Junk DNA turns out to have function again

_{Denyse O'Leary

March 31, 2015

Intelligent Design}

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Peter M. Waterhouse & Roger P. Hellens, ” Plant biology: Coding in non-coding RNAs,” Nature (March 25, 2025)

Dominique Lauressergues, Jean-Malo Couzigou, Hélène San Clemente, Yves Martinez, Christophe Dunand, Guillaume Bécar, & Jean-Philippe Combier, “Primary transcripts of microRNAs encode regulatory peptides,” Nature (March 25, 2015)

G C S Kuhn, “‘Satellite DNA transcripts have diverse biological roles in Drosophila’,” Heredity (March 25, 2015)

Go here for simple explanation.

Nick Matzke? Darwin book burner! Where are you when we need you to dump on all this?

You used to come at half o’clock and now you come at noon.

Otherwise, Biological Information

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Comments

DNA_Jock at # 40:
And my statement above is true. That is precisely the argument that you made;
No.
I understand you may wish to dial it back, given that you have just been touting the functionality of a 5 amino acid peptide.
That is simply false, but think as you like.
Why did you add the word “specific”? As I explained previously, an alpha helix can have a function. Whether it`s “specific” or not is irrelevant semantics.
I added "specific" because I meant a secondary structure that is necessary for ots function as signal peptide. That would be "specific", I believe. And it would be a possible condition for positive natural selection. Yoiu may consider all that "irrelevant semantics". I don't.
And you know this how?
You show how you know that they are. It's your theory, not mine.
I`ll agree with you that “A functional peptide, however short, is functional.”
How kind you are!
But when you write “Secondary structure in itself is not function, and is not selectable.” , you are merely repeating the same tired, unsupported assertion. This is why I asked you for facts to support your various claims about what evolution cannot achieve.
Again, I would appreciate examples of generic isolated alpha helices which are naturally selected because they confer a reproductive advantage in a biological system. Again, it's your theory, not mine. You have to show the supporting facts.
This is rather misleading. Yes, by looking at DNA sequences, we can detect the recent recombination of relatively large fragments.
Why these strange limitations? The sequences in ATP syntase have remained almost the same for about 4 billion years. The Helix-loop-helix domain in human myc shows clearly detectable homology with the same domain in the mxl-3 protein in C. Elegans: 72 AAs, 31 identities (43%), 44 positives (61%), expect = 4e-06. The DBD in human myb protein (about 46 AAs) can be detected in C. Elegans with 46% identity and an expect of 4e-06. The WW domain, maybe the shortest protein domain in classifications, of about 40 AAs or less, can be clearly identified in dystrophin in humans and drosophila, with an expect of about 1e-08. And so on. Of course, very short sequences (5-20 AAs) will usually evade a simple homology analysis for statistical reasons, but as you certainly know simple motifs can be identified and studied by associating other methodologies. You see, functional sequences are generally conserved, both long and short ones, and homologies can easily be detected, even after billions of years. As a lot of conserved sequences or anyway of recurrent motifs, some of them very short, are well known, you can certainly show the relevant role of those sequences and motifs in building up long and complex functional proteins by recombination and natural selection. You must only show how those long amd complex functional proteins are simply the sum of existing, selectable sequences and motifs.
But, as I went to considerable lengths to explain to you, the absence of detectable homology DOES NOT preclude common ancestry.
You seem a little confused here. First of all, I have nothing against common ancestry. I have a lot, instead, against common ancestry and derivation by simple RV + NS. There is a big difference. Moreover, even if two proteins could have common ancestry and lack detectable homology (which is perfectly possible), still you have to find other reasons to affirm the common ancestry, if you lack detectable sequence homology: for example, strong structural homology could be considered a sign in favor of common ancestry even in the absence of obvious homology. But, if you have no facts in favor of common ancestry, it remains just a product of your imaginatiuon, with no scientific importance. And, even if we detect some sign of common ancestry, we still have to understand the mechanisms of transition from one form to the other. IOWs, you have to show that your theory (for example, RV + NS) can reasonably explain the transition. Common ancestry is a concept common to both your theory and mine. But I would never affirm common ancestry of two proteins in the absence of any empirical evidence. I try to keep my expectations and scientific facts separated.
I think you may have been seduced by the awesome power of DNA sequence alignment (and its ability generate molecular phylogenies is truly awesome).
