A “completely unknown biology,” says a researcher. The paper on “glycoRNAs, or noncoding RNA strung with complex sugars called glycans” is still in preprint:
“There really is no framework in biology as we know it today that would explain how RNA and glycans could ever be in the same place at the same time, much less be connected to each other,” senior author Carolyn Bertozzi, a chemical biologist at Stanford University, told The Scientist in October.
Kerry Grens, “The Science News that Shaped 2019—“A completely unknown biology” ” at The Scientist
Remember when all that non-coding stuff was a vast library of junk that was evidence for Darwinian evolution?
Junk RNA? The Scientist doesn’t mention junk in either the article linked to, or the original report.
Bob O’H:
Here’s the start of the little blurb on this discovery:
Biologists are too embarassed to call “non-coding RNA” what once it was called, “Junk DNA.” But everyone around here remembers the argument. We remember the ENCODE project. We remember all the protestations. And we remember how wrong biologists were.
Of course they would be. It would show they were utterly clueless about basic biochemistry.
this post mentioned so called ‘glycans’….
honestly, how many of you heard of glycans and the glycome ?
from NewScientist:
“Move over, DNA. Life’s other code is more subtle and far more powerful
“Our cells use a sugary language to identify and interact with each other.
“It turns out that every type of cell in our bodies has a unique sugar coating.
“And whenever anything interacts with a cell, it must recognise that sugar code and use the appropriate secret handshake.”
“use the appropriate secret handshake.” ????
“use the appropriate secret handshake.” ????
in other words, to use a PASSWORD …
i am only a stupid mechanical engineer, but are biologists – natural science graduates – really suggesting, that cells use PASSWORDS ??? first DNA code, now this ?
and all that happened by random unguided natural process ?
It seems that biologists really believe in miracles …
Someone should call the doctor…
Full article is here:
https://www.newscientist.com/article/mg24132230-300-move-over-dna-lifes-other-code-is-more-subtle-and-far-more-powerful/
Bob O’H
From a paper
Dr. Palazzo has received several awards and is an editorial board member of the journal PLoS One.
It’s good to know that he’s clueless about biochemistry. It must certainly be true of everyone else he is connected to.
We might be tempted to pay attention to something they said.
Silver Asiatic – read what PaV wrote carefully.
Martin_r @4:
Excellent insightful commentary! Thanks!
From this OP:
“A completely unknown biology” huh?
Glycans May Bind to RNA?
Mammalian Y RNAs are modified at discrete guanosine residues with N-glycans
Silver Asiatic,
Thanks for the link you posted @5:
Non-coding RNA: what is functional and what is junk? (2015)
An atlas of human long non-coding RNAs with accurate 5? ends (2017)
From this OP:
“Junk” DNA?
The Science News that Shaped 2019
I assumed that Bob O’H was trying to say something, but that was my mistake.
An atlas of human long non-coding RNAs with accurate 5? ends (2017)
Thanks, OLV.
It certainly must be astonishing for people who believe the lies they tell themselves.
Another reminder that the basic dogma is wrong and that the evolutionary high-priests should be held in contempt. It’s not only that so much is unknown, but that explanations on what is already observed are false and must be rejected.
Silver Asiatic,
The information posted @9 & @11 is mostly a follow-up to what you posted @5.
Note the progression 2015-2017-2019.
Let’s see what we get in 2021.
🙂
There’s a debate? Interesting.
This finding “advances the debate”.
I think that means, “one side keeps losing”.
Silver Asiatic @12:
“It certainly must be astonishing for people who believe the lies they tell themselves”
Exactly! Good point. Thanks.
OLV
Thanks, yes. As above, the “debate”, keeps “advancing”.
I wonder when one side will eventually concede. Or will they hold out to the bitter end?
Silver Asiatic and Martin_r:
Have you ever been in a long flight and have seen the stuffs attached to the back of the seat in front of you? One is used to place the food trays they serve for breakfast, lunch or dinner. Another -at the eyes level- is used to display information.
