A.I. Reveals Autism-Linked Changes in “Junk” DNA | SciShow News

A.I. Reveals Autism-Linked Changes in “Junk” DNA | SciShow News


[♪ INTRO] Scientists know that autism has a genetic
basis. Studies have found that genetic factors may
explain anywhere from 56 to 95 percent of autism’s features. But so far, it’s been really hard to identify
exactly what those factors are. A new study in Nature Genetics suggests that
may be because researchers have been looking at the wrong
DNA. You see, earlier this week, a research team
announced that they’d used artificial intelligence to uncover changes linked to autism in the stretches
of DNA between genes— and that opens up a whole new avenue for autism
research. Autism Spectrum Disorder, or ASD, is a condition
that shows up early in childhood and usually involves challenges with social
skills, communication, and repetitive behaviors. But ASD isn’t just one thing. It varies a lot from individual to individual. While one person might have mild intellectual
impairment but socialize well, another might have genius-level intelligence
but struggle to communicate. So while scientists know that ASD has a strong
genetic component, the specific DNA changes involved are hard
to pin down. Researchers usually start by looking for changes
to protein-coding genes— the sections of the genome which actually
encode proteins of some kind. And they’ve found plenty. Specific variants of hundreds of genes have
been associated with having an autism diagnosis. But very few of them have been confirmed to
be causative. The few that have been sure bets — like,
one gene is responsible, and it’s passed down from parent to child — account for less than 10% of autism cases. Part of the trouble is that in most cases,
ASD stems from what’s known as a de novo mutation: a DNA change that a person doesn’t share with
their parents.. These are changes to DNA that happen in the
egg or sperm cell before conception or in the early embryo during
development. But even these de novo changes to genes only
seem to explain about 30% of spontaneous ASD cases— ones where both parents are neurotypical. And that’s where the new study published
in Nature Genetics comes in. They searched the rest of the genome for those
de novo changes. You see, despite their importance, protein-coding
genes are thought to only make up about 1% of the human genome. The rest is what was once called junk DNA,
because it didn’t seem to do anything. Of course, now we know it’s totally not
junk— and a lot of it is actually super important
because it controls the activity of genes. Like, it provides attachment places for proteins
called transcription factors which, as the name implies, speed up or slow down transcription—the
first step in gene expression. And though these sequences are called “non-coding”,
some do code for RNAs which play important roles in the processing
steps that occur after a gene sequence is transcribed. And that means, to really understand the genetics
of autism, scientists have to search through the DNA junk drawer. The new study isn’t the first to try, and
the work on this front has been promising; it’s just that it’s difficult. It’s pretty straightforward to find DNA
sequence differences between people. But just because there’s a difference doesn’t
mean it’s causing anything. No two people have identical DNA, and it’s
hard to tell the difference between a sequence change that does nothing and one that leads
to a specific feature or condition. When you look for gene changes tied to specific
conditions, you can narrow your search by using the genetic code to figure out if a
change actually alters a protein’s sequence. But we don’t have a similar way of knowing
whether a change to non-coding DNA will have an effect. So when studies have tried to look for changes
in non-coding DNA, they’ve ended up with too much noise in their datasets to tell if
there’s anything really going on. That’s why, for the study published Monday,
researchers tried a new way to sift through this messy genetic data: artificial intelligence. The team trained a neural network on more
than 2,200 different DNA-regulating features, so it could predict whether changes to a particular
section of DNA would likely make a functional difference. They also trained it on a large set of known
non-coding DNA changes and their effects. That way, it could generate a predicted impact
score for each change it encounters— basically, how likely it is that a given change
alters gene expression in a way that might lead to autistic features. And then, they fed it genetic data from actual
people. This data came from the Simons Simplex Collection,
which is a repository of whole genomes from nearly 1800 families, each that has a child with autism, a neurotypical
sibling, and two neurotypical parents. And, perhaps not surprisingly, they did find
significant associations between ASD and changes to non-coding sequences— in their dataset, almost as many cases were
linked to non-coding changes as coding ones. As you might expect, a lot of these changes
were predicted to alter gene expression in brain tissues. One thing that really stood out was how many
of these changes seemed to affect the expression of genes after the transcription stage— when the messenger RNA is processed and readied
for translation. As of yet, there hasn’t been a lot of research
on that part of the picture, so the researchers say those processes should
be examined more closely. And they also found that many of the non-coding
changes affected the same pathways and even the same genes as coding changes
that are linked to autism. So, it’s possible that studying coding and
non-coding changes together might be an easier way to zero in on the most influential genes— and that, in turn, might lead to a better
understanding of how autism arises in the first place. The researchers say that in the future, this
kind of analysis might even let scientists link non-coding changes to specific ASD characteristics. But the team says their immediate next steps
involve refining and expanding the algorithm itself. They say this is the first real evidence that
non-coding changes can underlie complex human conditions. And being able to accurately predict how these
changes affect gene expression could help unmask the hidden genetic components of all
sorts of conditions— basically, all those things we know are “heritable”
but can’t trace to single genes. Which is a lot of things. An unbelievable amount of information could
be right in front of us just waiting to be uncovered – written in overlooked stretches
our genomes. Thanks for watching this episode of SciShow
News! If you like taking a deeper dive into the
science behind the headlines, be sure to tune in every Friday for our news episodes. And if you want to get notified whenever we post
a video, hit that subscribe button and click the little notification bell [♪ OUTRO]

