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Science

Revolutionary Genetics Research Shows RNA May Rule Our Genome (scientificamerican.com) 80

Philip Ball reports via Scientific American: Thomas Gingeras did not intend to upend basic ideas about how the human body works. In 2012 the geneticist, now at Cold Spring Harbor Laboratory in New York State, was one of a few hundred colleagues who were simply trying to put together a compendium of human DNA functions. Their Âproject was called ENCODE, for the Encyclopedia of DNA Elements. About a decade earlier almost all of the three billion DNA building blocks that make up the human genome had been identified. Gingeras and the other ENCODE scientists were trying to figure out what all that DNA did. The assumption made by most biologists at that time was that most of it didn't do much. The early genome mappers estimated that perhaps 1 to 2 percent of our DNA consisted of genes as classically defined: stretches of the genome that coded for proteins, the workhorses of the human body that carry oxygen to different organs, build heart muscles and brain cells, and do just about everything else people need to stay alive. Making proteins was thought to be the genome's primary job. Genes do this by putting manufacturing instructions into messenger molecules called mRNAs, which in turn travel to a cell's protein-making machinery. As for the rest of the genome's DNA? The "protein-coding regions," Gingeras says, were supposedly "surrounded by oceans of biologically functionless sequences." In other words, it was mostly junk DNA.

So it came as rather a shock when, in several 2012 papers in Nature, he and the rest of the ENCODE team reported that at one time or another, at least 75 percent of the genome gets transcribed into RNAs. The ENCODE work, using techniques that could map RNA activity happening along genome sections, had begun in 2003 and came up with preliminary results in 2007. But not until five years later did the extent of all this transcription become clear. If only 1 to 2 percent of this RNA was encoding proteins, what was the rest for? Some of it, scientists knew, carried out crucial tasks such as turning genes on or off; a lot of the other functions had yet to be pinned down. Still, no one had imagined that three quarters of our DNA turns into RNA, let alone that so much of it could do anything useful. Some biologists greeted this announcement with skepticism bordering on outrage. The ENCODE team was accused of hyping its findings; some critics argued that most of this RNA was made accidentally because the RNA-making enzyme that travels along the genome is rather indiscriminate about which bits of DNA it reads.

Now it looks like ENCODE was basically right. Dozens of other research groups, scoping out activity along the human genome, also have found that much of our DNA is churning out "noncoding" RNA. It doesn't encode proteins, as mRNA does, but engages with other molecules to conduct some biochemical task. By 2020 the ENCODE project said it had identified around 37,600 noncoding genes -- that is, DNA stretches with instructions for RNA molecules that do not code for proteins. That is almost twice as many as there are protein-coding genes. Other tallies vary widely, from around 18,000 to close to 96,000. There are still doubters, but there are also enthusiastic biologists such as Jeanne Lawrence and Lisa Hall of the University of Massachusetts Chan Medical School. In a 2024 commentary for the journal Science, the duo described these findings as part of an "RNA revolution."

What makes these discoveries revolutionary is what all this noncoding RNA -- abbreviated as ncRNA -- does. Much of it indeed seems involved in gene regulation: not simply turning them off or on but also fine-tuning their activity. So although some genes hold the blueprint for proteins, ncRNA can control the activity of those genes and thus ultimately determine whether their proteins are made. This is a far cry from the basic narrative of biology that has held sway since the discovery of the DNA double helix some 70 years ago, which was all about DNA leading to proteins. "It appears that we may have fundamentally misunderstood the nature of genetic programming," wrote molecular biologists Kevin Morris of Queensland University of Technology and John Mattick of the University of New South Wales in Australia in a 2014 article. Another important discovery is that some ncRNAs appear to play a role in disease, for example, by regulating the cell processes involved in some forms of cancer. So researchers are investigating whether it is possible to develop drugs that target such ncRNAs or, conversely, to use ncRNAs themselves as drugs. If a gene codes for a protein that helps a cancer cell grow, for example, an ncRNA that shuts down the gene might help treat the cancer.