I don't think that I have been "seduced". Like you, I recognize that power, and try to use it in my reasonings. If I have been "seduced" by anything, that is certainly ID theory.
The bottom line is that we can observe, today, processes of mutation, indels, and recombination that do cobble together different bits of proteins. If you wish to make a claim that these processes are inadequate to explain protein evolution, you need to support that claim with something other than bald assertions.
No. My point is simple. If recombination of functional modules were really a fundamental component in protein evolution, as many on your side have bben affirming, then we shopuld be able, in the general case, to recognize the functional modules which have been recombined, and therefore be able to analyze the role of recombination according to facts. While it can be true that in some cases we would miss the sequence homology, that would be the exception, and not the rule. As you have recognized, the power of homology (and possibly of other techniques of analysis) is very high. We see strong homologies in distant, very distant proteins, when the function is really conserved. Therefore, affirming that there can be exceptions is not the same as saying (as you do) that we cannot find the evidence. If the theory were true, the evidence would be there in tons. With a few exceptions, which, as everybody says, confirm the rule.
I understand that you are taking the “Joe Gallien” position that functional proteins cannot grow longer. To each his own.
Who is Joe Gallien?gpuccio_{April 4, 2015
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Dr JDD, You have my sympathy regarding your dodgy internet connection. You ask
given all cellular organisms we know of have molecular chaperones what evidence do we have that a cellular organism could produce proteins from genes/RNA for cellular life without needing such aides for folding correctly? And also, given we can fold proteins in a test tube quite easily but these are usually homogeneous, how did such an organism fold their proteins without detrimental peptide aggregation, assuming more than handful of proteins are necessary for their existence?
to answer your question,
It is a fair point that many proteins can and do fold quite easily, given the right buffer conditions. Not all absolutely require molecular chaperones and other folding proteins as we can produce a lot of useful proteins in the lab quite easily
I cannot find a source to support the wikipedia claim that "most" proteins do not require chaperones. Frankly, I`m not sure I believe that myself*. But my case doesn`t require "most": given billions of years of evolution WITH chaperones around, there hasn`t been any selection for chaperone-free folding. My case rests on the fact that a significant number of (extant) proteins do not require chaperones. (It seems to be a common ID fallacy that "if X is essential today then X must always have been essential"; see, for example, Andre's confusion over PCD.) You do make a good point, however, that aggregation is more likely to be a problem at higher protein concentrations e.g. the cellular environment. The homogeneity of your purified protein is not relevant - it`s the effective concentration of exposed hydrophobic surfaces that matters. But, by the same token, both correctly folded proteins and polysaccharides (if you are willing to allow their existence) act as volume excluders. They may also have mild detergent / weak anti-aggregation ability. *It is true that the vast majority of proteins do not require specific chaperones.DNA_Jock_{April 3, 2015
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DNA_Jock: I just wrote a rather lengthy response that due to a dodgy Internet and tablet was just deleted, and I cannot be bothered to go through it all again as most of these points we will just go around in circles with. Maybe next week when I'm home on my desktop! So briefly, I believe as you know, the answer to your question I think is 0 proteins but that insisting the point completely and yes the point is could a complex multi-protein machine arisen through naturalistic means and no I mean the higher eukaryotic large (>150+ proteins) spliceosomal protein complex. A question for you then: given all cellular organisms we know of have molecular chaperones what evidence do we have that a cellular organism could produce proteins from genes/RNA for cellular life without needing such aides for folding correctly? And also, given we can fold proteins in a test tube quite easily but these are usually homogeneous, how did such an organism fold their proteins without detrimental peptide aggregation, assuming more than handful of proteins are necessary for their existence?Dr JDD_{April 3, 2015
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DNA Joke- Those links do not help you. They don't even address what I am saying. Who cares how many proteins it takes to excise an intron? Your position cannot account for editing and splicing.Joe_{April 3, 2015
