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

Piotr: 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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DNA_Jock: I cannot understand your reasoning. I have no problem in function for short peptides. Absolutely none. Short peptides work as signals. The same is true of siRNAs. Signals are signals. Their impèortance and function is due to their role in a network of recognition and meaning. What I definitely don't believe is that long and complex proteins, which effect important biochemical functions, like enzymatic reactions and so on, can be explained as the result of recombination of short functional motifs. That's the meaning of what I wrote, and that you kindly quoted: "Are you saying that you can explain the emergence of long and complex proteins or domains or superfamilies (whatever you prefer) as the result of reasonable recombinations of an existing pool of short motifs, each of which was expanded because in itself it conferred a reproductive advantage? Are you imagining some pre-LUCA whose main activity was to synthesize short alpha helices or beta sheets, selected in name of I don’t know what perspective, or short DNA binding motifs which bind DNA without having any other effect…" You should remember that, for RV and NS to work, two different things are necessary: a) Some functional sequences, short or long, must be selected, expanded and fixed. b) Those sequences must be intermediate states to the complex functional sequence of the final protein. Now, there may be a lot of short sequences which are functional, as signals or in other ways, and which may be more or less selected. In no way that helps your theory, unless you can show that the long complex sequences are "built" from those intermediate sequences, which can easily be verified by homology studies. So, unless you can show that functional peptides like miPEP171b are steps to, say, ATP synthase (or whatever you like), I cannot see any argument on your side. And I still wonder what is your problem, beyond misunderstanding my thoughts and words.gpuccio_{April 1, 2015
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Gpuccio,
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.
Care to cite that data? But, please, not Mattick's "Dog's Ass Plot" or, as Ryan T. Gregory puts it,
[any] graphical representation of data in any field that, through a lack of clear axis labels, selective inclusion/exclusion of data, visual presentation style, and/or other questionable characteristics, generates a misleading interpretation of the data in the viewer, especially by implying an illusory pattern that is not supported by the available data.
If lungfishes, salamanders, onions, Easter lilies, etc. are "anomalies/exceptions", how do you know that humans aren't? And how is complexity measured? What's more complex? An eagle or an ostrich? An opossum or a human? A mouse or a bat? And how do you know?Piotr_{April 1, 2015
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Dr JDD, I have been quite aware of the functionality of short peptides for over 30 years, siRNAs for over ten. What surprises me is that gpuccio should be such a fan. Previously, he mocked the argument I was making about minimally selective peptides thus:
Are you saying that you can explain the emergence of long and complex proteins or domains or superfamilies (whatever you prefer) as the result of reasonable recombinations of an existing pool of short motifs, each of which was expanded because in itself it conferred a reproductive advantage? Are you imagining some pre-LUCA whose main activity was to synthesize short alpha helices or beta sheets, selected in name of I don’t know what perspective, or short DNA binding motifs which bind DNA without having any other effect...
To which I replied:
Yup, pretty much, but without the unnecessary value judgments. I am imagining some pre-LUCA’s who synthesized short alpha helices, beta sheets, helix-turn-helix motifs, etc., etc. and concatenations thereof, selected in name of some minimal selective advantage, such as DNA binding motifs which inhibit transcription, until they were out-competed by their fractionally less hopeless cousins. But, unfortunately, all the selection and extinction that has occurred since that time has badly fogged our view of this era. I doubt that we will ever know the historical truth about how early proteins did emerge, but – thanks to in vitro protein evolution studies – we do know a fair amount about what is feasible.
which drew the following response:
So I can apply the random walk model to any step which does not include selection. And I will accept NS only if it is supported by facts, not as a magic fairy accepted by default because of a pre commitment based on personal (or collective) faith.
and
Again, refer to my discussion about what science is. Science is not about what is possible, but about what is supported by facts.