Now, let’s assume we don’t know what that stuff is for. We could get rid of all that stuff and test the plane to see if it flies. After confirming that the plane flies just fine without all that removed stuff, the airline starts to notice an increasing loss of passengers to other airlines that still have that “junk” attached to the back of the seats in long flights. That’s a surprisingly unexpected result, isn’t it? 🙂
Another way to look at this is by playing loud rock music to a crab dancing on a table. As we remove the crab legs one at a time we notice that the crab starts missing the rhythm and slows down considerably. After removing the last leg the crab stops dancing completely. Conclusion: the crab got completely deaf, hence its legs are associated with the hearing system. 🙂
Testing functionality is not a joke. It’s a serious task that must be done carefully and with open mind.
Silver Asiatic @16:
“I wonder when one side will eventually concede. Or will they hold out to the bitter end?”
No, they won’t concede. They will hold out to the bitter end. It’s the nature of the human nature.
We must humbly admit that we can’t change it. C’est la vie, mon ami! 🙂
Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification (2019)
Interactions between short and long noncoding RNAs
Here’s a clear example of the shamefully negative consequences of the dogmatic reductionist approach to research influenced by the close-mindedness associated with some Darwinian ideas.
Interplay Between ncRNAs and Cellular Communication: A Proposal for Understanding Cell-Specific Signaling Pathways
Why don’t we see more ID objectors in this discussion?
Are they afraid of serious scientific discussions?
We know that a few distinguished biology or biochemistry professors* have commented here in this website before, but have left after running out of valid anti-ID arguments. ????
(*) professors LM (UofT) & AH (UofK) for example
Jawa – I think most of us decide it’s not worth it. It’s been repeated many times that we know what a lot of “junk DNA” is, so we know it’s not functional for the organism (a lot of it is selfish transposable elements). We know a lot of it gets transcribed, but still isn’t functional for the organism. Finding another function for some non-coding DNA isn’t really a big deal evolutionarily: we already know a some of it has function.
This message never seems to get across, though. People around here seem to get triggered by “junk DNA” (as well as another phrase I used above: if you can’t guess what it is, just wait).
Bob- your position cannot account for DNA based organisms. You have to be given them to start. And even then you don’t have a mechanism capable of producing eukaryotes given starting populations of prokaryotes. All you and yours have are arguments from extreme ignorance.
Good luck with that.
Bob O’H
I’m sure you recall when evolutionists (with the same kind of confidence you are showing here) stated that Junk DNA had no function. They used this as evidence for evolution. Later, the same evolutionists were “surprised” to find some function. They claimed it was less than 1% of ncDNA. Then later, they were less surprised when that percentage increased.
So, to say now “it’s no big deal” to find function makes sense, yes.
But what we’ve seen is a breakdown in credibility among those who made bold claims and were proven wrong. It seems that today’s bold claims will suffer the same consequences.
If I was a researcher, trying to convince the public and “get the message across”, I’d be a lot more apologetic about recent falsifications of my own claims.
My first response wouldn’t be “it’s no big deal”. I think that would just undercut credibility more and indicate that the researcher is arrogant and can’t admit his own ignorance and blind-spots.
Silver Asiatic –
No, I don’t, even in the late 80s, when I started a Genetics degree and we didn’t know what junk DNA was.
Bob O’H
My point is that you still don’t know what it is.
As for the 1980s, and claims prior to that …
Ohno believed that non-coding base sequences had no function. Thus the term “Junk”.
Ohno’s views
Silver Asiatic –
Well, perhaps you should have written that, rather than “I’m sure you recall when evolutionists (with the same kind of confidence you are showing here) stated that Junk DNA had no function.” It’s difficult to respond to what you were trying to say when you actually say something different.