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Joe, Can. He. Understand. Basic. Biological. Science? See my 43 for links to the data. Re splicing, would you like to take a stab at my question
what is the minimum number of proteins needed to excise an intron?
or would you rather wait until Dr JDD comes to bail you out?DNA_Jock_{April 3, 2015
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Dr JDD, Re-reading this thread, I notice that you yourself wrote @38
That is to say, I think the evidence that short peptidic sequences with simple folds can combine over time to produce hugely complex proteins is very weak. I am not talking about repetitive sequences for example where proteins are involved in structural or architectural aspects of cells, I am talking about complex cellular machinery found all the way back to some of the most basic forms of life itself. [emphasis added]
which I took as a reference to collagen; but it could equally apply to titin and, given that you have published on titin, it seems safe to say that titin is an example of what you were not talking about. Regarding chaperones, my suspicion is that they originally arose as an adaptation to heat-shock; but once you have them, then the requirement that proteins be able to fold in their absence becomes moot.DNA_Jock_{April 3, 2015
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No DNA Joke, the data doesn't suggest otherwise. You have failed to provide any data for growing proteins. Also your position cannot explain splicing and editing- absolutely no data.Joe_{April 3, 2015
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Fascinating stuff, the spliceosome. Although someone reading your statement
the incredible complexity of the 150+ multi – protein spliceosome machinery
might make the mistake of thinking that 150 proteins are required for a spliceosome, rather than a 150 nucleotide snRNA... But do tell, what is the minimum number of proteins needed to excise an intron? A group I intron, for instance? I am happy to stipulate that life, as we know it, is complicated. The question is, could it have developed this complexity via natural processes? And what Joe wrote originally was:
additional amino acids will either alter or bury the active site. That is just the way it is.
The data suggest otherwise.DNA_Jock_{April 3, 2015
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7 - the incredible complexity of the 150+ multi - protein spliceosome machinery used to splice those 360-odd exons correctly. Titin is a fascinating protein regardless of your origins POV to be honest. But again screams design to me.Dr JDD_{April 2, 2015
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DNA Joke:
I agree that titin is complicated, but most of its size comes from duplication of the Ig-like domain, making it a terrible example for the lame argument “you cannot turn a small protein into a bigger protein”.
1- your position can't account for titin 2- It cannot account for the sequences it was allegedly duplicated from 3- It cannot account for exons and introns 4- It cannot account for alternative splicing 5- It can't even account for DNA 6- It definitely has no explanation for chaperonesJoe_{April 2, 2015
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LoL! I posted a typo tintin at first and auto-corrected it to titan. But anyway I am looking for evidence for a polypeptide to grow, starting small with some function and remaining functional as it grew to titin. Anyone?Joe_{April 2, 2015
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Dr JDD, I agree that titin is complicated, but most of its size comes from duplication of the Ig-like domain, making it a terrible example for the lame argument "you cannot turn a small protein into a bigger protein". Re protein folding, my comments re re-folding @48 were a response to your statement
However many proteins are extremely difficult to produce and impossible to refold in vitro, in particular membrane proteins and it is a fair point that some of the most important proteins in the cell will not simply refold on their own in the right buffer. [emphasis added]
which I hope you can see is somewhat off-topic. Hence my emphasis on folding during de novo synthesis. I mean, what are we to conclude from the extreme difficulty in refolding a membrane protein in vitro? Not a lot. P.S. I've been giving Joe the benefit of the doubt for a long, long time. ;)DNA_Jock_{April 2, 2015
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DNA_jock, You have to give people (Joe here) the benefit of the doubt - I've published on Titin and the number of times it was autocorrected to Titan while preparing the manuscript I am amazed it didn't get published as Titan. Of course the standard response would be that it is duplication. But it is incredibly complex and the 17kb exon is of particular interest. While there are a lot of domain repeats there are unique large functional sequences, and within the repetitions there is clear necessity for functionality. The novex-3 isoform is interesting as well, but as we can see here there are a couple of main repeat domains but also several others organised in a precise functional structure: http://www.embl-hamburg.de/~wilmanns/Titin-Figure1.png Secondly I say "re-folded" because how else do you fold a protein without an organism? For when you use an organism such as e coli or CHO or SF9 or whatever you are hijacking their cellular machinery rather than using a native buffer - which is the POINT here: early proteins in abiogenesis/organism evolution would not have had chaperones or other proteinacious machinery to help fold them and that is what is argued here. Thus the best example to use surely is that some proteins can be denatured in the lab and then resold in buffer alone, showing that SOME proteins do not require such help to refold from other proteins...Dr JDD_{April 2, 2015