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Revolutionary Genetics Research Shows RNA May Rule Our Genome

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  • by shilly ( 142940 ) on Wednesday May 15, 2024 @02:28AM (#64473095)

    It’s so interesting to see how strong a role emotional investment plays in scientific work. The idea of being outraged at the prospect of ncRNA having a biological function is simply a neutral concept to me, as a lay person: could be right, could be wrong, the evidence base will decide. But for professionals who have devoted decades to crucial work on understanding the molecular biology of cells, it’s clearly a hand grenade, because it requires such a major rethink of their lives’ work. Thomas Kuhn really was onto something about the structure of scientific revolutions (thank you, Cambridge, for offering history and philosophy of science as part of the natural sciences Tripos for those of us who realised we liked thinking about science and talking about science, more than we actually liked doing science).

    • by martin-boundary ( 547041 ) on Wednesday May 15, 2024 @03:44AM (#64473181)
      It's not that simple.

      Among all of the things in Nature that are True and False, there are many, many, many more things that are False than are True. It's not a good idea to pick something at random and say "I wonder if it's True or False, someone should look at it, as I am neutral".

      Science is under a strong resource constraint. There are only so many scientists, and only so many labs, and only so many datasets in the world. Being neutral about what should be investigated is a sure fire way to waste those resources. Smart scientists are extremely skeptical about changing multi decade research projects based on reading speculations in a paper. It's much better to let a new idea prove itself on the fringes over 50 years, and then if it's still there the next generation of scientists can investigate it.

      The bit that Cambridge undergraduate education fails to convey properly is the sheer slowness of human knowledge acquisition. One spends a few years ingesting millenia of elegant solutions without all the false starts and dead ends that accompanied them, then the pace halts to a virtual standstill, for those who go on to postgraduate work. It's frustrating, but there it is. Royal roads and all that.

      • by shilly ( 142940 ) on Wednesday May 15, 2024 @03:54AM (#64473193)

        I'm not saying it's wrong to be neutral, or treating this topic simplistically. You're literally describing the core concept of The Structure of Scientific Revolutions, and why and how and when paradigms do and do not shift. I was commenting on the fact that when I've previously thought about this topic, I've thought about it the way you have here -- about resources and constraints and the need for skepticism, but that this article's language made me also consider an additional factor, above and beyond: emotional investment.

        I am also not convinced you're right about the pace of human knowledge acquisition if you mean the pace for humans as a whole. The pace within paradigms can be very fast: look at the increase in the speed and reduction in costs of genomic sequencing, and what that's enabled. It's just that paradigm shifts are understandably rare. If you mean that the pace at which any single scientist is able to advance human understanding, then I agree.

        • by Anonymous Coward on Wednesday May 15, 2024 @07:06AM (#64473415)

          I've thought about it the way you have here -- about resources and constraints and the need for skepticism, but that this article's language made me also consider an additional factor, above and beyond: emotional investment.

          Don't forget that all of those emotionally descriptive words were put there by a non-scientific writer who at best is viewing science through their non-scientific lens, and at worse is only sprinkling them in like spices in a food dish.

          These same writers would look at the posts here between yourself and martin and describe it as "a heated argument over differences of opinion that only did not come to blows due to a separation over the Internet"

          To copy/paste quotes does not tend to attract eyes, which is the primary goal of the writer.

          I wouldn't put much faith in their implication that any scientists are actually outraged simply due to a scientist writing a paper that disagrees with another paper.

          • by shilly ( 142940 )

            That is a truly excellent point!

          • by mcarp ( 409487 )
            yes, i wanted to say its more likely reporter is exaggerating than outraged scientists. Also this new info about non coding sequences doesn't invalidate your life's work about protein coding sequences. Its just new and should be exciting
        • Reasonable points. I'll add a few more thoughts: human knowledge acquisition doesn't just go one way, it can also go backwards for all sorts of reasons. Without introducing social/nonscientific reasons here, consider for example that much of the studies filling the journals are not replicable. It's not like people haven't tried. Weak foundations in an area can collapse progress and cause chilling effects. This is particularly important today, as many people think that meta analysis of existing data via AI
        • look at the increase in the speed and reduction in costs of genomic sequencing

          This has increased dramatically, but most of that came from the Human Genome Project. Mapping out a human genome for the first time was very slow, because there was no way to know where each little DNA fragment fit into place, but once that map was made then identifying where each fragment fit in became pretty easy.

