New Genes May Arise From Junk DNA 110
An anonymous reader writes: Junk DNA (or noncoding DNA) is a term for section of a DNA strand that doesn't actually do much. Huge tracts of the human genome consist of junk DNA, and researchers are now finding that it may be more useful than previously thought. "For most of the last 40 years, scientists thought that [gene duplication] 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. ... 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."
This allows of big modifications (Score:5, Interesting)
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This is completely wrong. It is used for everything! Formerly called Junk DNA by ignorant people, it is now called Regulatory DNA. It is the code that calls the function calls that is the gene DNA. That is why the field is called Genomics now and not Genetics.
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I think you mean there are many subfields, including Proteomics.
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Absolutely. It was labeled "junk" because some egotistical scientist could not figure out what it does. If it befuddles him or her, who is no doubt really Smart, then it must be junk.
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And we definitely _know_ that most of it is junk - just a pile of SINEs, LINEs and other crap.
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What we don't expect is that a significant fraction of junk actually has a useful function.
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Here's more (with a nice plot): http://journals.plos.org/plosg... [plos.org]
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Junk DNA is junk DNA.
It may be "junk" in the sense that we can't currently ascribe particular functions to many such sequence elements, but it's also "not junk" in the sense that it's energetically expensive presence is at least not selected against (and might be favorable).
In my opinion, regardless of whether or not the sequences in question have specific functions, the term "junk DNA" is misleading and dismissive of the history of biological science.
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However, for bacterial cells (which are much smaller than eukariotic cells) DNA replication is a significant burden and so they have very l
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Some of the "Junk" DNA is packet headers with golay error correction codes and crc check codes. Some of it is activation switches. A lot of it is "mothballed" DNA that is saved for emergency situations.
Biologists need to have at least some network training, these days. 8-)
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magic super-power (more often than not, lethal)
As a general rule of thumb, things that insta-kill me in utero generally do not qualify as "super-powers" in my particular dialect of English.
I have a suspicion (Score:5, Interesting)
I suspect that in the future, scientists will laugh at the notion of "junk DNA" and think of it as just as much of a myth as "you only use 10% of your brain".
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Unless you think General Relativity is completely false, Dark Matter is some form of matter that acts upon visible objects in the universe. So take your pick, is Einstein wrong, or is there just a class of matter we haven't detected yet.
Science is wrong but becomes less wrong over time (Score:5, Insightful)
So take your pick, is Einstein wrong
Science proceeds toward understanding of nature that is less wrong* over time. So it's very probable that Einstein didn't have the whole story.
Aristotle was wrong about the relationship between mass and acceleration due to gravity. Galileo Galilei proved him wrong. Galileo was wrong about gravity being independent of location. Isaac Newton proved him wrong. Newton was wrong about the effect of gravity at what we now call relativistic speeds. Albert Einstein proved him wrong. Einstein was still wrong about "God doesn't play dice with the world." Each of them stood on giants' shoulders to become less wrong.
* Yes, "less wrong" is a thing. Assuming that "wrong" is an ungradable adjective [wikipedia.org] like "unique", "perfect", and "parallel" [wikipedia.org] is a fallacy [rationalwiki.org].
Re:Science is wrong but becomes less wrong over ti (Score:4, Insightful)
Likewise, NEWTON WAS NOT WRONG! That was the foundation for more than 200 years, from 1687 to 1915.
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No one said Einstein couldn't be wrong. But parsimony would suggest the simplest explanation is simply matter that's awfully hard to observe, rather than completely tearing the heart out of modern physics.
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Uh, no. There is nothing fundamentally incompatible between GR and QM, other than the piece that's missing that joins the two together.
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Aristotle was wrong about the relationship between mass and acceleration due to gravity. Galileo Galilei proved him wrong.
IMHO, this is the birth of science, rather than an evolutionary step. For example, back in Aristotle's days, projectile motion was understood as straight-line motion, until the object "runs out of steam" (impetus) and drops straight down. The general idea was that knowledge comes from wise men and old books, rather than actually looking at the world. With that kind of a mindset, it's impossible for the knowledge to evolve in an objectively better direction. To me, Galileo's big idea was to try and take the
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Einstein was still wrong about "God doesn't play dice with the world."
