Our “Junk DNA” Is More Important Than We Once Thought
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- Опубликовано: 15 мар 2023
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In the search for the genes that make us human, some of the most important answers were hiding not in the genes themselves, but in what was once considered genomic junk.
Thanks to Riley J. Mangan, Ph.D. Candidate, Molecular Genetics and Microbiology, Duke University for his help with this episode!
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References: docs.google.com/document/d/13... 
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The term “junk” DNA always made me think of the “use 10% of your brain” meme.
Pretty accurate! Both are misguided commonly held “facts”
It just means they don't understand 90% of neuroscience and 90% of genetics.
@@SoulDelSol I think the day we finally understand neuroscience will be the start of when AI actually gets some I
@@SoulDelSol the 10 % claim is more related to only having 10 % of the brain active at any time, not only understanding what 10 % does. When in reality all neurons firing at the same time would just be a major seizure
@@calsta619 Junk DNA is real, this video is extremely misleading. There are multiple lines of positive evidence that point to most of the genome being junk including lack of selection pressure against junk DNA in eukaryotes, mutational load and vastly different genome sizes among even closely-related organisms.
I'm currently doing a master's in biotech and the difference in what we know is staggering. I remember that in my undergrad, it was still called junk DNA. Now, professors are very much "nah, you thought this was going to be easy 😂"
Biology is getting exceedingly complex
@@LuisSierra42 it always was. We were just innocent.
"The more you know, the more you know you don't know."
In the early 90s I was in high school and in bio I thought, “junk DNA? No way. It’s got to have reasons for being there.”
@@burnte "junk" = "nonsense" = "science can't explain that...."
I had a teacher (around 1970. It's been a year or two) who made extravagant mockery of me when I described tectonic plate theory to her. (It was a theory then.)
I made the mistake of learning something outside class. One of the things I learned was that my teacher was a vile old baggage.
Now I understand that "non-coding DNA" is a short form of saying "non-protein-coding DNA". The sequences made from A, C, G, T are still code, but code unrelated to building proteins.
I'm a programmer and I found it very interesting how DNA genes and programming codes work in similar way. If you ever coding something, you know, more than 3/4 of your codes would not create anything (same as non-functional genes), but to ensure the other functional code will work "as expected". We called them "validate codes". Through lot of developments, the size of these validate code keep getting bigger and bigger to the point, they usually take 80 -> 90% of total code size. Funny how junk genes also have characteristic in similar ways.
Interesting!
This is kinda akin to docstrings too. lol
Exactly!
It means we born to die?
Neat! Thanks for sharing!
My PhD is on Red-backed Salamanders. They got rid of their lungs and their aquatic life stages and are only a few inches long at most. Despite appearing so simple, they somehow have a genome over 4x as large as ours. It's so big we can't properly sequence it all yet. Even their genome size is just an estimate that differs depending on who you ask.
Would studying haploid cells save time?
It’s like you go to school for decades just to tell everyone what they already know…nothing. Sorry just tired of RUclips commenters citing their credentials
@@geigercourtier Oh, if you wanted to talk about the thermal preferences of Redbacks and their impact on competition and trophic cascades, I could go on all day. My advisor and I probably know more about that than anyone else in the world (since we’re the first to experimentally study it in nature). Even then, there is still plenty of more work to be done.
But their genome? It’s not a matter of education or credentials. These are things that simply haven’t been discovered yet. It’s an active work in progress no different from cancer research (literally when it comes to the regenerative abilities of axolotls).
@@geigercourtier Chill. His comment fits the topic very well and I think it's interesting. I can feel you though. There are so many out of place comments under certain videos ^^'
@@mikeycrackson your comment makes no sense. We were never ‘Monke’. Even if your thesis was conceptually viable, we would not ‘return’ to a ‘Monke’ state, we would just continue on into some NEW form, one that might be similar to ‘Monke.’
I got my masters in molecular genetics back in 1994. It’s amazing how far we have come in nearly 30 years. I was recently going through my library of books and found a genetics book. While reading it, it was amazing how complex it was back then, while today it’s just the basics.
So by saying that, you mean that today it takes the whole book for just the basics whereas back then, there was enough space to cram in some of the messy stuff also? :)
If so, that message was nicely hidden ;)
And yet the Supreme Court of the US wants to take you back 150 years! Go figure!