          The parent is right about the overall pace of advancements. Scientific advancement is slower than science reporting would suggest, though I suggest that it's less about resources than it is ab

      • by gtall ( 79522 )

        " One spends a few years ingesting millenia of elegant solutions without all the false starts and dead ends that accompanied them"

        My own opinion is that merely ingesting the elegant solutions without plowing through the false starts tends to make learning a bit less deep since the false starts give one a perspective of why an elegant solution works the way it does.

      • by cusco ( 717999 )

        We're acquiring knowledge on an exponential curve now. The idea of waiting 50 years to start investigating a paradigm shift in a field like genetics is absurd. Less than half that time ago it took billions of dollars, thousands of scientists, and hundreds of labs to analyze the DNA of a single person over several years. Today a tech puts a cheek swab in the machine and emails the results in the morning. I could use free online tools to design a new gene and for a few bucks get a million copies mailed to

        • Exponential curves are difficult to detect or estimate, and in general they do not happen in complex systems. There's always some other factor that acts as a bottleneck, a resource that gets depleted and plateaus the curve, or even causes a crash or boom bust cycles. That other factor is obvious in hindsight, and impossible topredict in foresight.
          • by cusco ( 717999 )

            I don't think the rest of the world is going to be content to advance at the 19th century rate that you propose, they certainly weren't during the 20th century. The current acquisition rate of data comes out to something like one Library of Congress per hour just from IoT devices. The tools we have available to analyze it weren't even imagined a decade ago. The ability to distribute that analysis happens at exceedingly close to light speed. An exponential curve is easy to see once it has reached the 'kn

    • by Jerrry ( 43027 )

      From TFA: "Some biologists greeted this announcement with skepticism bordering on outrage."

      That fit's this quote to a T:

      "All truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident."--Arthur Schopenhaur

    • by backslashdot ( 95548 ) on Wednesday May 15, 2024 @11:01AM (#64474225)

      No. The article is fluff, really. First off we've known this about ncRNA for a while, maybe the whole extent of how much of a role it plays was not fully elucidated .. and is still not btw. That aside, we've known ncRNA is important. We've known it does things. Just look at the wikipedia article on ncRNA biological roles section: https://en.wikipedia.org/wiki/... [wikipedia.org] So, to be clear, 1. nobody's mad or shocked about this 2. No scientist I've know (and I know plenty) ever thought ncRNA had no function. In spite of that, the media for the past few DECADES has been claiming "scientists shocked that non-coding RNA/DNA has function" (references: https://phys.org/news/2009-10-... [phys.org] https://www.scientificamerican... [scientificamerican.com] https://www.dkfz.de/en/presse/... [www.dkfz.de] ) because one scientist FIFTY years ago referred to the non-coding region as junk DNA .. ironically in a paper wherein he literally proposed that it *wasn't* junk. I have been in science for decades and not one scientist I know has ever referred to or thought of the non-coding RNA or non-coding regions of DNA as useless. I'm telling you journalists go prodding scientists for skepticism. Yes, scientists are skeptical about EVERY new publication even when it confirms something we already knew .. and the media can inflate that. This new publication shows that ncRNA plays perhaps an even bigger role than anticipated .. BUT nobody is mad about it .. nobody's angry and sure as hell they're not mad about it in the sense that the Pope was mad at Galileo.

  • If we can find out what is going wrong in autoimmune diseases like MS or UC, we are now on track to tell the responsible genes to STFU?

    Where do I send money to?

    • If we can find the genes we........... might be in for a wait. Unfortunately while global emergencies can compress the lead times from discovery to invention to release to a couple of years, the aches , pains, and terminal calamities of us mere mortals are looking at decades.

      I'd sure as hell like them to figure out this ageing nonsense. No matter what we tell the kids, it pans out getting older is complete nonsense and I'd rather like my old body back.

      • Agreed. I would like my old back, back.
      • If we can find the genes we........... might be in for a wait. Unfortunately while global emergencies can compress the lead times from discovery to invention to release to a couple of years, the aches , pains, and terminal calamities of us mere mortals are looking at decades.

        I'd sure as hell like them to figure out this ageing nonsense. No matter what we tell the kids, it pans out getting older is complete nonsense and I'd rather like my old body back.