100 thoughts on “A.I. Reveals Autism-Linked Changes in “Junk” DNA | SciShow News

  1. I'm autistic, and I just want to say you guys did a great job with this episode. Too often, autism is put under a negative lens, or the research is used to eradicate us. It's very frustrating.

    I'm happy to see a video that simply presents autism as a subject of research. You frequently call it a "condition", even though many people (including the dsm-5) call it a disorder.

    We don't view it as a disorder so much as a difference.

    Thank you for your coverage on this. Neural networks never stop ceasing to amaze me.

  2. So-called "junk DNA" is a classic example of how blind faith in the evolutionary hypothesis has stiffled scientific progress. For decades creation scientists were calling for further study into what all that extra DNA did but as the evolutionary hypothesis dictates that useless DNA must exist, funding for such research was consistently denied. Just as it's come to be known that no vestigial organs exist, what will be said when it's finally found that all DNA has a purpose? This is because it was designed that way.

  3. I feel like it's rather limited to only look at the parents, you can inherit genes from previous generations too…. After all that's how recessive genes tend to work. Like even on a superficial level; my brother's appearance is a mix of our two grandfathers, he doesn't have much in common with our parents beyond what THEY inherited from THEIR fathers. If you were only looking at our brown eyed parents, his green eyes make no sense for example.

    Like I'm autistic, as are two of my cousins (who aren't siblings). I suspect my father might be, but that's about it as far as my parents go for autism. But the fact that I have two biological cousins who are also autistic, as well as my brother being autistic, might indicate a familial trend – and thus a hereditary nature to our autism.

  4. in this videos they always talk like if they were in a rush plush they repeat the same words over abc over 🙄 pathetic

  5. Heavy metals in our immunizations, like mercury and aluminum, end up in the brain tissues of our youngsters. There's your autism.

  6. I'm on the autistic spectrum because i was born with a non hereditary condition and have 3 sex chromosomes instead of 2 doctors explained to me that the more sex chromosomes a person has the more likely they will have autism and in some cases Down syndrome.

  7. Certain aspects/types of autism are arguably useful if especially for specialized tasks.
    Maybe we can use the AI as a combination finder for using Crispr without getting unwanted side effects.

  8. It's great we're finding out all this stuff about genes, but I'm fairly certain that the root cause of autism isn't genetic. I read a paper once that made a solid connection between (often allergic) inflammation in the brain as a fetus and autism.

  9. I've always wondered if I could be on that autism spectrum but I've never been tested in any way. I'm considered smart by some and very, very smart by others (personally I don't think I'm very smart at all and that not only do I not know enough about anything but that I'm not very good at much at all. Which is what drives me to learn and do more). It's my social and communication skills that are very much terrible. Very, very, very terrible. I don't know if that's because I could be on the spectrum or if it's because of the environment in which I was raised. Growing up I had zero friends and funny enough I still have no friends and my family has never been the talkative/share our thoughts and feelings type. So I suppose I just was never able to develop those skills and chances are it's too late, or so I've been told. At work I'm considered very weird. Then again, I can never find anyone to talk to about the things I'd like to talk about; the many things that I'm passionate about and that which fascinates me most: poetry, classic literature, music, physics, math, other sciences, technology, philosophy and other languages. Well, that's it I suppose. That's all I wanted to share. As usual, fascinating video SciShow. I can't wait to learn more with you.