Spotted the atheist troll.
Spotted someone unfamiliar with Einstein's public statements about his disbelief in quantum mechanics.
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astronomy it is dark matter or something similar
Dark matter is not some astrophysics catch-all explanation. Dark matter and dark energy separately refer to a specific observed discrepancy for which we don't have an answer yet.
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so.... a catch-all for what isn't known. Gotcha.
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No. "Specific" and "catch-all" are pretty different.
Dark energy, for example, is essentially the discrepancy between the observed expansion rate of the universe and the quantity of detectable matter in the universe.
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same thing in other sciences. archeologists say anything unknown was a religious ritual. astronomy it is dark matter or something similar
I can inderstand that, since the public punishes anyone who says the words "I don't know". Even if it is the best truth known...
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a message from Visual Studio 2038 (Score:1)
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A better analogy might be huge blocks of code that's been commented out. It may have been unable once, and may be unable in the future but right now it can't do anything other than get copied along with everything else.
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except that it's a physical system, and the commented sections may play a role in spacing, separation, structure, provide binding sites for regulatory proteins etc.
just because it isn't transcribed doesn't mean it's not critical to proper function.
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:) i'm not about to argue that we know what the rest is. but i'd also argue that our genomes are a bunch of hacked together spaghetti code where even commenting some bit out could end up being super critical to proper function.
*how the hell did deleting a comment break the fucking program?*
*i don't know, but it works, so just fuck off*
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My impression of so-called 'junk DNA' is that they're like some conditional (if/then) statements in a programming language: the condition required to run that code may rarely, if ever, occur, therefore that code sits there 99.9999999999% of the time doing absolutely nothing. Except, of course, for that one time when it does run. We've made much progress in the last 100 or so years with regards to understanding the mechanisms of life, but we're far, far away still from understanding all of it.
Hmm, Mod Up or Reply, tough choice, but I have to go with reply - hopefully someone else will mod your comment up - because I agree with you completely. The old "90% of the brain is unused" thing is exactly the right comparison to make, one I've been using for a long time whenever the subject of junk DNA comes up. The fact is that nature simply doesn't operate so inefficiently. The idea that evolution would have maintained huge tracts of completely unusable genetic code serving no purpose at all for million
Re:I have a suspicion (Score:4, Informative)
Scientists haven't thought "junk" DNA as junk for years. It's a shorthand expression for genes that have no obvious expression, though they've known for a long time that junk DNA may have regulatory functions, and that most certainly junk DNA is a potential seed bed of evolution because the likelihood of deleterious mutations in junk DNA sequences is much lower.
Huh? (Score:5, Interesting)
What is heretical about novel new genes arising out of junk DNA? Molecular biologists have known for many years that so-called "junk" DNA played a number of roles; regulatory, and that most certainly novel genes could arise.
Oh, I get it, this is the idiotss otherwise known as "scientific journalists" hyping up a rather unremarkable finding, and fixating on the word "junk" much as they, in ignorance and the need to sex up stories, concentrated on the word "God" in the "God particle"
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Quit touching my junk
Your junk is microscopic; be glad that anyone is willing to go to the trouble of touching it.
Re:Huh? (Score:4, Interesting)
What is heretical about novel new genes arising out of junk DNA?
Labeling it "heresy" is just bad journalism. Biologists have long suspected that new genes could arise from "junk" DNA. The news is that now there is some actual evidence, rather than just conjecture.
Re:Huh? (Score:4, Informative)
As I said, it's a fairly unremarkable finding. I remember references to junk DNA sequences having the potential to be expressed in the early 1990s.
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This is part of the problem of the public understanding of science.
You hear idle speculation 20 years ago and, with clenched fists and tears welling up in your eyes, whisper "it's gospel truth" and go around believing, wholeheartedly, unsubstantiated nonsense.
Now, far off in the future, someone says "hey, here's some evidence that indicates that this idea may have some merit" you scoff and complain that this is "unremarkable" old news.
You'd be amazed at how many "scientific" beliefs people have that are no
The Goddamn Particle (Score:2)
"God particle" appears to have originated in Dell Publishing's censorship of "goddamn particle", which was originally chosen because of the difficulty faced by particle physicists in producing an excitation of the Higgs field. Had the title of the book [wikipedia.org] instead been The G.D. Particle, there probably wouldn't have needed to be as much "sex[ing] up".