@@levnzt6949 I don't think that's what was meant!
From your experience do you think intelligence, or the ability to learn, could partly be genetic? Is it a possibility?
We will soon began at last harness all these disconnected areas of Biology and began to steer our Evolution in the new direction that few if single contemporary mind can even imagine!
He Jiankui, Robert Plomin, Svante Paabo, David Reich, George Church in truly amazing times we live!
We also lack understanding of molecular biology from physical perspective.
Jack Tuszyński has proven in 2020 that for example Tryptophan has hugely Quantum properties (Legget Effects) lasting in coherence up to milliseconds. Jim Al-Khalily didn't even scratch the surface when he wrote his grandiose book!
The other thing we only began to appreciate is that GWAS are going to be eventually far more powerful than any painstakingly slow and only mediocrely accurate tries and errors to understand individual genes at molecular level!
There's reason why they now call introns "Genomic Dark Matter "
ruclips.net/video/U4qhyiqbxiI/видео.html
Wherever "mind emerges from matter" is not so obvious but certainly Mind Does Emerge from Biology!
And Numerous also neuropsychological studies prove now in paralel that indeed Introns are anything but "junk"(term coined by declared Marxist Lewontin.
Our genes literally make our Minds! No reasonable scientist can deny it anymore!
ruclips.net/video/Vc-egHHIEJo/видео.html
I wonder if the appearance of brain and stomach genetic changes at about the same time could be related to the adoption of fire and cooking. That allowed more available calories, which allowed a smaller gut, and also freed up calories allowing a more energy-expensive brain to co-evolve with the smaller gut.
This makes a lot of sense to me.
People take for granted just how much energy we can extract from our food just by cooking it, imagine if your body plan has for millions of years that relied on mostly raw foods, suddenly was able to get so much more calories just by heating it up, something that you would otherwise not satisfy your hunger suddenly does, its puts a pressure in terms of incentive to figure out how to replicate the process, so we get smarter further requiring more and more energy to fuel our intelligence until it plateaus, as our intelligence at that point have reduced the physiological need to specialize since we make up for it in terms of technological advancement. Why waste evolution points/energy on bigger stronger muscles when a sharp rock on a stick made using your intelligence can do so much more?
I had the exact same thought
Does cooking actually change the caloric content?
@@kekeke8988 No, you can't produce more energy out of nowhere. but it makes food, especially protein, more digestible, thereby increasing the AVAILABLE calories.
I think the "human shares 99% of our dna with chimps" is like looking at two books of completely different size and length and saying they're 99% identical because they use the same paper and have some similar words
Please do an episode about what happens at the genetic level when a selective pressure emerges in an ecosystem.
One of the most baffling things to me is how cells know how to differentiate themselves, especially starting from just a single one after the egg has been fertilized.
How cells that contain the exact same DNA manage to perform completely different functions and are able to coordinate themselves to form a complex functioning organism is just fascinating.
If I had to guess, I'd say that the coordination of the expression of the genome requires more information than the sum of all the proteins which are coded within the DNA.
The recipe to make a brick is simple, the art comes from how to sick a bunch of them together to form a building.
you don't need to make a guess, a lot of it is figured out to an extent. you just need to study it. but to share the little I know to get you started. every cell does have all the information necessary to create you, however that information is turned on and off in a pre-programmed manner, making the cells shape and differentiate in specific ways. its like a compacted digital file, it doesn't have all the information to create the complete file, but it has the information to unfold that file into the bigger file, and the compacted file and the information to unfold it are both much smaller than the complete file. meaning that with very little information and through the use of proteins to communicate when to turn specific genes on and off, its capable of creating extremely complex organisms.
what is fascinating is that very little has changed in that process since the first multicellular organism. when the eggs is developing it basically goes through all the stages of development of its ancestors. because evolution works with what it has, so if a process works, it doesn't need to change it. like how a snake develops limbs buds in its early fetal state, but then it suddenly stops developing, and then the buds fuse together at the end and become part of their gonads instead. or how our vertebrae develops like the tail end of a fin, and then grows larger like a tail, but then it stops growing and the tail end fuse together and become internal, becoming the tailbone.