  10. Do we really want to know the recipes for certain conditions?
    I mean, with the ever growing quandary of designer babies, it seems possibly even more dangerous. Like you said, there's varying levels on the spectrum. Geniuses, disabled wards, and everything in between. A totalitarian regime could theoretically master human gene editing as to not only control who has autism, but in what form. If the state wants obsessive scientists or a docile public, they can do it. Am I on the right track?

  11. If we are experiencing an epidemic of autism and de novo mutations are highly correlated to autism, are we also seeing a spike in de novo mutations, and if so, what is causing it?

  12. Learning more about the inner mechanics of Autistic genetics is interesting, but it makes me uncomfortable to see it studied this way. Humanity is still very eugenicist, and the moment we "figure out the why" of autism, the next question people ask is going to be, "How do we prevent it?"
    This is seriously scary.

  13. "Oh no… that's junk DNA, it just randomly accumulated" we've been told for decades. Meanwhile they tell you straight down their nose that there's absolutely no chance our genome was designed or engineered in any way (i.e. by other life in the universe) while at the very same time they work on genetic engineering, designer babies, and creating life in the lab. Remarkable how many people in both the scientific community and the public can't see this absurdity, or think… whoa, I don't want to mention "design" and be accused of being a christian whacko, hmm okay I'll put my head back in the sand and pretend like we are the only life in the universe alla pre-copernicus times. Hint: science is the loser in scenario.

  14. ehh, what is this?
    Is Autism really a Scientifically accepted condition?
    I've met "Autistic" people before and they are super chill dudes that go to school or work and like anime like me.
    Even if Autism is real and has its origin in genes is it even ethical to remove? You're altering someone's personality. I hate what schools in the US do with "Autistic" kids. They give them a label, everyone has to treat them differently, and they drug them.
    Why do we do this? I disapprove everything about this discussion.

  15. Why can't you normal people accept us for who we are instead of demonizing us and saying something is wrong with our DNA.

  16. Now i wait for a gene therapy using viral loads to edit and repair my DNA. Yes I am Autistic, it sucks btw.

  17. I look at other people and I don't fully understand how anyone functions, and everyone is incomprehensible in a different way. I guess the reason for that WOULD be in those stretches and stretches of DNA we don't yet grasp.

  18. There have been studies showing links between non-coding DNA and some very specific forms of autism for years now, this is not the news.
    What the new study did, was showing a faster way to look up which strands of DNA could be causing neurological problems. This is not new science, it is a new tool, for doing science.
    Like a sorting machine for tools, instead of finished products.
    It should also be noted that they used the Simons Simplex Collection, which is a very specific dataset. The other thing is that they did not show their findings to cause autism, they just confirmend that they caused the expected DNA changes, without knowing what those realy do or if those are realy the ones responsible for autism.

  19. I'm just going to guess; you're irresponsibly reporting on someone applying a machine learning algorithm to a sample set – something that is well understood to mathematically find any possible pattern, with zero implication of significance… while horribly misrepresenting the longstanding myth of 'junk' DNA… annnnddd yup.
    Instead of taking a moment to educate viewers on post-transcription factors and how gene->phenotype thinking has long been known to be nonsense – you make your viewers less informed for having watched this.

    I'm almost certain that if I go check out the article in Nature that it probably explains this too, and how it's a kind of obvious thing to check.

  20. We all know that it is VACCINES that cause autism. Autism can be cured by eating gluten free, raw food diet, don't trust big pharma or Monsanto. Resist vaccination.

  21. If you call something "junk" in the material you research, then you can safely call your research junk as well…

  22. Q:If genes are identified and are screenable / adjustable- Do autistic folks take issue with the idea of new parents selecting against (or even for) those genes for their kids?

    I could easily see there being strong hostility against other potentially genetically influenced behaviors, if the genetic components became parent-decision-capable.