        I'm beginning to view things like Logan's Run as a bright possibility compared to the life we have to live. Past 35 life is pretty much a useless churn of obligations to other people, while everything you hold dear is stripped away from you by those obligations that can't be escaped. Granted, this is coming from an American, where hope is deemed evil and the only prayer any of us cling to is the prayer that we die before we bankrupt our entire family when our lives begin to ebb.

        Escaping the doomer in me for

        • by Kokuyo ( 549451 )

          I am glad that I am not you guys. My outlook kinda seems to make me more resilient despite the four individual incurable chronic diseases I have.

          Good luck to you anyway.

        • by mcarp ( 409487 )
          Lack of imagination, there's all that outer space to explore.
          • Lack of imagination, there's all that outer space to explore.

            And look at the absolute apoplectic spasms that people get into trying to say there's nothing worth visiting out there. As much as I'd love for us to get off this rock at some point, I don't think we have the long-term thinking required anymore. Two generations of MBA "ROI in one quarter or less" bullshit has humanity convinced that nothing is worth doing if it takes effort before ROI is realized.

    • What they'll find is that most of the non-encoding RNA is the biological small-print: legally binding EULA and a hard-boiled NDA, having any research institution's legal counsel quaking in their tan brogues.
    • Gene silencing techniques have been fussed with, but what this will show is more of the feedback loop between RNA and non-protein biological activities. Fussing with the behavior may be tricky as it could come down to turning particular cellular behavior up or down rather than on or off.
    • Viruses look to be one of the root causes if not the root cause. Other factors play a role because not everyone that gets the virus get MS.

      EBV, a herpesvirus that infects most people by adolescence and then lies latent in B cells throughout life, has long been a prime suspect. People who have had mono are at higher risk for MS. But although 99% of MS patients have had an EBV infection, 95% of those without MS have, too, making it difficult to pin down the virus’ effects.

      Ideally, researchers would track a group of young people who haven’t yet been infected by EBV to see whether those who contract the infection are more likely to develop MS than those who don’t. A team led by physician and epidemiologist Alberto Ascherio of the Harvard T.H. Chan School of Public Health found a clever way to do that. They probed a medical records database of 10 million active duty U.S. military personnel who enlisted between 1993 and 2013 and gave a blood sample every other year for HIV testing.

      Eventually, 955 soldiers developed MS. Of the 801 with sufficient blood samples, 35 were negative for EBV in their first blood test; all but one became EBV positive during the study before developing MS on average 5 years later. By comparison, only half of 107 MS-free study participants used as controls became EBV positive during the same period, the researchers report today in Science. That means an EBV infection multiplies a person’s risk of MS 32-fold, comparable to the increase in risk of getting lung cancer from heavy smoking, Ascherio says. None of the other common viruses Ascherio and his team tested for showed an effect. To bolster their case, they showed that people who eventually developed MS had a rise in levels of a protein linked to neural degradation after their EBV infection. Ascherio believes the study clinches the case. “How do you explain the fact that you don’t get MS unless you get EBV? There is no other alternative explanation,” he says.

      Hanan Polansky has the theory that many of these diseases with unknown causes are actually caused by latent or dormant viruses. Since that theory came out, there have been advances in knowledge. Viruses are contained within our genome, HERV-K, HERV-W. There's also something some scientists call transposable elements like LINE-1 transposons, that have some virus characte

  • "It appears that we may have fundamentally misunderstood the nature of genetic programming"

    Is that a concern for the genetic programming in the wild already, bio engineered crops? I am ignorant on the subject and assume it's different to gardeners cross breeding roses.

    • It is something that needs to be watched, but commercial biotechnology efforts would generally catch any issues. The modified plants are carefully tested and selected to insure that they have the desired properties. That noncoding DNA controls gene expression is not really a huge surprise to those in the industry. It is more the extend of the DNA that is involved. I would be more concerned with medical applications and university work, where the testing is usually much less complete. After all it is ha
    • by HiThere ( 15173 ) <charleshixsn.earthlink@net> on Wednesday May 15, 2024 @09:05AM (#64473745)

      That particular line is clearly wrong. We *did* assign the wrong weights to various factors, but the concept of control regions goes back at least 50 years. And we probably (almost certainly) still need to fine-tune many of the weights.

      E,g,: The cytoplasm of the Ovum contains a LOT more RNA machinery than does that of the sperm. What does this imply about heritable traits?

