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New Genes May Arise From Junk DNA
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."
Thanks for the post!!
One of the properties of junk DNA is that it can endure brutal mutations since it's not used for anything. So over time it can change a LOT. Then suddenly another mutation suddenly activates it by mistake and *poof* you have a new magic super-power (more often than not, lethal). Starting from a crucial gene won't work since the slightest modification will reduce your survival rate, since by definition it's crucial.
Non-Linux Penguins ?
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".
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"
The world's burning. Moped Jesus spotted on I50. Details at 11.
... is declaring something you don't understand "junk". I always found the concept of junk DNA to be unbelievably short-sighted.
That's always been the key to genetic evolution. This is somehow new??
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.
Lost at C:>. Found at C.
I know that there's a big difference between "hey, i've got a cool idea" and actual scientific proof, but as is usually the case in such things there were a lot of precursors to this "once-heretical" idea gaining traction. Greg Bear's Darwin's Radio is one of the more famous SF examples (though certainly not the only, and quite possibly not even the first) of speculation that junk DNA could actually be useful for something. It came out in 1999, and although i don't know if he based his ideas on any research that was happening at the time it certainly wouldn't surprise me.
This Space Intentionally Left Blank
I always felt dismay when people would talk about "junk DNA". Who came up with that ridiculous moniker? Why not just tell the truth, namely, there is a large proportion of DNA that we have (had?) no clue what it is for? The message that has been sent for years was that such DNA was doing nothing, was therefore evolutionary dead weight, hence the ghastly "junk DNA" naming. Biologists should have protested far more strenuously against what probably was, for the most part, journalistic exuberance (not the word I would otherwise use, but we all know the context.)
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 in the end, as it controls the level of expression and timing of transcribing DNA, the whole LOGIC of the system.
They don't call it genetics any more for a reason. They realized how ignorant it was to only look at Genes. Now it is called genomics, as in whole genome is important!
WARNING: Unreachable codon detected
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 like "unique", "perfect", and "parallel" is a fallacy.
That's what happens when we eat too much junk food.
EINSTEIN WAS NOT WRONG! That is the foundation of the last 100 years of science!
"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 instead been The G.D. Particle, there probably wouldn't have needed to be as much "sex[ing] up".
Likewise, NEWTON WAS NOT WRONG! That was the foundation for more than 200 years, from 1687 to 1915.
... is that hybridization might play a very big role in the appearance of new species, 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.
Maybe we deserve this world ?
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.
Its just poorly understood DNA sections. The ENCODE project studied non-coding DNA and estimated that up 80% could be important. Some codes for RNA which until recently was hard to measure because it decays so rapidly. Some may encode for epigentic control like methlyation locations. Some may control the folding of histone-DNA complexs, forcing sections sections DNA to be nearly one another for reasons we dont understand yet.
Clever biochemists will figure these out soon enough.
It seems pretty simple, if a gene was useful in the past at some time, it is possible it might be useful in the future. Therefore it is handy to write down old unneeded sequences just in case. How many you write down would be related to the desire to facilitate mutations or prevent them as the case may be. FYI this was actually hinted at by creationist who pointed out the probability of gene sequences spontaneously forming being astronomically low. Clearly biology was cribbing from previously useful sequences.
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).
The first rule of intelligent tinkering is to keep all the pieces.
-- Aldo Leopold.
Uh oh, now I am afraid an HERV will suddenly get activated, pop out, and start infecting people.
This posting is provided 'AS IS' without warranty of any kind, implied or otherwise.
... tracts of junk DNA!
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, but at the rate we're going with overuse of fossil fuels, you might need that soon.
-- Tigger warning: This post may contain tiggers! --
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.
The world's burning. Moped Jesus spotted on I50. Details at 11.
There is some evidence of non-random mutations, which has been called a "risk management strategy for evolution". Only certain parts of DNA chains tend to mutate, causing things like coloration and size to alter, and not the cartoon mutations of growing odd horns and limbs. It has been suggested that those regions of DNA, the "hot spots", are marked by the presence of "pseudogenes".