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Dr JDD, Re protein folding. Agreed. I would note that protein re-folding is far more difficult that protein folding during synthesis. Asking if a protein can re-fold is asking the wrong question. Strange to relate, but most proteins fold rather well as they are synthesized. Especially if they are expressed in a host from the same kingdom.DNA_Jock_{April 2, 2015
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Thank you Dr JDD for the clarification. Joe`s references to titan puzzled me. Nobody looking at the structure of titin would ever think that it arose via the duplication of the same simple sub-domains over and over and over again. No sirree. [/sarcasm] Best own goals evah.DNA_Jock_{April 2, 2015
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It is a fair point that many proteins can and do fold quite easily, given the right buffer conditions. Not all absolutely require molecular chaperones and other folding proteins as we can produce a lot of useful proteins in the lab quite easily (although a lot of the time we get bacteria to do the work for us). However many proteins are extremely difficult to produce and impossible to refold in vitro, in particular membrane proteins and it is a fair point that some of the most important proteins in the cell will not simply refold on their own in the right buffer.Dr JDD_{April 2, 2015
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What's the problem Joe? Do you not see how a 244 protein domain molecule with 363 exons one being >17kb in length alone can just come through selection of small peptides coming together over time? Maybe 244 different proteins decided to join together randomly alongside extra peptides to form the largest functional protein known in humans with a length of 1um. Seems plausible given enough time. After all it was necessary to come around to enable proper muscle and cardiac function.Dr JDD_{April 2, 2015
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DNA Joke- none of that even addresses what I said. Obviously you are deluded. Please provide the evidence that one of the small polypeptides gpuccio discussed can grow into something like titan. Or admit that you are a goal-post moving chump.Joe_{April 2, 2015
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I, too, am extremely fond of these kind of observations. It goes to the heart of the matter: IDists are impervious to evidence. See https://uncommondescent.com/evolution/exon-shuffling-and-the-origins-of-protein-folds/#comment-551488 in particular: https://uncommondescent.com/evolution/exon-shuffling-and-the-origins-of-protein-folds/#comment-551647 https://uncommondescent.com/evolution/exon-shuffling-and-the-origins-of-protein-folds/#comment-551663 The simple fact is that (more often than not) heterologous gene expression and fusion proteins work as expected, including fusion proteins created with libraries of peptide fragments (e.g. yeast two-hybrid systems). Random recombinations between large proteins, OTOH, have a much more spotty prognosis, as expected, but some do have novel functionality.DNA_Jock_{April 2, 2015
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Joe: Meaning it doesn’t do any good to “grow” a protein if you don’t also have the proper accompanying chaperone(s)
I'm extremely fond of these kind of observations. It goes to heart of the matter: the cell is a whole. Under materialism one cannot insert an unrelated part into it - similarly one cannot just throw in an unrelated memory card into a computer. Regulation - in the broadest sense of the word - has to be in place.Box_{April 2, 2015
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DNA Joke:
I understand that you are taking the “Joe Gallien” position that functional proteins cannot grow longer.
It isn't my position. I take the position of those biologists and biochemists who I have read. They say that proteins are not like stalagmites and stalactites, meaning they are not just growths of amino acids. You don't get to titan by adding on to one of those short polypeptides all the while maintaining some function. Also:
It has recently become clear that protein folding in the cellular environment is not a spontaneous, energy-independent process akin to that observed when chemically denatured purified polypeptides are refolded in vitro. Rather, in vivo protein folding strongly relies on accessory proteins known as molecular chaperones and foldases.--Molecular Chaperones and Foldases (bold added)