To borrow the house analogy, the people building the house are your chromosomes and some are plumbers and they tell certain stem cells to become digestive tissue. Some are electricians and tell others to become your nervous system. So on and so forth. That's why sometimes you get people who are genetically XY but have a fully functioning uterus and ovaries, the Y chromosome didn't turn on at the right time so the baby developed female organs instead of male.
Unlike a house though, if a group of workers don't show up on time, or don't show up at all, development doesn't get halted till things are done in the right order. The rest of the workers still keep going, many times with tragic results.
You will probably find Evo Devo (Evolutionary Developmental Biology) of interest, have a look at HOX genes/proteins. There was a good book written about all this called “Endless Forms Most Beautiful”, by Sean B Carroll
Some is definitely known.
A lot has to do with positioning. Where a cell is in relation to neighbors is one cue used.
Blastocoel is a cool phase you should look up!
One fun fact is there's a big clade division between embryos that form the mouth first or the ...exit...first. (hehe guess which we vertebrates are 😮 or 🍑 lol)
A dimple forms and cells fold in making 3 layers. The ectoderm makes skin/nerves/brain
Mesoderm makes muscle and connective tissue. Endoderm makes the guts.
Those are the basics I remember and hopefully all the technical terms are accurate.
As far as internal signaling mechanisms, I don't know details :) Cytokines, DNA methylation, and receptors are involved and where they are helps determine what does what.
One last thing, from a research lab project I was on in undergrad. The body reuses a lot of things. PAR-4 is protein apoptosis response 4, and it tells prostate cells to self terminate. We were studying it because in the brain (of men and women) the same protein is involved in depression related behavior through dopamine (and pain sensitivity when the gene is removed in mice).
Basically, different cells can repurpose the same molecules, and even produce the same molecules under different circumstances : )
People directly studying your question could blow your mind. I'm just a warm up act 😜
@@danilooliveira6580 can u give some references?
Having taken college-level biology in the late 90’s, the term “junk DNA” never sat well with me. After watching this, “junk drawer DNA” seem much more appropriate.
Now I'm curious what that "junk drawer DNA" is doing in other species, they probably don't have 90% of useless codes just sitting around if humanity's genome has so many other functions in that.
It's not the size of the genome that is important, it's how you use
Right, size doesn't matter as long as you know how to use it
That's what she said
As a retired doctor and epidemiologist I love spending time on a whole heap of science topics and this episode crystalised some information I was thinking about and more exactly presented information I did not even have any idea about, so thank you guys.
But I’m not even wearing jeans!
Shorts for life!
Dad jokes incoming
You’re not wearing jeans because you have nothing but _junk_ to fit one.
Junk because DNA, get it? I’ll see myself off stage now.
Angry up vote
Not a huge fan of dad jokes, but funny is funny. And this comment *was* funny 🤣
This video was very impressive (all the more so for helping to address a nagging uncertainty I'd long felt about the entire concept of "junk DNA"). BTW, yours was the first presentation to help me understand the difference between "genes" and "DNA writ large". Thank you.
His gripe with the grape is great.
It's not just in biology that researchers will categorize data that can't be classified as 'junk'. Astronomy, physics, chemistry have all fallen into the trap of lazy thinking.I am heartened that there are those who are willing to face ridicule and investigate the dung heap to find the gem that shows us how much we really don't know.
This video was very informative and well thought out, nothing less than can be expected from PBS.
I'm an IT guy so I guess we used to think that we would find what makes us by looking at tables in a database, when all the important stuff were actually the triggers at the back end.
IT guy as in working in an IT department or generally information technology?
In my college experience in human development (I graduated in 2013) we would muse that "junk" DNA must have a purpose because humans were way too complex for genes coding proteins to explain such variation. Lovely to see the growth in the field.
At the end of this scientific journey, we're going to find out that what makes us human was inside of us the entire time. 😁🧬
👍🏻 I love what you did there. 😜
My jeans are all Wrangler, and on the outside I might add.
Monks, yogis and many spiritual leaders who've been privileged with the time to explore, investigate and study their own "inside" directly have known this for thousands of years. And I don't mean mythology and metaphor. . . these people were and are scientists of their own consciousness. We've had many answers for a long time that modern science is now confirming/catching up. Unfortunately that science gets clouded by faux "spiritual" teachings that are often inappropriately aligned with it. 🙏
Um, yeah, just like every piece of matter that ever existed and every living thing that ever did some living. It would really be astounding if we discovered the contrary.
only if you only look at nature and ignore nurture.