      • The cytoplasm of the Ovum contains a LOT more RNA machinery than does that of the sperm. What does this imply about heritable traits?

        My take: That they are in fine control of the allocation of precious resources.

        The sperm is a messenger, trying to deliver its copy of the plans to an ovum (the only one, or one of a very few, within reach) in competition with hundreds of millions of others, not all necessarily from the same male (or to bias the race toward others that have versions of the plans more like its

  • how much we think we know vs how little we actually do know. Reminds me of that StarTrek scene where McCoy call the 20th century doctor a barbarian.
    • by gtall ( 79522 )

      Yes, but this does not show that. It is merely anecdotal in that it is a single instance of science correcting a defect. A single case does not an induction make.

  • by labnet ( 457441 ) on Wednesday May 15, 2024 @04:04AM (#64473195)

    Being a Christian and believing God created our amazingly complex biological machines, I remember hearing scientists saying most of DNA was junk left over from evolutionary processes.
    I thought, nah, they will be proved wrong with time!

    • Correction; most of DNA is refined by evolutionary processes.
    • If anything this sort of thing supports the 'RNA world' origin of life hypothesis, if true. There's still plenty of junk in the genome, from the summary. This would explain why some of the noncoding elements were preserved so well over time.
    • Let me guess: you think God put a bunch of broken retrovirus genes in our DNA because that is the perfect design?

      • by Tablizer ( 95088 )

        No, evangelicals will claim The Devil messed stuff up. It's like epicycle ring layers: throw enough magic personalities into the mix, and anything is eventually "explained".

    • I remember hearing scientists saying most of DNA was junk left over from evolutionary processes.

      I recall, back in the sixties, a co-worker speculating that, considering the genome as a program and presuming a creator (or creation engineering team), the non-coding DNA might be the program's comments.

      And wondering whether, if so, they should be considered "holy writ".

  • by Baron_Yam ( 643147 ) on Wednesday May 15, 2024 @06:32AM (#64473369)

    The problem with the original conception of DNA is that it was conceived of by humans, who - even when not religious - are looking for a rational, organized design in whatever system we are investigating. There is of course organization, but it was not designed by anything other than random chance. We had that part down, "random variation and natural selection", and we seem to have missed some of the implications.

    For DNA, there are no start and end points with some kind of program running sequentially from one to the other. It's chemistry that happened because it worked, like stars happen because gravity and fusion work. It's insanely complicated, but it did have billions of years to get that way and that's a really, really long time that is difficult to fully comprehend with a human brain. We are not biological machines assembled at birth, we are the current state of an unbroken chain of chemistry going back almost 4 billion years.

    We're made of stuff that fell together and kept going if it kept going and not made of stuff that didn't. Every bit of us is part of the 'program', we're a soup of chemicals constantly reacting with each other. The current state of the cellular environment is part of that 'program'. The way your DNA is twisted up exposing some bits and shielding others is part of the 'program'. And the current state of DNA-RNA interactions is part of the 'program'. Billions of simultaneous processes all ongoing simultaneously, all interacting wherever they happen in proximity to each other.

    It's honestly amazing that we've managed to figure out how to fiddle with any of it without breaking it all.

    • by shilly ( 142940 )

      That is very nicely put, and reminds me of this fantastic series here:
      https://www.bbc.co.uk/programm... [bbc.co.uk]

      • No mod points so I'll just reply on that I agree as well.

        DNA co-mingles data and code. We figured out the data portion, at least the codons for amino acid sequences that become proteins. But the idea that the rest of the DNA is "junk" is kind of silly.

        DNA is expensive to maintain, from a biological stand point. Why would nature select for simple pairs chromosomes but fill them with 90%+ junk. Why not "spend" your DNA budget on tetra+ chromosome groups and less junk? The answer is that there is much mor

        • DNA is expensive to maintain, from a biological stand point. Why would nature select for simple pairs chromosomes but fill them with 90%+ junk. Why not "spend" your DNA budget on tetra+ chromosome groups and less junk?

          Because such clean-up requires a mechanism, which doesn't exist until it gets evolved. Carrying along some broken-and-disabled junk in long-term program storage doesn't cost enough to be a strong selection pressure, so under just mutate-and-select it can hang around for a long time.

          Also, if i

    • by Tablizer ( 95088 )

      I know incompetent programmers who write comparable "organic" spaghetti code.