As for Ohno, you seem to be confusing one person’s opinions from the early 70s with what was known in the late 80s. Quite a lot happened between those two times.
Bob O’H
Ok, I’m sorry I made that more difficult. Ohno – an evolutionist. Stated Junk DNA had no function. I think that’s an illustration of what I said. Evolutionists claimed that Junk DNA had no function, but in fact, they really didn’t know.
In the 70s, Ohno claimed he knew what Junk DNA was, but he was wrong even though the name he gave it and his understanding of it was retained for a long while. Yes, as you said, in the late 80s, you didn’t know what Junk DNA was. Now you still don’t know. But you assured us that whatever we discover about it in the future will not be a “big deal”.
Given the points above, I can’t put a lot of trust in what you said.
how did this appear on the scene?
Molecular choreography of pre-mRNA splicing by the spliceosome
ID on steroids? 🙂
Sonic hedgehog in vertebrate neural tube development (2018)
More ID
Development of the basal hypothalamus through anisotropic growth
SA – I guess you’ve conceded that I can’t “recall when evolutionists (with the same kind of confidence you are showing here) stated that Junk DNA had no function.” And when did Ohno, even, state this? Certainly not in his So Much ‘Junk DNA’ in our Genome paper, where he suggests possible functions (an points to centromric sequences as non-coding but having a function).
And where did Ohno claim he knew what junk DNA was? He made some suggestions, but what he wrote was clearly speculative – he didn’t present a lot of empirical evidence (certainly not or what we now know as pseudo-genes). Of course, we now know that he was largely wrong – although there are pseudo-genes, we actually know that a lot of junk DNA is ERVs and the like – selfish DNA.
another evident ID showoff? 🙂
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach
Bob O’H:
There are now articles saying that transposable elements–what you seem to now consider as ‘junk,’ is the real driver of evolution.
Pav – Can you point to these articles? I’ll predict that that’s not what they say.
DNA Transposons and the Evolution of Eukaryotic Genomes
https://www.annualreviews.org/doi/10.1146/annurev.genet.40.110405.090448
Diversification of the Caenorhabditis heat shock response by Helitron transposable elements
https://elifesciences.org/articles/51139
Helitrons on a roll: eukaryotic rolling-circle transposons
Helitrons seem to have a major role in the evolution of host genomes.
https://www.cell.com/trends/genetics/fulltext/S0168-9525(07)00270-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0168952507002703%3Fshowall%3Dtrue
Thank you Pw, but I’m not sure those are the papers PaV was thinking of.
PaV claimed “There are now articles saying that transposable elements … is [sic] the real driver of evolution.”
What does “DNA Transposons and the Evolution of Eukaryotic Genomes” say?
So, a major source not “the real driver”. i.e. there are other sources, indeed other major sources.
Next, “Diversification of the Caenorhabditis heat shock response by Helitron transposable elements”. This doesn’t say anything about whether TES are a major force, or the major driver, of evolution. It does give one example where a transposon seems to play a large role in the evolution of stress responses.
So how about “Helitrons on a roll: eukaryotic rolling-circle transposons”? Does this show that TEs are “the real driver of evolution”? Alas not: what they do say is “Helitrons seem to have a major role in the evolution of host genomes.”.
So these don’t support PaV’s claim. Perhaps PaV himself has some references to back him up.
Bob O’H
Ohno created the term Junk DNA because he claimed that non-coding DNA had virtually no function.
He was proven wrong.
I’ve been responding to your statement:
The falsification of Ohno’s claim was a big deal. His prediction based on evolutionary theory proved false.
Now you make a prediction stating that finding more functions for non-coding DNA is not a big deal.
At the same time, you don’t know what Junk DNA is.
So, your prediction has no substance and deserves no credibility.
You’re trying to make a prediction about an entity that you haven’t even understood fully yet.
From there, you use sophistry and hair-splitting to try to score a point.