Can you do an episode on epigenetics? Could that explain some of the variance we see despite our smaller number of genes?
I've been amazed about how little we know about human genetics and yet also how available genetic testing has come. I'm closely connected to the medically complex community and many many people have health issues that are likely genetic but science is not able to identify the reason.
The evolving of "junk DNA" into useful components reminds me of the usefulness of polyploidy in plants for evolving new adaptations without threatening the original
I learn more from this channel than others- topics I wouldn’t necessarily be interested in, I’ll dive into because Eons covered it! Love your content
Great vid. And it showed how out of date my (limited) knowledge on genetics was. To think, just over 20 years ago with the first (almost!) complete humand genome sequencing it seemed like job all but done - a bit of mapping of genes to structure and the role of the odd control genes, variation, and that's human genetics wrapped up. Any more delving into genetic structure/function would be welcome!
Yep. We've had the 'text' of our genetic code for decades.
Learning to decipher it; looks like we've only started.
Re-watch it ... "Some experts think that", "Somehow they affect" ... it's unproven guess work.
I've also often wondered why number of genes doesn't seem to be related to complexity of the organism.
Because they only encode for proteins, not for function, not for complexity.
Also because grapes (grapevines) are still more complex than we like to admit.
Flowering plants are just as complex as us, maybe even more so.
as Luiz said, number of genes doesn't necessarily translate directly to function and complexity. simple structures for example can require big proteins to form, and those proteins require a lot of genetic material to create. but at the same time humans are not necessarily more complex than most organisms, remember that we lost a lot of "special powers" to focus on our brains. our varied diet also allowed us to have a simpler gut and not need to synthesize some essential nutrients, like Vit C.
@@danilooliveira6580 - Luis, Luiz is not a name in any language.
@@LuisAldamiz my mistake, Luiz is a name here in brazil.
The part of my brain that should of been a sociologist starts with "But our experience is also critical to what makes us human".
What makes us human is the friends we make along the way
Ditto. But do not forget the enemies, they also deserve a little spot in our heart, even if it's full of bile.
@@LuisAldamiz you have no enemies Thorfinn
@@LuisSierra42 - I, Loki, have many enemies in Valhalla.
Excellent video. Incisive, informative, and aesthetically pleasing. Keep it up, Eons!
Love these kinds of episodes - updating old information.
I’m doing my PhD in biochem/biophys, so it’s great to see a PBS video tangential to my field.
Very informative.. thanks for making such great content!
Just more to add to my list I'm working on. One day, we should hope to use all of these to check our knowledge in living organisms
Very good video! Very good explanation of our genes and non-coding portions of our DNA!
That was absolutely fascinating!
This is my favorite Eons presenter so far! I mean, I like all of them, but this guy is my fave!
So cool, thanks for sharing such great content!!
Great article, love it, want more.
Please do an article on evolution of thinking and memory.
That would be based on studies of hunter gatherers and the art of tracking. Hunter gatherers are the most ancient homo sapiens societies in exsistence. They have lived the way our ancestors did for hundreds of thousands of years. For reference look up the RUclips video "The Intense 8 hour Hunt" by the British Broadcasting Corporation and read about Lois Liebenberg, a studier of hunter gatherers and tracking. His book "The Origin of Science" helps explain.
When we came across the whole epigenetics thing during this discovery process, things turned even more complicated. Suddenly human evolution didn't even just concern the long-term evolution over thousands of years, but even between single generations. It's amazing how quickly even a bit of complexity can turn something deceptively simple into something so complex as the human body and its ongoing evolution.
Keep these videos coming we need to keep this knowledge and share it with everyone 😊
Another amazing video! Love these guys 👍👍
I loved this so much, thanks.
Love your videos!
This is (understandably) very human-centric, of course. You've got to wonder what commonalities you'd find in the "former junk" of other sets of closely related species in other clades across the tree of life that are unique to them...