  23. I'd like to consider myself the 'genius' variant, but in reality I'm a dumbass both socially and intellectually. 🤷‍♀️

  24. As someone with both a disorder called peutz-jeghers syndrome (look it up it’s to long of an explanation to put here) and asbergers (a form of autism on the high functioning end of the spectrum) I’m not suprised that autism could be caused by a mutation in genetics

  25. you mean if i skip over sections of the book ill have gaps in my knowledge? i would never have guessed.

  26. Actually, it's because of vaccines. They have a chemical in them called "Dihydrogen Monoxide" in them which can have toxic and mutagenic properties. My aunt told me so. Google it.

  27. I'm a little worried they'll find the root cause. We're already treated horribly as it is, we don't need to be prevented from breeding and parents don't need to be encouraged to abort a child they would otherwise want just because we are "defective." We really don't suffer from ASD nearly as much as we suffer from mistreatment and neglect. And even if we are "defective," that doesn't make us any less human or any less worthy of respect and care. That aside, THANK YOU SO MUCH for noting how different ASD is for each individual. Lots of people like to paint us with the same brush, and really, we're as varied as can be. Lots of autistic people can't or won't speak, but lots of us do, me included. I seem normal at first glance so people are dismissive when I tell them I'm autistic. The worst symptoms usually only show up when I'm distressed. Addressing that each case is different is really helpful to all of us autistic folk! Thanks!

  28. I'm autistic and that makes me feel…. neutral. It can help a lot with other conditions and understanding more of the spectrum, and how it affects our wide range of characteristics… but I fear that it'll push to genetic editing to erradicate the spectrum altogether and that's a terrible prospect tbh.

  29. Dependence on AI will lead to so much suffering. It will really change nothing for the better. Only shifting more power into the hands of the few. The Luddites might have been right all along.

  30. If DNA encodes the mechanism for transcription, then it probably encodes the entire decoding process, making it self referential like C, which has compilers written in C.

  31. Why on the Internet everybody has autism? The autistic people I've seen are continuosly making weird noises and can't write or spell, meanwhile in youtube they appear to be writers or something.

  32. Some vaccines have microorganisms (that have DNA), and that DNA mix with our own and causes autism!!
    BOOM solved!!!

  33. Recent studies have actually shown that one of the key characteristics used to disgnose autistic people – a supposed defficiency in social intellect – is actually skewed. Why? Because autistic people generally have no problem communicating WITH OTHER AUTISTIC PEOPLE. The difference is rapport. Also, autism is often misdiagnosed as something else, or something else is misdiagnosed as autism, precisely because allistic ideas of what constitutes 'correct' social skills skew the data. So maybe it's time they started researching themselves, and let actual autistic people dictate what studies need to be done on us, and listen to us when we talk about ourselves, instead of treating us as some alien anomaly that needs to be 'cured.'

    That being said, fascinating video. My rant technically has very little to do with the video, btw. Just putting it here to help start countering misinformation that continues to occur through the fact that people still go off old ideas of what autism is when talking about it.

  34. The event that really changes gene expression in brain tissue is the occurrence of encephalopathy. What is the most frequent cause of brain inflammation in infants? Vaccines

  35. I think the most interesting piece of this is left out. My "autistic features" vary on a day to day and week to week basis. It would be great to see a study looking at actual autistics habits and expression of features over a period of time and analyze which factors had an effect on the features.

  36. I'm autistic and this terrifies me. Blood tests and the like for autism opens up the door for even more of us to be murdered, like we were as a result of being "discovered" by Hans Asperger. Some people have different personalities and traits. Just let us be.

  37. I've suspected epigenetics to account for many autism cases. Seems like it would be a useful advantage to our evolution

  38. The expression "junk DNA" is embarrassing. It provides a snapshot of the unwitting arrogance we often bring to our study of the world.

  39. So what about autism mmh?? It wasn't my fault that all the other children were not able to talk at age 0.75.
    Wanna bet that "junk-DNA" is far from "junk" and more important than it is wildly believed?

  40. Junk dna , aka the dna you can control when you meditate heavily . Turning genes off and on.
    Yes, genes do turn off and on based on environment . It’s true .

  41. I hope they can use this new method to study the genetic factors relating to other dissorders too like ADD and Dyslexia. Very exciting!