That’s defensive and shows a lack of integrity in your theory itself. This is your life’s work – you shouldn’t need to nit-pick. But the failure of claims about non-coding DNA being Junk is now upheld as a failure for evolutionary theory so I understand your defensiveness.
I know how the game is played.
Ohno (and all of his disciples) were proven wrong.
For you, this is “no big deal”.
If, however, he had been proven right, his claims would be held up as great vindication and a victory for evolutionary thought.
It’s a double-standard.
So, you down-play the failures of the “junk” predictions. Ohno was just “speculating”. If he had been correct, he would have been “advancing evolutionary theory”.
I find this kind of game-playing to simply underscore the weakness of evolutionary theory. It lacks integrity. You’re willing to make claims about what functions we might find for non-coding DNA in the future.
There’s already work being done to overturn your notion that it is selfish DNA:
Not so selfish after all ? Key role of transposable elements in mammalian evolution
https://www.titech.ac.jp/english/news/2019/045702.html
This summary on recent findings was published last month:
https://evolutionnews.org/2019/12/jonathan-wells-was-right-noncoding-dna-continues-to-show-function/
SA –
If you read the paper I linked to, you would see that he was actually suggesting functions for it.
In comment 22 Jawa asked “Why don’t we see more ID objectors in this discussion?” My response was to point out it’s not worth it. I think you’ve proven my point very well: unlike you, I actually read what he wrote, and found out that you were wrong (Ohno was actually suggesting functions for junk DNA). Your response? Ignore it, and keep repeating the same falsehoods. If you want to have a serious discussion about science, that would be great. But it means you have to be serious about it.
Bob
I pointed out that you were making claims about what future discoveries of function in non-coding DNA would mean (“no big deal”), at the same time while you don’t know what NC-DNA is.
Ohno’s claim about Junk DNA was proven wrong, and it was not his suggestion that it might have some function.
I noticed that. You talked about what the early theorists about Junk DNA said before you had read Ohno’s paper. Then you read it this week, searching for a “gotcha” as when he said it might have some function. So, you weren’t informed about it before now.
If you think you’ve scored enough points for evolution to win this battle, then you shouldn’t have a need to post here any more. But I think you’re going to find increasing challenges to your theory, and such things do continue to be a big deal.
But we do know what most of it is! There’s even a wikipedia page on them.
Read the paper and stop repeating falsehoods. It was his suggestion that junk DNA had a function. And FWIW, he was actually not totally wrong: some non-coding DNA is indeed pseudo-genes. I’m not sure if his spacer theory has stood up, but I haven’t checked.
Bob
I believe you are trying to say that evolutionists never made false predictions about Junk DNA. That it was known and predicted that non-coding DNA would have the functions we now know it does, right? The term “Junk DNA” was never meant to signify “the remains of nature’s experiments that failed” like “fossil remains of extinct species” and there never was a challenge to understand why non-coding sequences were conserved?
Regarding the spacer theory, in the item from Evolution News I posted they mention it.
Sa
No, I’m certainly not saying that. It was certainly predicted by Ohno himself that junk DNA would have a function, but certainly wasn’t “known” when he made the prediction. His prediction was not entirely wrong: some junk DNA is pseudo-genes, although most isn’t.
Bob O’H:
I just did a Google search: https://www.cell.com/trends/genetics/pdf/S0168-9525(17)30112-9.pdf
The first sentence of, I presume, the abstract ( I don’t have access):
And here’s something from 1998: https://www.eurekalert.org/pub_releases/1998-02/UoG-TEMH-090298.php
The title of the article: “Transposable Elements May Have Had A Major Role In The Evolution Of Higher Organisms.”
PaV – thank you for giving a link to another paper that doesn’t support your claim “that transposable elements … is [sic] the real driver of evolution”. Yes, they affect evolution, and I don’t think many people would object to the claim that they have a major effect. But the drivers of evolution? That’s a different claim, and I’m still waiting for you to provide the evidence.