The paywalled paper’s Abstract reads, in part, “We reflect that a broad misunderstanding of pseudogenes [“formerly, junk DNA”], perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution.”
Now, even “pseudogenes” is pejorative, never mind “junk DNA” (cites as evidence by Darwinists)
Calling the shift in perspective “simply incredible,” Evolution News and Science Today reports,
A variety of other non-transcriptional functions are documented in the paper, including stabilizing chromosomes, mediating transcript-splicing, and regulating recombination. Thus, in many cases copy numbers of pseudogenes seem to have functional importance, where deviations from the normal genetic state causes disease. They predict: “It is expected that further links between human pseudogene polymorphisms and complex diseases will be identified in the coming years”
The implication is that one reason we presume pseudogenes are functionless is because we haven’t been looking for their functions. And why didn’t we look for their functions? Because we presumed they were functionless! So there’s a circular aspect to the reasoning here. It has created the science-stopping junk-DNA paradigm, which has prevented us from understanding what pseudogenes really do.
Evolution News, “Nature Reviews Genetics — Pseudogene Function Is “Prematurely Dismissed” at Evolution News and Science Today
The authors of the paper, of course, avoid pointing out that the presumption of uselessness was anchored in the comfortable fit between useless junk in the genome and the idea of unintelligent evolution.
Evolutionary thinking is the cause that ultimately created, nurtured, and sustained the junk DNA paradigm. Yet the paper adopts a wholly evolutionary approach, and for this reason never identifies evolutionary thinking as the root problem. The closest the authors get is when they recount how the very first paper to identify a pseudogene (published in 1977) dismissed its potential function as a “relic of evolution”: …
Evolution News, “Nature Reviews Genetics — Pseudogene Function Is “Prematurely Dismissed” at Evolution News and Science Today
But Darwinism seems destined to die in small doses.
Never mind, Jonathan Wells’ The Myth of Junk DNA seems to be holding up well.
Dawkins illustrated the importance of this issue (at least for people like him):
It’s not much of an argument:
Junk DNA is non-functional.
Therefore, God does not exist.
When function is found for Junk DNA then it is evidence that God does exist, right?
‘When function is found for Junk DNA then it is evidence that God does exist, right?’.
Hehehe. Atheist theologians will find a way during their next conclave to solve the dilemma.
‘It is ‘junk’. ‘Oh wait, it is functional!’ ‘We guessed it!’ ‘Oh wait, but not ‘functional-functional’. ‘Functional as we see fit!’ ‘Did we say ‘junk’? ‘Oh my dawkins, ain’t Science (with caps, unlike ‘god’) cool’?
Insert philosophical add-on (e.g): ‘God does not exist! We know it, although our brains are kluge! Evolved brains are un-reliable except when related to atheistic Evolution (with caps, unlike ‘god’!). Then you can trust them! No doubts! And no faith required here! You do not even need to think about the details! It is true and it will be forever and ever. For sæcula sæculorum.’ Amen.
Are introns mostly junk?
The Function Wars: Part I. Quibbling about the meaning of the word “function”
OK Sev, why don’t you put your genome where your mouth is: how much of your DNA do you want to get rid of as “junk”? Just think, if 90, or 50 or even 20% of your genome is really useless junk, then you don’t need it. Your cells would be more efficient without all that junk, right? Just think, you’d be a superman without having to carry around that excess baggage! So go ahead, which parts do you want to toss out? In a few years you’ll be able to find a clinic willing to delete “bad” genes, so why not remove all the “junk” you have identified. No takers? Oh, maybe you’ll hang onto all that DNA? After all, if the functional parts have gone from 2% to 10% to 30% or even 80%, who knows, maybe science will find out 98% of it is needed by some cell or other at some point in your development.
This is sort of like the “we don’t use 90% of our brain” myth that was common a few decades ago. I did not see many people sign up for voluntary lobotomy.
‘@5 Fasteddious: ‘This is sort of like the “we don’t use 90% of our brain” myth that was common a few decades ago. I did not see many people sign up for voluntary lobotomy.’
Oh, that silly one 🙂 I had thougth science and myth were opposites.
‘We do not know the meaning of ‘function’. But we know for sure that when that meaning embarrasses us, then it is not the good one’.
4. Researchers routinely construct intronless versions of eukaryotic genes and they function normally when re-inserted into the genome.
You can live without one of your two kidneys, without your tonsils or your spleen. And even without your two legs.
That does not mean they are ‘functionless’.
Question about this point, Sev:
>”About 98% of the introns in modern yeast (Saccharomyces cerevisiae) have been eliminated during evolution form a common ancestor that probably had about 18,000 introns…”
Since all we have to work with are the modern forms of yeast, how do they know there used to be more introns which are now gone?
EDTA – the paper that found this is here (and there’s a blog post here). From the blogpost:
In the paper, the authors explain that they mapped 250 introns in 20 yest species, and looked at their patterns of loss and gain (using a standard phylogenetic approach).
Bob O’Hara claims that
Translation, they simply assumed that common descent (their unproven hypothesis) was true.
Small problem with their unwarranted assumption of common descent, They have no empirical evidence that the transformation of one species of yeast into another species of yeast is remotely feasible. For example, as “one (evolutionist) explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”
Dr, Hunter further comments on the disingenuous nature in which Darwinists tried to ‘massage the data’ in order to give the preferred answer that fits their theory of common descent.
