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Can new genes arise from junk DNA?

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From Quanta Magazine:

Emerging data suggests the seemingly impossible — that mysterious new genes arise from “junk” DNA.

Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration.

For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions.

Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.

The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. “Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis. More.

Hmmm. Whenever scientists use terms like “somehow springs into existence,” find your boots, your bicycle lock key, or your car keys.

But this is a good conversation to be having.

Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.

Evolution isn’t what we used to think.

See also: The Myth of Junk DNA

and

Talk to the fossils: Let’s see what they say back.

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Comments
wd400 @23, You are certifiably insane.Mapou
August 25, 2015
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What's the average size of a de novo gene? What functions to they play?wd400
August 25, 2015
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wd400:
It is certainly true that we didn’t think de novo genes would play a big role in evolution. But if they do it seems that biological function is easier to find in sequence space than we had previously thought.
Even if the size of the sequence space is 4^23000 ? Not a chance if all you have is Darwinian RM+NS. The math never lies. Your lying soul is the problem.Mapou
August 25, 2015
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Deep down, all Darwinists know that the combinatorial explosion, aka the curse of dimensionality, kills Darwinian evolution dead. After all, the mathematical argument against DE designing just one gene is simple and brutally unforgiving. The average human gene consists of about 23,000 nucleotides. The search space for a single gene is 4^23000! That's 4 raised to 23000! No stochastic search algorithm has a chance of finding anything in such a huge space. Having a massively parallel computer as big as trillions upon trillions of universes would be no better than a wooden abacus. The "Scrabble tiles dumped onto the floor" metaphor is a joke in comparison. And that's just for one little gene. Now imagine how big is the search space of an entire genome with its thousands of genes. All Darwinists are certifiably insane. As Feyerabend once wrote, "it's time to cut them down to size and give them a lower position in society."Mapou
August 25, 2015
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bFast
However, the ID scientists have been talking for a long time about the statistical chance of a gene arising from junk. They would suggest that even the “one or two” position is painfully implausible. That de novo genes are common, and important, is just so very “not predicted” by the Darwinian model.
I'd say that if we take the calculations of Doug Axe and Steven Meyer seriously, we'd have to conclude that if we looked at 10,000 proteins in each of the 20 million species on earth and then looked at a trillion identical planets each with 20,000,000 species with 10,000 proteins its extremely unlikely we'd find a single de novo protein. After all, he calculated the likeliness of coming up with a single folded protein domain as 1 in 10^70. So ID is proven or is completely demolished on this one observationREW
August 25, 2015
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SA,
“Why do you think this is a problem for evolution”? Then days later. “We knew about all of this decades ago.”
It's certainly very common for IDers to make a bigfuss about some new finding without saying why it's relevant to evolution. News here, for instance, has dedicated many column inches to HGT without ever explaining why it a problem for evolutionary biology. Likewise, people frequently make a lot of noise about topics that are actually core evolutionary biology. My favorite is that radical idea that the environment influences gene expression (i.e. quantitative genetics). Those points seem relevant, so I often point them out.wd400
August 25, 2015
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Complex organisms can gain complexity through De novo gene arisal…which needs junk DNA…which complex organisms have more of…which is WHY they are complex…which is why junk DNA has pervaded NS despite being such an expense to the organism to replicate
That's not possible, of course. But something not so far from it might well be. For a big hulking multicellular creature the cost of one more ALU/SINE/repeat/transcript is so small as to make little difference. So such junk accumulates. There is good evidence for this by the way. All else being equal, creatures with high energetic needs (bats and birds for instance) for which selection agaist junk would be stronger have smaller genomes than those with little eneregetic constraint (salamanders have huge genomes). Likewise, organisms with large effective population sizes(and therefore strong selection) generally have smaller genomes. Multicellular creates of course generally have low effective population sizes. So, if de novo genes do indeed play an important role in evolutoin, complexity could indeed beget complexity. Complex organisms, by their nature, are more likely to accrue junk. That junk is more likely to generate new complexity and away we go. Something not unlike the idea of constructive neutral evolution. I have to admit I don't quite understant the glee in the rest of the thread. It is certainly true that we didn't think de novo genes would play a big role in evolution. But if they do it seems that biological function is easier to find in sequence space than we had previously thought. It's hard to imagine, for instance, that humans are carrying around a Poldi because it was designed to later become a gene in mice!wd400