  • ...once they find the ncRNA sequence that regulates penis size gene.

    • You jest but a few years back 23andMe put out a paper on the genetics of breast size and density. Unfortunately it turns out thereâ(TM)s a nasty correlation between density+size and cancer.
      • I am not jesting. Between this, AlphaFold, and other AI, we're about to enter an age of genetic level body modification--at least for those that can afford it.

      • Curing baldness could really be a money maker. It costs about $5k to 20k for a hair-transplant*, depending on dodginess of the shop. If ncRNA tweakers can devise a cure with a price below $5k, they'll be zillionaires.

        * Which takes about 6 months to grow enough to hide the scabs and scaring. The misleading ads don't tell you that. They should be sued.

    • But that same setting also inversely controls brain size.

  • This is just crazy complexity in the cellular function that makes it vastly harder to understand or manipulate. Imagine a protein that does some function, let's call it a hammer. Then you have these random bits of ncRNA floating about that basically determine whether or not the hammer is needed in the first place, or how many are needed. It is such an indirect and subtle method of controlling cell function (probably relying on mechanical type physics to impede or control protein expression) that it would be

    • by Tablizer ( 95088 )

      > Its far different than the more "computer like" encoding

      I'm not sure I agree; more like we found it's not just controlled by just Boolean data, but also lots of numerics (continuums). That doesn't necessarily make it non-simulate-able, but rather just requires a much larger and fancier simulation.

      • That doesn't necessarily make it non-simulate-able, but rather just requires a much larger and fancier simulation.

        Yes, that's what I said.

        it would be incredibly difficult to observe and then simulate in some way.

        Imagine you have a million computers, and say the computers run at different speeds depending on the ambient temperature. They all run asynchronously of course, each doing their own thing. Now you're controlling how they interact and mesh as a whole by increasing or decreasing the temperature of different batches of computers so that they somehow are all in synch and doing things in the correct order at the correct time.

        Or imagine a million computers, each with printers that output o

    • And many many registers. It's a mess.
  • by timeOday ( 582209 ) on Wednesday May 15, 2024 @07:46AM (#64473503)
    I was going to say this is cool because I remember disappointment being expressed that the Human Genome Project had not yielded more revolutionary results. But then in looking to back it up I found out that even in 2010, recognition was growing that the Project was leading to a change in the understanding of RNA:

    A decade ago biologists and nonbiologists alike gushed with optimism about the medical promise of the $3-billion Human Genome Project. In announcing the first rough draft of the human âoebook of lifeâ at a White House ceremony in the summer of 2000, President Bill Clinton predicted that the genome project would "revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases."

    Fast-forward to 2010, and the scientific community finds itself sobered and divided. The problem is not with the genome project itself, which has revolutionized the pace and scope of basic research, uncovered heretofore hidden purpose in what used to be called "junk DNA" and even detected traces of Neandertal DNA in our genomes. Cancer researcher Bert Vogelstein, echoing a widespread sentiment, says, "The Human Genome Project has radically changed the way we do science." The problem is that research springing from the genome project has failed as yet to deliver on the medical promises that Collins and others made a decade ago.

    ...a few brave voices are suggesting that the rabbitâ(TM)s hole of human biology may go still deeper than a focus on DNA sequences and proteins can reveal. Traditional genetics, they say, may not capture the molecular complexity of genes and their role in disease. The vast areas of DNA that do not code for proteins, once dismissed as "junk," are now known to conceal important regulatory regions. Some DNA stretches produce small bits of RNA that can interfere with gene expression, for instance.

    https://www.scientificamerican... [scientificamerican.com]

    Biology is hard. Untangling all this stuff is a very long and slow process. Yet, it progresses.

  • More turbo cancer
  • The human body is complex but efficient in its use of resources as it has to be. Why on earth then would one imagine that DNA would contain useless bits? It doesn't make any kind of sense. Mercifully some biologists have some common sense and have endured the slings and arrows of their colleagues to pursue the search for knowledge.