Yet, no matter how much Darwinists may ‘massage the data’ in order to try to get the data to fit their preferred theory, the fact of the matter is that, number one, they have no evidence that the transformation of one species into another species is remotely feasible,
Number two, the genetic data, when looked at clearly and soberly without Darwinian blinders on, actually supports Intelligent Design not Darwinian evolution:
‘But in the past few years, the tide has shifted within the field. Recent studies have revealed a wealth of new pieces of noncoding DNA that do seem to be as important to our survival as our more familiar genes. Many of them may encode molecules that help guide our development from a fertilized egg to a healthy adult, for example. If these pieces of noncoding DNA become damaged, we may suffer devastating consequences like brain damage or cancer, depending on what pieces are affected. Large-scale surveys of the genome have led a number of researchers to expect that the human genome will turn out to be even more full of activity than previously thought.
In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, “turns out to be doing stuff.”
For Gregory and a group of like-minded biologists, this idea is not just preposterous but also perilous, something that could yield bad science. The turn against the notion of junk DNA, they argue, is based on overinterpretations of wispy evidence and a willful ignorance of years of solid research on the genome. They’ve challenged their opponents face to face at scientific meetings. They’ve written detailed critiques in biology journals.’
https://www.google.com/amp/s/www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.amp.html
‘Junk DNA’ plays a vital role in embryo development’:
‘Strings of seemingly nonsense DNA play a surprising structural role in the early development of embryos, writes Michael Lucy.
In mammals, almost half of the genome is made of repetitive stretches of DNA known as retrotransposons whose purpose has baffled scientists. Historically this genetic code has been known as ‘junk DNA’, though in recent years it has become clear that it is anything but disposable.
In a paper published in Nature Genetics, a team of German and American researchers has now shown that retrotranspons play a surprising and significant role in the development of embryos’.
https://cosmosmagazine.com/biology/junk-dna-plays-a-vital-role-in-embryo-development
Earth to Bob O’H- Your side cannot explain the existence of introns. You have nothing that can explain gene editing and splicing. So please, get a grip and buy a vowel.
Fasteddious @ 5
Wrong. The point about “junk DNA” is that it’s assumed to be neither good nor bad. It could be removed without affecting the organism one way or the other. Cells would not become more or less efficient, they would just chug along the way they are. If neuroscientists could reliably identify the DNA that has no useful function then I would have no objection in principle to having it removed but why undergo the risks of neurosurgery to remove something that is not doing anything one way or the other?
@ Seversky: ‘The point about “junk DNA” is that it’s assumed to be neither good nor bad. It could be removed without affecting the organism one way or the other. Cells would not become more or less efficient, they would just chug along the way they are’.
Wrong.
‘In a paper published in Nature Genetics, a team of German and American researchers has now shown that retrotranspons play a surprising and significant role in the development of embyros.
The researchers looked at a kind of retrotransposon known as LINE1 elements, which were known to be involved early in the process of embryo creation. These elements are “highly expressed” in that phase, which means that they are read by the cellular machinery in order to produce RNA.
By blocking or promoting the reading of the LINE1 elements at the two-cell stage of development in mouse embryos, the team found that too much or too little expression made development stop’.
No development = no cells ‘chugging along’.
https://cosmosmagazine.com/biology/junk-dna-plays-a-vital-role-in-embryo-development
“Saved By Junk DNA: Vital Role In The Evolution Of Human Genome”.
‘Stretches of DNA previously believed to be useless ‘junk’ DNA play a vital role in the evolution of our genome, researchers have now shown. They found that unstable pieces of ‘junk’ DNA help tuning gene activity and enable organisms to quickly adapt to changes in their environments.
https://www.sciencedaily.com/releases/2009/05/090528203730.htm
Sev @ 16. The improved efficiency would be in the cell replication process. If the vast majority of your DNA does not have to be copied into every daughter cell, every time, then the process requires much less energy and matter, i.e. occurs more efficiently. This would, of course, affect more than your brain since all your cells have the same DNA load – information to pass on to their daughters.
Bob O’H @ 11,
And a thanks to BA77 for bring out the point I was leading to: if one has to assume common descent in order to conclude that introns are being lost, then the claim of introns being lost cannot be used as evidence for evolution: circular reasoning.
EDTA – eh? Where did anyone say that intron loss was being used as evidence for evolution?
Evolutionists, beware before calling something ‘useless/junk’. Will you ever learn?
‘Tonsils are small organs in the back of the throat. As part of the lymphatic system, they play an important role in the health of the body. Tonsils were once thought to be a useless part made obsolete by evolution. When bothered by an infection, doctors once prescribed the removal of the tonsils through a tonsillectomy. These small organs are actually quite useful, though’
‘Though small and seemingly useless, tonsils have several uses. The tonsils prevent foreign objects from slipping into the lungs. Think of them as goalies for the throat. They also filter bacteria and viruses. On top of all that, they produce white blood cells and antibodies, according to the Mayo Clinic’.
‘According to the American Academy of Otolaryngology, these bumps on the back of the throat are the “first line of defense as part of the immune system.” For example, tonsils sample bacteria and viruses entering the body through the mouth or nose and flush them using lymph. Lymph is a clear and colorless fluid; the name comes from the Latin word lympha, which means “connected to water,” according to the National Lymphadema Network”.
https://www.google.com/amp/s/www.livescience.com/amp/62447-tonsils.html
Bob @ 21.
I mis-read; never mind.
So ‘junk’ DNA a.k.a. ”we make **** up as we go along / typical evolutionary mindset / saying we do not know is forbidden” regulatory properties are, after all, important.
But they knew it, of course. 🙂 We never said ‘junk’!
Tumor-driving mutations discovered in the under-explored regions of the cancer genome
“Looking into the non-coding genome is really important because these vast sections regulate our genes and can switch them on and off. Mutations in these regions can cause these regulatory switches to act abnormally and potentially cause—or advance—cancer,” says Helen Zhu, student at OICR and co-first author of the study.
https://m.medicalxpress.com/news/2020-01-tumor-driving-mutations-under-explored-regions-cancer.html