Oookaaay. So I anticipate gpuccio arguing that, although short peptides are selectable in a modern context (as both of you insist), they are not selectable in a pre-LUCA context. All I ask for is some facts to support this position, not just "a pre commitment based on personal (or collective) faith".DNA_Jock_{April 1, 2015
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Why is it a surprise that short sequences are functional? Do you know what siRNA is? If RNA sequences si short can be so powerful why not peptides? Do you know anything about MHC class 1 peptide presentation?Dr JDD_{April 1, 2015
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DNA_Jock: I am afraid I don't understand your point, if you have one. Maybe my old age...gpuccio_{April 1, 2015
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gp, I'm just surprised to see you admit it openly. When you respond, citing "context", be careful to hold yourself to the same standards of evidentiary support that you demand of "evolutionists".DNA_Jock_{April 1, 2015
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tjguy #3, Exactly. And they are saying that we have the problem of the gaps )EugeneS_{April 1, 2015
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DNA_Jock: Yes, that's what the paper says. Why are you surprised? I believe that short peptides have already been considered functional in many cases. This is just one example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764427/pdf/fpls-04-00352.pdf "Small signaling peptides arise from genes that typically encode an N-terminal signal peptide region, one or more conserved peptide domains and variable regions that flank one or both sides of the discrete peptide domains. There are two structural classes of signaling peptides: small (5–20 amino acids) posttranslationally modified peptides, which are the focus of this review;" Emphasis mine. So, why are you surprised?gpuccio_{April 1, 2015
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JoeCoder: I will start with your point about the c-value enigma. I absolutely agree. 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. Obviously, there are many extreme exceptions and anomalies. But I believe that they should be studied individually, rather than considering them as a reason to derive a general conclusion. So, I agree with your points about that, which are very well expressed.gpuccio_{April 1, 2015
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A 20 amino acid peptide and a five amino acid peptide? And they're functional? Really?... I`ll get me coat.DNA_Jock_{April 1, 2015
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DNA_Jock: "How long are these “short regulatory peptides”?" In the quoted paper, in "Extended Data Figure 1: Characterization of the M. truncatula miPEP171b", two "short putative ORFs" are represented, one of 20 AAs, one of 5. I suppose that's a good example.gpuccio_{April 1, 2015
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gp, How long are these "short regulatory peptides"? ThanksDNA_Jock_{April 1, 2015
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JoeCoder: I have looked at your arguments, and I must say that I agree with many of the things you say. However, I will try to take time to give my perspective too, while wd400 prepares his answers. :)gpuccio_{April 1, 2015
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wd400: "Such sequences will continue to be found, people that think genomes are almost junkless will keep harking on them, all the while ignoring the good arguments for very junky genomes." Until, in the end, the genome will be found to be almost completely functional, and the "good arguments for very junky genomes" will remain as a very good example of bad arguments defended for a long time by a lot of intelligent people because of cognitive bias.gpuccio_{April 1, 2015
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Hi Joe, I did miss your commen. it'll take a little while to respond to your points, but i will try to in the next few days.wd400_{March 31, 2015
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@wd400
ignoring the good arguments for very junky genomes.
Yesterday I replied to your arguments on junk DNA in a previous thread, but that thread was almost dead so you probably didn't see it. I would appreciate your thoughts and feedback because I want to know whether I'm right or wrong :)JoeCoder_{March 31, 2015
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And, as correctly stated by Dr JDD, the point is simply that other sequences (like those in the primary transcripts of miRNAs) have revealed completely unexpected function
In ~0.005% of the genome. Such sequences will continue to be found, people that think genomes are almost junkless will keep harking on them, all the while ignoring the good arguments for very junky genomes.wd400_{March 31, 2015
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Mapou: "Yeah, science is the real enemy of Darwinists, not religion." Absolutely. Science (indeed, reality itself) is definitely on our side!gpuccio_{March 31, 2015
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wd400: And, as correctly stated by Dr JDD, the point is simply that other sequences (like those in the primary transcripts of miRNAs) have revealed completely unexpected function. And the whole field of unknown short regulatory peptides is still there for us to investigate.gpuccio_{March 31, 2015
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wd400: Thank you for meeting my expectations (see post #2) :) OK, your comments are welcome anyway. At least you give facts, which cannot always be said of others...gpuccio_{March 31, 2015
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The .005% is from all the primary transcripts of miRNAs -- the same sequences used in the paper. In the human genome alpha-sattelite sequences make a couple of percent of the genome, some of those, in the centromeres, are required. Other satellite classes add up to very little.wd400_{March 31, 2015
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Actually wd400 are they not about miRNA precursors of which much less were known as it included additional sequence space originally not included as "functional"? So what % of the genome does satDNA make up then?Dr JDD_{March 31, 2015
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gpuccio @2, Yeah, science is the real enemy of Darwinists, not religion.Mapou_{March 31, 2015
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Andre:
if you are sceptical about RM & NS you are no doubt a bible bashing fundamentalist that have no IQ.
Throwing a rabid dog in the arena is a favorite tactic of materialists and Darwinists. It will come back to bite them in the ass. Sooner than they think.Mapou_{March 31, 2015
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The trend is in one direction only
Well.. yeah. Could it be otherwise? But y'all might want to keep some perspective. Two of these links relate to miRNA in plants. Most people wouldn't count miRNAs as junk DNA to start with. Even if you did, all the miRNAs in the human genome adds up to about 0.005% of the genome.wd400_{March 31, 2015
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I'm sure this will just go down as "what they expected" as per every other discovery that dents their idealistic interpretation of the data...Dr JDD_{March 31, 2015
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This is getting more and more embarrassing for the believers in junk DNA! The trend is in one direction only and it is relentless. The places they can still hide in are getting fewer and fewer in number. They are still safe for now to be sure, but they gotta be getting worried as they watch purpose and function encroaching on their space.tjguy_{March 31, 2015
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One small step at a time, our understanding increases. Luckily. Our darwinist friends will certainly be busy to count their remaining treasured "non functional DNA", like a miser who counts his remaining coins. The era of the epigenetics of cell regulation is only at its starting point. Understanding can only increase, and new multiple levels of designed complexity will emerge. But, as Andre says, RM & NS can do anything after all. And Wagner will readily argue that all epigenetic regulations derive from multiple platonic networks of functional states. What's the problem?gpuccio_{March 31, 2015
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Darwinian evolution predicts that everything has function RM & NS can do anything, even replace all designers, seriously, and if you are sceptical about RM & NS you are no doubt a bible bashing fundamentalist that have no IQ. Evolution optimizer for function and that is a fact sure as oxygen.Andre_{March 31, 2015
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