Meaning it doesn't do any good to "grow" a protein if you don't also have the proper accompanying chaperone(s)Joe_{April 2, 2015
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Gpuccio writes:
DNA_Jock:
You have shifted your argument. On the FSCO/I vs needles thread, you argued that the sort of short peptides that might be accessible via random walk (I used the example of a stable alpha helix) could NOT confer a selectable advantage
Not true. The problem is not that whether a peptide is short or long. A signal peptide is functional because it is part of a recognition network.
Ah, yes, the context argument I predicted @27. And my statement above is true. That is precisely the argument that you made; I understand you may wish to dial it back, given that you have just been touting the functionality of a 5 amino acid peptide.
I have no idea if the miPEP171b peptide has a specific secondary structure or not. My point is that an alpha helix, in itself, has no specific function.
Why did you add the word “specific”? As I explained previously, an alpha helix can have a function. Whether it`s "specific" or not is irrelevant semantics.
And that longer proteins are not built by adding some generic isolated functional alpha helix to another one and to another one.
And you know this how?
Again, homology can detect recombination. Secondary structure in itself is not function, and is not selectable. A functional peptide, however short, is functional. Maybe selectable. Whatever its secondary, or tertiary structure. But if it is not an intermediate step to a longer functional sequence, it does not explain the longer functional sequence.
I`ll agree with you that “A functional peptide, however short, is functional.” But when you write “Secondary structure in itself is not function, and is not selectable.” , you are merely repeating the same tired, unsupported assertion. This is why I asked you for facts to support your various claims about what evolution cannot achieve. However, your response did offer a clue as to why you think the way you do (other than confirmation bias, of course…) : You wrote
Again, homology can detect recombination.
This is rather misleading. Yes, by looking at DNA sequences, we can detect the recent recombination of relatively large fragments. But, as I went to considerable lengths to explain to you, the absence of detectable homology DOES NOT preclude common ancestry. I think you may have been seduced by the awesome power of DNA sequence alignment (and its ability generate molecular phylogenies is truly awesome). The bottom line is that we can observe, today, processes of mutation, indels, and recombination that do cobble together different bits of proteins. If you wish to make a claim that these processes are inadequate to explain protein evolution, you need to support that claim with something other than bald assertions.
Is this so difficult to understand?
I understand that you are taking the "Joe Gallien" position that functional proteins cannot grow longer. To each his own.DNA_Jock_{April 2, 2015
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DNA_Jock: "You have shifted your argument. On the FSCO/I vs needles thread, you argued that the sort of short peptides that might be accessible via random walk (I used the example of a stable alpha helix) could NOT confer a selectable advantage" Not true. The problem is not that whether a peptide is short or long. A signal peptide is functional because it is part of a recognition network. I have no idea if the miPEP171b peptide has a specific secondary structure or not. My point is that an alpha helix, in itself, has no specific function. And that longer proteins are not built by adding some generic isolated functional alpha helix to another one and to another one. Again, homology can detect recombination. Secondary structure in itself is not function, and is not selectable. A functional peptide, however short, is functional. Maybe selectable. Whatever its secondary, or tertiary structure. But if it is not an intermediate step to a longer functional sequence, it does not explain the longer functional sequence. Is this so difficult to understand?gpuccio_{April 1, 2015
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DNA_jock, The reason people who oppose Darwinian evolution call such things fairy tales is these hypotheses are oft touted as fact - but they can only be considered factual as if they were not we would struggle to be able to accept or explain UCD otherwise. That is to say, I think the evidence that short peptidic sequences with simple folds can combine over time to produce hugely complex proteins is very weak. I am not talking about repetitive sequences for example where proteins are involved in structural or architectural aspects of cells, I am talking about complex cellular machinery found all the way back to some of the most basic forms of life itself. FYI I would not be personally surprised if short proteins could merge (I.e. the genes) and give a functional protein but functional here is again quite