This and the idea of "co-opting" genetic material have been kicked around for some time now. But coming up with where some "random" mutation might come from is pointless in the face of hereditary traits being a limiter. Charles Darwin was inspired by animal breeding. Animal breeders are well aware you cannot cross breed two very different animals. They are also very aware that any odd mutation being bred with the general population that does not share that mutation will produce a hybrid. Breeding hybrids with the general population that does not share that mutation tends to "breed out" the mutation. We have this issue with white tigers. It's not albinism, but rather a specific mutation. To continue the mutation, we have to inbreed them, and the practice has been outlawed for obvious reasons. So no matter how many different ways a "random mutation" is explained, it still has to occur simultaneously in a large enough population that "breeding out" the mutation is not an issue.
But then again, sexual reproduction seems to confuse many people. Add science nerd joke here.
I'm not fat, I just have more junk in my DNA trunk.
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.
No no no no NO! Ptolemy was not wrong. Say it AGAIN! Ptolemy. Ptolemy. Yaaaaaaay, Ptolemy!
I thought it was "God does not play dice with the universe."
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 human out of the loop, using precise and systematic experiments to gain more direct knowledge of the world.
Escher was the first MC and Giger invented the HR department.
If Einstein is right then quantum mechanics is wrong. Either way something big is wrong...
Uh, no. There is nothing fundamentally incompatible between GR and QM, other than the piece that's missing that joins the two together.
The world's burning. Moped Jesus spotted on I50. Details at 11.
http://theory.caltech.edu/people/jhs/strings/str115.html
You can find any number of people discussing this if you search "general relativity quantum mechanics incompatible". It is a commonly accepted "fact". It could be wrong but you are against the consensus here.
Mosquitoes carry viruses between mammals. Some of these virus are mammal specific, but a number of unknown virus are transmitted regularly, that have cut sections of DNA from organism A and then inserts it into organism B via arthropod borne viruses. Interestingly, we do not look for these because they are asymptomatic. But, they still transfer large DNS sequences , with some genes, between us.
I prefer the "u" in honour as it seems to be missing these days.
I had two. The doctor was quite pleased when I let him keep them. He did most of the appendectomies in Brussels and had never had a patient with two until I showed up.
My Flemish doctor told my Mom I was a big faker. I don't know what my Mom told him after I nearly died.
But you don't listen. if scientists weren't so preoccupied with being liberal, grant grubbing fraudulent little shits, we'd get some work done.
I misread this as "old drunks".
"stuff we super-brilliant science types have not yet figured out but are too arrogant to admit ignorance of".
Just as the appendix was written-off as a "vestigial" organ for many decades (it's function was unknown by all-knowing scientists... so it HAD to be "leftover junk") and fault lines were just mysterious leftover cracks from the Earth's creation back when science denied plate tectonics (only finally accepted in the 1960s). For many decades, the experts were convinced, and told the public, that stress caused ulcers (now known to be caused by a particular bacteria). All the genetic material currently classed as "junk" will eventually be understood and history will label the current crowd of authoritative genius experts as closed-minded neanderthal knuckle-draggers akin to flat-Earthers. Of course, there are quacks out there with all sorts of quackery that OUGHT to be dismissed after being properly exposed, but the existence of quackery does not automatically give legitimacy to this sort of dismissal of something unexplained that is right before our eyes.
These dismissive labels slapped onto stuff by the scientific establishment (of any generation) are in fact supremely anti-science. These areas of the real world that are such a mystery are EXACTLY where new younger scientists should be probing with all their efforts in search of a Nobel prize and eager to make their predecessors look like out-dated dinosaurs; science needs this turmoil and churn in which the old fossils of the institutional ivory towers who've become too comfortable and set in their ways are nudged aside in favor of people with fresh eyes and big questions. History is FULL of scientists who stood on their authoritative pronouncements and reputations - and were later shown to be completely WRONG.
the human biome ?