August 25, 2015
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Dr JDD: Will the tautologies ever end? No need answering.PaV
August 25, 2015
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But Begun and collaborators found several genes that were present in only one or two species and not others, suggesting that these genes weren’t the progeny of existing ancestors. Begun proposed instead that random sequences of junk DNA in the fruit fly genome could mutate into functioning genes. Yet creating a gene from a random DNA sequence appears as likely as dumping a jar of Scrabble tiles onto the floor and expecting the letters to spell out a coherent sentence. The junk DNA must accumulate mutations that allow it to be read by the cell or converted into RNA, as well as regulatory components that signify when and where the gene should be active. And like a sentence, the gene must have a beginning and an end — short codes that signal its start and end.
You'll notice that this is exactly how IDers approach these types of questions. Yet, when we do, we're told we don't understand probabilities, we don't understand evolution, etc., etc. But, then, when it comes to analyzing how novel genes come about, they use it to rule out the possibility of the new gene arising from nowhere. So, I guess we do understand evolution, and we do understand probabilities.PaV
August 25, 2015
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Actually, I see this one being spun around to fit the narrative. Complex organisms can gain complexity through De novo gene arisal...which needs junk DNA...which complex organisms have more of...which is WHY they are complex...which is why junk DNA has pervaded NS despite being such an expense to the organism to replicate....but the junk DNA provides benefit as it allows complexity through novel gene appearance. Just what was predicted all along.Dr JDD
August 25, 2015
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This one is beyond belief. I would have thought it was a satire.
“Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis.
He obviously doesn't understand evolution. First we have junk. Then we have new genes. He's confused. They don't "spring" into existence. They "arise" or in some cases "emerge". Ahhhh - even better. They don't "spring into existence", they're actually "selected" from junk. :-) They might be able to salvage Darwin that way.Silver Asiatic
August 25, 2015
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the logic! the logic! It's a good thing we had that junk DNA around because it provides us with de novo genes... It's a good thing my parents named me Rob, because that's what everyone calls me...Robert Sheldon
August 25, 2015
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Cue wd400: "Why do you think this is a problem for evolution"? Then days later. "We knew about all of this decades ago."Silver Asiatic
August 25, 2015
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Moreover, the essential genes were somehow incorporated into the 'bicycle' while the bicycle was being peddled, i.e. while the cell was busy being alive.bornagain77
August 25, 2015
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// follow up #9 // The irony is killing. A novel gene from junk-DNA, it sure is every atheist's dream, right? Okay, now we find de novo genes in abundance — let's assume, arguendo, that they magically appear from junk-DNA. Only now they start to realize that — given materialism — there is (still) absolutely no way forward from here:
Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said. “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
It makes one wonder what the big idea was all along.Box
August 25, 2015
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“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
Exactly my question. Assume that a perfect new gene is offered by random mutation. What is the next step towards expression / function? Where does the regulation come from? Without regulation there is no function. Will there be some random placement of transcription factors — a blind search for the starting and end position? Preceded by nucleosome / histone modifications? If a new protein is produced, what regulates its concentration so that it can be tolerated by the organism? How does the protein get to its proper position? And so forth. IOW how do you build gene- and protein-regulation from scratch? And how does all the experimenting stay within the boundaries of homeostasis? How can an unregulated (or even poorly regulated) new gene not be a huge threat to the organism?Box
August 25, 2015
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PaV:
Now, the EVO’s can’t get away from the fact the de novo genes are abundant. This ought to, right now, without a second’s more delay, debunk Darwinism, population genetics, and the whole nine yards. But, don’t hold your breath.
Darwinian evolution has been debunked many times over. One more humiliation will neither hurt it nor help it. But this fight was never about science, right?Mapou
August 24, 2015
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Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.
