack of strong consensus sequences at SJs of many introns may be compensated by the presence of m6A that could eventually attract splicing factors to exert their function.

    Our study shows that the crucial role of m6A on SED as well as on alternative splicing is position dependent.

    m6A deposited in intronic regions sort transcripts to a slow-track processing pathway and is associated with alternative splicing while m6A deposited at exonic boundaries of SJs sort transcripts to a fast-track processing pathway and constitutive splicing.

    Awesome stuff on selective splicing and processing!

  408. 408
    DATCG says:

    Dionisio! there you are!?! 🙂

    Gpuccio@403, you are always generous to your detractors.

    And Arthur was on topic and kind as well. It’s one reason why I was hoping for more of his insights and input on the discussion.

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