There are some things common across species. Some "junk" DNA as it was once called helps make sure chromosomes bundle properly in the nuclei of cells... and if that didn't happen, there'd be a dead cell... Then there's therir role in producing substances that enhance or inhibit other genes' expression/replication/etc. It's nto junk. It's just not coding for proteins. Those differences, btw, in "junk" are key to speciation is the more recent thinking. What's most fascinating, to me, anyway, is that generally, evolution tosses DNA that has no use. So what use is all that stuff we thought was "junk"?.... And that's the next 30 years of molecular biology!
Hey, here's am obvious principle: knowledge gets more detailed, not less. That looks like a principle of the evolution of information to me, like info dynamics.
I think it’s amazing how scientists can figure out how even one one gene function. It’s wild how they’ve learned so much and still have so much more to go
Love the junk drawer reference.
This was fascinating. Thanks
I mean that makes a ton of sense. It's way easier to evolve (probability wise) by picking from a sequence of dna you already have than to hope that mutation occurs randomly.
"We'd missed them."
Interesting way to say "ignored."
I'd love to see a video on ungulates, especially what we know on how they came about, when and human domestication in the fossil record!
Super interesting! I hope more videos about human genetics follow :)
I think what makes us human is some combination of elements that just came together
Thank you
What I really think we're talking about here is the difference of our consciousness.
The best question to which is not how but why.
To me it only seems fitting that the more chaotic portions of our genes should inform our nature.
This non-scientist considers this PBS vid may be one of the most important. It informs us of the essence of ourselves.
It makes sense; as humans we often forget to flip the coin and observe the other side. I think about how activating an arm for an action, such as a punch, requires that some muscles are activated, and it is just as important that other muscles are relaxed. There exists this dance between action and inaction that determines the composition and motion of a movement. I presume this idea can apply to the functioning of most of the human body.
I suppose it makes a lot of sense. Having a useful gene that makes a protein and then several genes that decide when and where that gene is activated. The "junk" is a playground that helps with rapid adaption to new niches if they arise.
i actually think this is a much better name for this episode!!! sounds way more interesting!!!
Where can we buy that Polo shirt? :) Outstanding video - as always!
Great episode 🤘🤘🤘
Water flea is the common name for a number of species of tiny crustaceans in the genus Daphnia. Fish love them! Frozen and freeze-dried farmed daphnia is a common food in the aquarium hobby.
Thank you!
Great video!
you also share 60% of your DNA with grapes.
I have a hypothesis* granted I’m not a biologist or a specialist but just a programmer. I suspect genes are shaped and tooled by the environment via epigenetic and stored within memory cells and their DNA. After all, genes cannot “see/hear/taste,” but we can. As such, our experiences shape not only our own lives but our genes as well, passing on these changes via the “junk” portion of our DNA. Maybe our memory cells take cues from our gut (via microbiome), our immune system, endocrine system, and code these changes to help better cope with changes in our environment.
On one hand, it can’t change /too/ rapidly (unless it’s beneficial to that life form) or else we may lose vital components or functionality we need. On the other hand, the changes have to translate through somehow or else we would never adapt.
Junk DNA is a library of classes, objects, and methods used by life for a long time.
You need actual evidence to back up that theory or it’s just a hypothesis. Not to discredit a hypothesis, but you’re need to take a step back lol
@@orishaeshu1084 That’s fair. There is some evidence for what I say- particularly how traumatic experiences in the mother can be passed on/imprinted onto their child. Still, we’ll just say “hypothesis” since we’re talking more of a scientific sense.
It’s amazing how much we know, it’s daunting how little we know.
Whom told you so ?? 🤔🙄
Gut's response: "Hey, it's not the size the matters, but how efficient it is, TYVM".
😆
We did harness fire and externalized a substantial part of digestion via cooking, so I guess it's a catch 22 for the gut-brain relationship.
Interesting episode!
The march of science is the constant finding out that we were dead wrong about whatever we felt confident in.
Fascinating!
Great work there
Love this channel
Mates need to collect all that dad jokes and compile a book or something.
_"What makes us human? Is it the way that we walk? Or talk? Or how our face disintegrates into chalk?"_
maybe the thing that makes us human is the friends we made along the way ✨
Love the science divulging work
one man’s junk really is another man’s treasure after all
A link to the rest of the story would be nice. I scrolled through quite a few videos, trying to find the rest of this one. I even found a video explaining why weasels are skinny can’t tell you what either of the viruses are in the content of this RUclips short but I can educate myself on why weasels are thin I feel so enlightened. Please human being that is in charge of this site and the creation of this video short, could we please have a link to the remainder of this story, so that we can educate ourselves instead of thinking that we were duped by Clickbait
I didn't realize grapes wore those... I have like 4 pair myself.