Possibly labelled heresy because... (Score:5, Interesting)
What is heretical about novel new genes arising out of junk DNA? Molecular biologists have known for many years that so-called "junk" DNA played a number of roles; regulatory, and that most certainly novel genes could arise.
There is a small percentage of biologists which really, really would like acquired traits to be heritable (as a work study job in college, I worked in the lab of one of them, and we were cautioned not to talk about his theory outside the lab).
Every so often, one of the proponents of the idea of heritable changes due to environmental pressure, or more formally, either Lysenkoism or Lamarckism, tries to find a mechanism that could make it work. Even though it's never been demonstrated (the biologist in the lab I worked at was attempting experiments with, among other things, chelodina longicolis diets, to force physical changes, which he hoped the offspring would inherit, even though not on that diet).
This theory is what's known as "soft inheritance".
The main premise for its development in the first place was that Joseph Stalin was all pissy about genetic being a non-Soviet idea, and wanted an nice, Soviet alternative that better fit the ideology he put forth. This actually influenced a lot of decisions in Soviet agriculture that didn't work out badly enough that they ended up importing wheat from the West.
The last go-round was trying to use introns as a mechanism whereby he introns were involved in making traits heritable (and before that, it was endogenous viruses, such as PERV - Porcine Endogenous Retro Virus). Those were the main ones. The've also tried to explain it with varying degrees of gene methylation, and so on. Todays flavor is non-coding DNA (the correct scientific name for "junk genes").
Unless the can demo it in plants, mice, or fruit flies, etc., don't expect that the idea will go anywhere directly.
The sad part is, if they had concentrated on the punctuated equalibria model, which the article mentions, instead of trying to explain it as a short scale inheritable phenomenon, the might have had a really great argument.
(Yes, I am in the 90% who are skeptical about this, without further evidence and perhaps a demo).
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how about DNA methylation? There's some evidence that it might be heritable
It is, generally as undesirable mutations, although must such methylations are repaired by the MATA mechanism based on the p50 gene and the genes at the end of the long arm ob c20.
Typically, you can get "thalidomide effects" and similar mutations, if done at exactly the right time, and impacting a germ cell involved in the gametogenesis, but no long chain mutations of the type this article (and Lysenkoism) is interested in have been demonstrated in the lab.
In order to trigger them, you have to specifically
Hubris (Score:2)
Re:Hubris (Score:4, Insightful)
It's short hand. Scientists haven't thought of it literally as junk in many years. It's like "black hole" and "god particle", funny little shorthand references that don't necessarily reflect what researchers think at all.
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Well no shit... (Score:4, Informative)
That's always been the key to genetic evolution. This is somehow new??
Genetic spare parts? (Score:4, Interesting)
So basically there's a bunch of spare stuff laying about which, under the right circumstances, can actually change into something new and unexpected.
This is good, because it means we have more potential than what we already have. It also explains why organisms aren't constrained by things which came before them.
I still get the impression we still don't understand how all this works. Which is good. Because people start thinking science has answered everything, only to find out there's tons more to go.
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We don't. We have laboriously identified the purpose of specific areas, but you can't a priori deduce the function of arbitrary DNA turned into a protein, and you can't currently simulate the working environment of the enzyme, or understand the full extent of the "reactome" chain of related processes and consequences of a particular change.
Lots of what we have learned is transferred from in vivo experiments of gene suppression. Fortunately the massive similarity between many living organisms allows us to po
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Is it likely that there are more hidden gems out there? Sure. Is it likely that a significa
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More than the past few years (Score:2)
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As far as I know, a moniker is a 'nickname' you give yourself, so unless there's some highly creative recombination going on, it was likely some science journalist who coined the term 'junk dna'!
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No such thing as junk DNA, known for ages now! (Score:2, Interesting)
The term Junk DNA is a laughing stock within the scientific community for ages now.
It was 'blank slate' and 'we are all the same under the skin' retards pushing for such an ignorant assumption.