key in terms of complexity and also necessity. the other aspect of this is it is quite clear that many of these non coding regulatory RNAs that are being discovered are actually quite necessary in the control of the genes they help to regulate nd other processes necessary to life of that organism. Therefore this in a very simple sense raises 2 aspects of increasing the level of complexity that evolution must account for: 1) even less mutations are allowed than previously (as in this non coding space which is functional mutations are more likely to be deleterious to the organism) 2) even more than just a gene must arise through evolution, and many coordinated so with their regulatory counterparts as several studies are showing that many of these non-proteinacious products of the genome are in fact misregulated or mutated or aberantly expressed in cancer and other disease states. These to many people with an open mind to the ID vs materialist debate cause further doubt on the ability of naturalistic processes to solely account for this level of complexity in the genome.Dr JDD_{April 1, 2015
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Interesting, gpuccio. You have shifted your argument. On the FSCO/I vs needles thread, you argued that the sort of short peptides that might be accessible via random walk (I used the example of a stable alpha helix) could NOT confer a selectable advantage, yet here you are touting the functionality of a 5 amino acid peptide. Now you appear to be hanging your hat on the idea that functional proteins cannot grow larger -- the "Joe Gallien" position, as it were. Is this correct?DNA_Jock_{April 1, 2015
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There are many data suggesting that, in general, the proportion of non coding DNA is related to the complexity of organisms. Mattick has defended that concept in many papers.
Mattick has said this is many papers -- if he's ever made a genuine effort and defending such a claim I've not read it.wd400_{April 1, 2015
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Gpuccio,
Indeed I quoted Mattick. You seem not to like him. And so?
You didn't quote Mattick; you mentioned his name. Why do you think I don't like him? I only disagree with the idea illustrated with his (in?)famous plot. The relation between "complexity" and the amount of noncoding DNA is spurious, in my opinion. It's fair to say that eukaryotes (especially multicellular ones) are structurally more sophisticated than prokaryotes. But among eukaryotes there's very little if any correlation between phylogeny or complexity (however defined) and the amount (or proportion) of noncoding DNA. Even the contrast between prokaryotes and eukaryotes is not necessarily connected with their "complexity"; a more probably reason is the vast size of bacterial effective populations, making them susceptible to extremely small selection pressures. I'll explain that in detail if you want. Anyway, there are eukaryotes with hardly any noncoding (let alone junk) DNA, and they are not "simpler" in any way from their close cousins. Whatever the human complexity, the amount of noncoding DNA in our genome is not particularly outstanding, even among mammals (for example most marsupials have got significantly larger genomes but more or less the same amount of coding DNA; ditto for tarsiers, aardvarks, armadillos and many other mammal groups), not to mention many amphbians, lungfishes, and even shrimps. Parrots and corvids are thought to be very intelligent, but they have much less noncoding DNA than ostriches.Piotr_{April 1, 2015
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Aurelio, There isn't any theory of evolution and there isn't any evidence that prokaryotes can evolve into something other than prokaryotes. That means universal common descent can't even get started. As for ATP synthase- that "progress" has nothing to do with unguided evolution.Joe_{April 1, 2015
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Piotr: I apologize for the duplicate post. There was a problem with the upload. I am not trying to make my arguments "heavier" by sheer brute force! :)gpuccio_{April 1, 2015
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Piotr: Indeed I quoted Mattick. You seem not to like him. And so? My simple point is that there may be real effects and exceptions, and that exceptions should be understood, before building theories upon them. Regarding complexity, while I can agree that there is no simple way of measuring it in species, I would definitely say that a general gradiemt of complexity can be traced, in form, functions, biochemical networks, epigenetic regulations. With more complex forms emerging later than simpler forms. Would you question that eukaryotes are mopre complex than prokaryotes? Or that metazoa are more complex than unicellular forms? Just to know. And, even if maybe you are not available to think that humans, with their extremely complex nervous system and their cognitive abilities, are more complex than other metazoa, well, I tend to think so.gpuccio_{April 1, 2015
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