    Sadly this is all biology is, a bunch of bio technologists poking around seeing what they can find in the absence of any kind of first principles to guide them. Not science, j

    • Solipsistic nonsense. You can read some of the junk and tell what it was, whether dead and disabled endogenic viruses, broken genes, useless transposons that replicate nonsense. But we have known for decades that you can't just clip it all out, some of the bits in there that don't code were clearly doing more than just soaking up extra mutagenic radiation. Because science works we're learning more about these processes, not in spite of it.
      • Not being able to clip it out didn't mean that it was doing something though, hence further study was needed. It could have just been acting as a delay timer...

        • Exactly, its like creationists excited to find that a vestigial organ still does something small and hoping this advancement of human knowledge by biologists somehow undermines biology itself when updating our knowledge is the whole point. And to your point more specifically, there'd also be need for there to be room for RNA or proteins to bind correctly to different coding sequences, but what sequence the spacer is may be irrelevant.
    • by Tablizer ( 95088 )

      > Why on earth then would one imagine that DNA would contain useless bits?

      One conservative joker called them "union genes". Agree or not about unions, it's funny.

    • by kackle ( 910159 )
      I agree with the efficiency aspect; even dumb me suspected that about our DNA and I thought the same thing a long time ago when I first heard that only X% of our brains was actually used. "Nah, that doesn't make sense." Have you seen how densely compacted our abdominal organs are? It's amazing we can move as well as we do.
  • by ISoldat53 ( 977164 ) on Wednesday May 15, 2024 @08:25AM (#64473587)
    As Max Plank is normally summarized: "science advances one funeral at a time"
  • This rouses my curiosity. Non-coding DNA is not conserved, i.e. is not preserved during evolutionary changes, If it is crucial to life how do random evolutionary changes affect ( or not affect) its function?
    • by shilly ( 142940 )

      Have you got any background on ncDNA not being conserved? I didn't know that

    • Some noncoding bits were known to be conserved but not known in function. There is lots of readable cruft you can tell is dead viruses or broken genes, but this ncDNA model is explaining why some of the conserved bits are conserved. Depending on their mode of action they may be less sensitive to mutation than coding genes as well (which already have some flexibility in that the third element of the codon rarely matters but that's another story)
  • "what all this noncoding RNA -- abbreviated as ncRNA -- does. Much of it indeed seems involved in gene regulation: not simply turning them off or on but also fine-tuning their activity."

    Next we'll discover that other noncoding RNA fine-tunes the activity of the ncRNA that does gene regulation. And other stuff fine-tunes that too.

  • since the discovery of the DNA double helix some 70 years ago, which was all about DNA leading to proteins. "It appears that we may have fundamentally misunderstood the nature of genetic programming,"

    How could they miss a potentially significant portion of genetic machinery for that long? Usually somebody notices an odd repeatable phenomenon in say worms that hints at something new or bigger. Is this "mass subtlety"?

    • Yeah sounds like it is tuning the degree of expression, not on/off. Much harder to measure. You'd disrupt the processes underway try to see how much of which RNAs were there.
  • 1954-2024: "Most DNA is junk DNA; it doesn't do anything. Anyone who tells you otherwise is a conspiracy theorist."
    2024: "Most DNA is not junk DNA. Conspiracy theorists were right."

    • by Tablizer ( 95088 )

      > Anyone who tells you otherwise is a conspiracy theorist.

      That's misleading. Most would more likely have called it "backing a highly speculative theory(s)".

      Do note just because one "conspiracy" turns out to be true doesn't mean all are true. Conspiracy theorists are kind of like addicted gamblers: they remember the (rare) big payoffs far more than they remember their losses.

    • Nice trying to peddle your "conspiracy theories are true" narrative. No scientists since the 1970s and likely before thought of it as useless or junk, many if not all felt that it was useful but didn't know how. See my other comment for some links. Since the 1970s various functions of the non-coding DNA have come to light .. and no it wasn't viewed with skepticism (other than the normal "we need more confirmation/proof" skepticism that is normal in science).

  • Back in the 80s, I lost a grade for arguing with a prof in class over this. Clear back then, the argument was less than 5% coded or did any work. Yet, that argument flies in the face of how efficient/effective life is. Plants, animals, etc are extremely efficient. We save off extra energy as fat for long-term storage. But animals like bears, whales, etc took it even further and use it as insulation. Why? Efficiency.

    The ONlY dead / unused parts of DNA are going to turn out to virus that inserted into the w

And on the seventh day, He exited from append mode.

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