We have known for a while now that essentially all non transcribing DNA is highly used as "regulator factors". This is the DNA that controls the transcribing DNA. You can think of the 'gene' DNA as function calls. The 'junk' DNA is the code that calls those function calls, where and when! It is the most important DNA
New genes may arise from junk DNA (Score:1)
And another 'heretic' theory... (Score:4, Interesting)
... is that hybridization might play a very big role in the appearance of new species [macroevolution.net], in several different ways:
- apomixis, producing some (most often aneuploid) news organism (which then clones itself indefinitely by fragmentation, budding or parthenogeny, becoming a distinct species all by itself)
- polyploidization, where the different DNA sets just add up and coexist side by side (like in pretty much every angiosperm on the planet, and many other plants, as well as many fish, reptile and salamander species - like Ambystoma platineum)
- symbiotic association, as seen in lichens and also in how mitochondria fused with bacteria into eukaryotes
- recombinational stabilization (a.k.a allohomoploid nothospeciation), where the slightly mismatched chromosomes from different DNA sets of compatible but different species pair up into complex heteroduplexes that end up fragmenting or fusing chromosome segments when the first generation of hybrids starts mating - which very well might be how two chimpanzee's chromosomes fused into our own bigger Chromosome 2.
In the cases mentioned of TFA some of the 'exotic' genes may be explained more simply as introgressions from a past hybridization event with a different species followed by backcrossing [wikipedia.org].
big surprise (Score:4, Interesting)
so I'm not carrying all this stuff for nothing. I'm so glad to be a member of a species that thought otherwise for so long. I like my appendix too, by the way, also the other 80% of my brain, thanks very much.
Re:big surprise (Score:5, Interesting)
Almost everything you can summarise in a line is bollocks news headlines. Science is, unfortunately, a lot more complicated than that.
We (probably) use all our brain. Just not all on conscious intellectual thought. It's not hard to see that - cut into the brain and you ALWAYS lose something, it just might not be immediately obvious what.
The appendix may well be a store of gut bacteria that reseeds the gut in the case of illness. Which kinda makes sense, the same way you save some of the cheese by-products to help make the next cheese. And also explains why when it blows it's quite so serious - it's basically an inactive mini-gut getting infected and exploding.
It's just that it's hard to prove these things definitively because they were never DESIGNED to do that. They just happen to do so. And so they may be doing ten jobs well or one job badly or no jobs at all and it's incredibly difficult to say which for a global population at any static point in time.
Similarly "junk" DNA is as it says - noncoding. We think. But it might be doing other stuff. Hell, it may just be purely structural, or it may be remnants of old coding, or it may just have got mixed in the same way you accidentally mix in insects into basically every foodstuff you eat (yes, literally) but because it "just works" and nobody notices, it doesn't really matter.
Or, maybe, it's coding is not as simple as we expect. Nobody's every really SEEN things like DNA do their jobs. You can look at it, you can simulate it, but nobody really knows exactly what's going on in the millions of full strands inside a HUMONGOUS cell that replicates billions of times over in the space of a matter of months.
The problem is that science is so complicated that you can't understand it, and headlines are all you pick up. How many moons does the Earth have? Depending on which scientists you ask, and which definition of "moon" you use, it can be zero, one, two, twenty-seven or hundreds. Nothing is as simple as you can explain in one sentence. Or even one article. Or even one research study and paper. Or even one field of expertise.
junk may not really be junk (Score:4, Interesting)
Clever biochemists will figure these out soon enough.
Junk DNA is not Junk (Score:2)
keep all the pieces (Score:1)
The first rule of intelligent tinkering is to keep all the pieces.
-- Aldo Leopold.
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The first rule of intelligent tinkering is to keep all the pieces.
-- Aldo Leopold.
Good point.
Biological systems are very wasteful in many ways, but very conservative in others. It is quite possible that those are kept "just in case", so to speak. 8-)
Fear (Score:2)
siRNA mRNA miRNA circRNA not new (Score:2)
Basically, it's a frame shift method of writing code. If any of you had ever had to use old style 4 bit encoding schema to store data, you'd know that.
It allows one set of instructions to adapt for different environmental conditions. We don't just bootstrap our DNA, we use it to fold and generate proteins when we need them, and then we discard it when we don't need it. But the instructions are still there.
Now, that said, some of it is inserted viral code from infections, or instructions on how to grow gills
and not just out of the 'junk' dna (Score:3)
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