  42. Can DNA-based explanations, including this one, explain the changes in prevalence over time?
    https://rd.springer.com/article/10.1007/s10803-018-3670-2

  43. Hey SciShow, how far off do you think we are from custom DNA to the point where parents can make their child before a zygote is actually formed? Physical features would obviously be easiest, but what do you think about passing intelligence, empathy, or other possible personality traits that aren't directly relative to how the child is raised?
    Also if the possibility was there, would it be ethical? Some might lose their minds about the lack of variation from random DNA. But it could be remedied with proper research to make super humans. Would be the next leap for our species..

  44. I think we should be cautious and/or wary of research into the causes of autism, because the usual end-goal of such research tends to be a "cure". Since it's flat-out impossible to make an autistic person not autistic (and almost none of us actually would want to be cured), this supposed "cure" can only mean eugenics. I am autistic and the sentiment that people like me are an undesirable burden that should be eradicated from the earth is unnerving and hurtful to say the least.

    So while this is utterly fascinating from a scientific point of view, it comes with a bit of concern for what this research will actually be used for in the future.

  45. The more I read everybody’s comments, the more I feel my 5 year old daughter will do ok in life. God’s willing. God bless

  46. I've seen these studies, and I still lean toward the theory that Autism is environmental.

    NO not freaking vaccines! Gosh, I'm talking science here, not conspiracy theories…

  47. It shows up in early childhood–and has nothing to do with vaccines.

    It definitely runs in my family. My great-great uncle was placed in an asylum prior to 1900 with symptoms that sound very much like Autism. Two of my mom's cousins had it, as do my brother and a cousin of mine, all from the same genetic line.

    And before anyone criticizes, yes, I know asylums in the day were HORRIBLE places. People weren't' as knowledgeable back then. Furthermore, my great-great grandmother died quite suddenly in a time when, if that happened, a man sent his children to an orphanage, remarried, and had more children. Instead, my great grandmother, the oldest of eight children, begged her father to keep them, and he agreed if she helped raise them. She was hardly more than a child herself and she raised six children before she went on to get married and have five children herself, one of whom died tragically, another of whom was excessively premature.

  48. Grunya Sukhareva noted in her studies of autism that a lot of the relatives of autistics had similar traits.

  49. As cool as science is, I as an autistic person don't want the genes that might cause autism identified, because that seems likely to just lead to negative eugenics of autistic people. Despite autism being primarily a social disability and not a medical one, neurotypical people would certainly love to prevent us from ever being born. Hell, look at the most popular non profit surrounding autism, Autism Speaks! Their whole point is they want to eradicate us and our neurodivergence.

  50. I really don't understand why so many autisitc people don't want to be cured. I mean is it pleasent to many times be the last one who understand what to do in classroom, if you cannot listen to what a boss wants from you because your brain doesn't process the task wished from him correctly, I mean you cannot remember what he wants from you.

    It isn't a socail problem, it's a problem of limited processing/slow processing/different processing information in general. It means often lower intelligence in new situations but higher intelligence seen long term.

  51. The key to figure out the causes might not be in studying single genes but a NET of genes. Let's think of it this way; imagine a picture from Picasso. Seen very closely you just see dots which doesn't say anaything about the structure as a whole; even if this dot of a color is "impaired", the whole pictures can still be beautiful and vice versa. It's the interplay of various colors ('pixels') which makes the individual pictures "beautiful and positively unique" or "boring, unesthetic and ugly".

    So the key might lie to observe the relationships of various genes to each other and if this pictures CONVERGES to a common pattern in all autsitc people. It's this general pattern , and the relationships which matter, not the individual impaired genes.

  52. I know I might sound stupid, but what if human consciousness is as unique as the fingerprint and has a huge part to play in all this. What if all human structure begins with the fundamentals of human consciousness??? What if our brains are just an amazing organic processor and consciousness is the most important thing??

  53. I have aspergers and I outperform the majority of my co workers to the point where I often feel that I'm working with children. Don't call my autism 'junk'. The goal of the neurotypicals is to screen us out? Well, I hope they'll enjoy being back in the stone age once they've managed to destroy themselves, because everyone's iq will be scraping the bottom of the barrel by then.

  54. What's the likelihood that they will discover that vaccines cause the changes in the DNA? Can't you hear it already? 😉

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