Articles, Blog

12 magnets show how viruses are built

December 21, 2019


DNA is often referred to as the instruction manual for building an organism or the blueprint for an organism. And I like that. It’s a good one sentence summary of what’s going on, but obviously it leaves this huge gap in understanding. Because, if you think about it like, what really is DNA, like on the molecular level? Well in simple terms DNA is a really long molecule made of smaller molecules chained together, and there here are four possible small molecules that DNA can use they’re called A, T, C, and G for short. For example, maybe this is a adenine, this is thymine, this is cytosine, and this is guanine, and the particular sequence of A’s, T’s, C’s, and G’s that make up this chain of DNA is like a code and it’s a code that tells a cell how to build proteins. The way your cells build proteins based on the code that’s inside DNA is really interesting. Basically, you’ve got these giant molecules inside your cells called ribosomes, and a ribosome is basically like a robot. I mean it is a robot. It’s just a molecular size robot and a ribosome will grab ahold of one of these chains that we’ve been talking about, one of these A, T, C, and G chains, and it will pull the chain through itself, and the particular sequence of A’s T’s C’s and G’s as they pass through the ribosome will cause the ribosome to grab different components from its environment. And so, for example, suppose the sequence coming in is A, A, T. Well, then the ribosome is going to grab hold of an asparagine molecule, but if the sequence is G, G, C then it’s gonna grab a glycine molecule. There are 20 possible molecules to choose from they’re all called amino acids, and actually the ribosome doesn’t grab the amino acid directly instead it grabs hold of a carrier molecule. Those are shown in green in the animation and a little red blob on the end. That’s the amino acid that it’s carrying. And actually when I say grab, the ribosome isn’t reaching out and getting these things. It’s just that they’re all jumbling around in solution, And occasionally the right carrier is going to come along to match the sequence of “letters” that’s currently inside the ribosome, and the ribosome is chaining these components together to form the protein. So you’ve got this chain that’s being pulled through the ribosome, and at the same time the ribosome is spitting out a new chain, and that new chain will fold up into some complex protein. So, you can see how the specific sequence of A’s, Ts C’s, and G’s defines the sequence of ingredients that are pulled in by the ribosome to form the specific protein that it wants to build. So that’s how DNA codes for proteins. I have actually missed out a step where a copy of the DNA is taken first. The copy is called RNA and all the T’s are switched for U’s. But here’s the thing, when the ribosome is finished building the protein it just spits it out, and the protein is then just swimming around in solution. It’s moving around aimlessly in the fluid inside your cells. And, that seems like a really random process, really undirected, and And, that’s where the chasm of understanding is. You’ve got this really stochastic looking process: the building of proteins, and then them sloshing around in solution . And then, on the other end, you’ve got the organism which seems really directed, really deliberate, like, you know, five fingers go on the end of this thing five fingers go on into this thing So, you can get from one to the other. You can fill in the gap between the stochastic process going on at the molecular level and the very deliberate process of the organism. And, this video is going to look at the early stages. So, how do you get from these molecules and proteins moving around in solution to some kind of meaningful structure. And it turns out, that the way viruses reproduce is a really good example of how meaningful structure can arise from molecules swimming around in solution. A virus is basically just a relatively short piece of DNA surrounded by molecular shell called the capsid. The capsid protects the DNA inside. Actually, viruses sometimes store their genetic code in RNA molecules instead of DNA molecules, but the point is, viruses are really small and really simple. There’s no room for molecular robots like ribosomes So, for a virus to reproduce, it needs to hijack the molecular machinery of a host cell Once a virus gets inside a cell, the protective capsid falls away leaving the DNA or the RNA exposed, just floating around. Let’s assume it’s RNA in this case. Eventually it will bump into a ribosome, and ribosomes will just blindly read whatever RNA it comes across. So, the ribosome is feeding the RNA into itself and spitting out proteins according to the genetic sequence that’s encoded in the viral RNA. In other words, the cell starts to produce new viral proteins. And here’s the really clever part, these viral proteins are just floating around aimlessly in solution, but, they’ve been built in just such a way that when they bump into each other they snap together, and they snap together at just the right angle. Here’s what happens when you’ve got a whole load of them jiggling around together A meaningful structure arising from a random process You might have noticed that the virus has icosahedral symmetry or dodecahedral symmetry it has twelve identical faces, like this, and that’s really common for viruses. And the brilliant thing is, the RNA of the virus only needs to code for this one single protein to build its protective capsid shell. If you pump out enough of them, eventually twelve will bump into each other and form a capsid. In reality, one of these faces of the capsid may be made of a handful of different proteins, but still, it’s a really efficient use of genetic code. One of my favorite examples is a family of viruses called circoviridae. The DNA of these viruses codes for just two proteins: one that forms the outer shell capsid of the virus, and the other that helps with DNA replication. The DNA is so short. It’s just half a kilobyte in size. That’s as much data as you could store in a 22×22 pixel grayscale image. For comparison, the human genome is 700 megabytes in size Not all viruses have this Icosahedral symmetry, some have spiral symmetry but again, it’s really efficient use of genetic code because it’s made of just a handful of repeating protein units. Among the most complex viruses are ones that infect bacteria, because bacteria have a cell wall that needs to be overcome. So, bacterial viruses have evolved a way to inject their DNA into the bacterial cell from the outside. And yet, the Assembly of the virus inside the cell happens in much the same way, just a jumble of proteins coming together and snapping into the right position. This video is made possible by my patrons on patreon, but I’m also really grateful for the continued support of brilliant.org who are sponsoring this video. Two new things? I want to say about Brilliant that You probably don’t know yet. Well, actually first of all, if you don’t know what it is it’s a website full of amazing maths, science, and engineering problem solving courses. The two new things are well, first of all, it’s gotten really interactive, which I’m really enjoying. Like, a lot of time, you’re not just looking at a static image. In most of the courses and challenges you’re dragging things around and stuff like that, really interacting with the problems. The other thing is they’re introducing offline courses. So, it’s already available for iPhone and it will be available for Android very soon. So you can take courses offline, and you can work on them on your commute where you might not have internet. I really like the way the courses are structured, like, the rate at which it gets harder. You always feel like you’re making progress and it’s really satisfying as you go along. And if you ever do get stuck, there’s a whole community of learners just like you discussing the solutions. So you’ll get there eventually So check it out for yourself today. Go to brilliant.org/SteveMould. The link is also in the description. The first 200 people to use that link will get 20% off annual membership. Which gives you full access to the entire archive of courses and daily challenges. Thanks also to Hamish Todd who lent me his virus self-assembly model. He makes really interesting interactive content. I’ll leave a link in the description for his stuff, and thanks also to Arthur Olson who actually devised that model. I hope you enjoyed this video. If you did, don’t forget to hit subscribe, and I’ll see you next time.