I actually got to meet the scientist who decoded which codon sequences code for which amino acids. I went to church with his secretary.
Lmao.
I love those videos! I have a question: what is the mechanism with which those non coding sequence affect the cell? mRNA copy? Change on the line of working proteins, on how the double helix folds? What could it be?
Many noncoding regions act as identification sites for different DNA polymerases that read the genes for processing. Some areas are mostly structural and used to manage the shape of the DNA in the cell. Certain regions called transposons are thought to be ancient viruses left in our DNA that can move freely within the genetic code. Some areas do code for mRNA and tRNA as well as ribozymes which are RNA molecules with enzymatic function. So most junk DNA has some purpose but that purpose is not necessarily just for making proteins.
@@TheRedKnight101 thanks you very much!
Basically, non-coding DNA regulates when and by how much some nearby gene(s) is transcribed to RNA by interacting with regulator proteins. Others may produce non-coding RNA molecules, like microRNA, that can either generate protein variants by controlling the splicing process of its messenger RNA (mRNA), or suppress the translation of specific mRNA, or even regulate other distant genomic regions.
2:40 FOXP2 didn’t “pick up” a mutation. It was *mutated.* Someday you’re all going to accept that the “animals” are evolving themselves. On purpose. They move into a new niche or engage in novel behavior… and the mutations follow.
Awesome one, well, now that I know about my uniqueness and we solve this mysterious riddle - we'll, I can go to sleep calm and peaceful Zz
please wake me up in the next eons.... Awesome one!!!
Being complicated is backed into our 🧬 , I love being human ngl 💛
Awesome!
If genes are the tools, it’s sounding like the junk DNA is ‘software’ that controls how to use them (though I’m sure it’s way more complicated). Another step in understanding how our brains work. Nice vid.
Don't forget we start to cook around 2-3 million years ago, so for sure we somehow made food more easily digestible, hence the trade off between gut and brain was not only advantageous but indeed somewhat unavoidable.
This was a great episode
What we have yet to understand is so vastly larger that what we do. Yet, we act with such hubris till we are smacked square in the face with unintended consequences.
That 2022 paper came out just as I graduated, I feel like I just missed a good lecture series that was yet to be written when I was in uni ahhaha
This suggests something very interesting to me, about how this may have happened. What happened is that the body started using less energy on its gut and used the surplus on its brain, and that it happened sometime before the last common ancestor
It sounds to me like what happened is when homo erectus started cooking meat over fires, the body suddenly needed to do much less work to digest the food, so the stomach would first have quickly started needing less resources in energy to function, and then through random mutations some individuals would have the dna to start sending the surplus to the brain and then through natural selection those genes would fix in the population over a long time, while at the same time because of the cooking fire they can spend the evening staying awake and getting smarter
The real human gene is the friends we made along the way
I feel 'junk DNA' needs to be phrased as 'hoarder DNA', since these molecules have plenty of room withing the nucleus and seem to hang on to all past information.
Buen video, se complementa con antroporama y su video de las áreas aceleradas humanas, algunas menciones de estos genes indirectamente sería secreto of nimb aka la ratoncita valiente y bagi the monster of mighty nature de ozamu tezuka.
I played bass for Expensive Tissue Hypothesis.
The really like the metaphor of genes as tools! SubAnima has a great video about promiscuous enzymes that can be used on a bunch of different molecules, just like a hammer and nails ig
I preferred the thumbnail with the small shrimp that has more genes than us. I just didn't have time to watch it when I first saw it.
I kept thinking the coding dna was a loading bar and I was ready for it to fill up the non coding dna
VERY NICE
What if non-coding dna is there like a standard, the same for many many organisms, because it is necessary.
Like certain lines of code for games, programs, browsers, apps, or certain scientific methods that are used (and credited) in many research papers.
"The basics", the foundation upon which the organism is built. I dunno, I'm stoned.
maybe if you get more stoned, you'll figure it out?
@@therattusrattus I don't have the capacity, I just dream.
Yes.