"De novo genes make up a significant part of the genome." This was NOT predicted by evolution. The opposite was predicted. In other words, the whole theory of evolution was based upon false assumptions about the genome and now we see that the genome does not support their claims. "Scientists have little idea of how many there are or what they do." Or, for that matter, of where they came from! Yet, evolution is a fact and the genome is evidence for evolution??? I see. I wonder if the text books will be changed to reflect this fact/reality or if kids will simply continue to be snowed with evolutionary claims that are not supported by the data. Mutations in these genes can cause catastrophic failures - and these are the genes that are least understood! Yet evolution is a fact??? It seems these mysterious genes are the most important ones yet no one knows how many there are, where they came from, or what they really do. Yet evolution is a fact. There is no need to sweat the minor details. And these evolutionists complain when people don't believe them and swallow their ad hoc explanations whole. It seems to me that they aren't as bright as they seem to think they are. Or perhaps, we are not as dumb as they think/hope we are.tjguy
August 24, 2015
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The development of gene families seems potentially darwinian. We still, of course, have to wrestle with where the first gene in the family came from. If there were a single gene family -- if all genes could be traced back to a single ancestor gene, then Darwinism would be writing a compelling story. I remember dialoguing a few years back on a different site. I was dialoguing about de novo genes with what appeared to be a biologist. He suggested that the human lineage should have no more than one or two de novo genes, and that those genes should play a minor role. This smacked of a message that wasn't too inconsistent with Darwinian prediction. However, the ID scientists have been talking for a long time about the statistical chance of a gene arising from junk. They would suggest that even the "one or two" position is painfully implausible. That de novo genes are common, and important, is just so very "not predicted" by the Darwinian model. I see de novo genes to be a major challenge to the theory.bFast
August 24, 2015
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The article that keeps on giving:
Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said. A human-specific gene called ESRG illustrates this mystery particularly well. Some of the sequence is found in monkeys and other primates. But it is only active in humans, where it is essential for maintaining the earliest embryonic stem cells. And yet monkeys and chimps are perfectly good at making embryonic stem cells without it. “It’s a human-specific gene performing a function that must predate the gene, because other organisms have these stem cells as well,” McLysaght said.
"A human-specific gene performing a function that must predate the gene . . ." So, if the ancestral organisms don't have the gene, then where did it come from? Yet, even if they didn't have the gene, they must have had the function, else the stem cells would have been affected. However, if the ancestors have the function, then advantage can NS use to "evolve" the gene? [What came first, the chicken or the egg?] The EVO's must not be sleeping well at night these days.PaV
August 24, 2015
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Some more from Quanta:
Yet if life’s toolkit is so limited, how could evolution generate the vast menagerie we see on Earth today? “If new parts only come from old parts, we would not be able to explain fundamental changes in development,” Bornberg-Bauer said. The first evidence that a strict duplication model might not suffice came in the 1990s, when DNA sequencing technologies took hold. Researchers analyzing the yeast genome found that a third of the organism’s genes had no similarity to known genes in other organisms. At the time, many scientists assumed that these orphans belonged to families that just hadn’t been discovered yet. But that assumption hasn’t proven true. Over the last decade, scientists sequenced DNA from thousands of diverse organisms, yet many orphan genes still defy classification. Their origins remain a mystery.
Ouch!!! This has gotta hurt.PaV
August 24, 2015
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From Quanta:
Some scientists say they may even be common. Just last month, research presented at the Society for Molecular Biology and Evolution in Vienna identified 600 potentially new human genes. “The existence of de novo genes was supposed to be a rare thing,” said Mar Albà, an evolutionary biologist at the Hospital del Mar Research Institute in Barcelona, who presented the research. “But people have started seeing it more and more.”
This mirrors the dilemna that electrophoresis created for Darwinists in the 60's, leading to Kimura's "Neutral Theory." NT is Darwinism without natural selection: an oxymoron. Now, the EVO's can't get away from the fact the de novo genes are abundant. This ought to, right now, without a second's more delay, debunk Darwinism, population genetics, and the whole nine yards. But, don't hold your breath. With the rise of whole genome analysis (WGA), with it becoming more prevalent, accurate, and cheaper, this was the risk the Darwinists were running: that de novo genes would appear, not allowing them to any longer rationalize how new genes (and functions) could arise via gene duplication. The day of reckoning is upon them. They're running out of "just-so" stories (although I might be very wrong in underestimating their ability to imagine implausible scenarios, and then swallow them. For example, the NT was first vilified before being swallowed up into Darwinian lore.). We're living in interesting times.PaV
August 24, 2015
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"For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse:"JDH
August 24, 2015
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“Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis.
Not very Darwinian, I would say. Where is the natural selection? Where are the random mutations?Mapou
August 24, 2015
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