100 Comments

  • Reply Steve Mould April 19, 2019 at 10:35 am

    A lot of people are asking how the genome of the virus is replicated and how it gets inside the capsid. Great questions! Genome replication depends on the type of genome (DNA or RNA etc). Simple example is DNA where the replicating machinery of the host cell blindly replicates the viral DNA. This can be slow when the cell is not in "replication mode" itself. Which is why viruses often code for their own replication machinery. As for how the new genetic material gets inside the capsid, well it has a "high affinity" for the inside face of the capsid proteins. In other words it easily sticks to the inside of the shell as it forms.

  • Reply うんあ うん August 29, 2019 at 5:40 pm

    5:55 is something i do every night

  • Reply Diamonds 555 August 29, 2019 at 7:02 pm

    Haha, one second off of 10 minuites!!

  • Reply Quarnozian August 30, 2019 at 2:22 am

    Wasn't there some experimentation going on with virii to make them exclusively target cancer cells?… One virus cell infecting and destroying a cancer cell to make more cancer destroying virus cells? Sounds pretty awesome in theory.

  • Reply Just A Bit Of Rye August 30, 2019 at 2:22 pm

    So what things do I need to expose due of my genes to turn into like an argonian lizard person thing?

  • Reply KRASH KIDD August 30, 2019 at 3:39 pm

    May I inquire as to how I might acquire your virus demo model/magnets? Brilliant teaching tool!

  • Reply AstralPotatoe August 30, 2019 at 5:02 pm

    At 7:53 the bacteria virus is moving its legs like an animal, do they really do that? or do they move randomly, and snap onto the bacteria randomly without moving anything.

  • Reply Mike Corleone August 30, 2019 at 10:49 pm

    Wow. Totally leave out that DNA is composed of a 4 character, irreducible, biological computer code that instructs not only what you are, but continually runs quality control programs to ensure your DNA doesn't mutate into having anomalous malfunctioning segments.

  • Reply Mike Corleone August 30, 2019 at 10:54 pm

    Are you serious. Ribosomes simply grab random molecule out of the cell? They aren't sent by other molecular machines that received instructions from the ribosome? The cell's internal transportation system is more complex than the New York transit system, and this simplistic explanation does the subject a disservice.

  • Reply Zulfburht August 31, 2019 at 5:30 am

    Basically what I’m getting is a photocopying machine that reads code and prints out results. Or a scantron.

  • Reply Corruptorr September 1, 2019 at 12:55 am

    oh no he made a super virus

  • Reply Anthony Ortiz September 1, 2019 at 1:04 am

    So in other words the Ribosome is taking a shit…

  • Reply Depressionbomb September 1, 2019 at 8:53 am

    Tbh, we could probably manipulate HOX genes to give us another pair of arms and we can play piano in a way that would be impossible for one single person to do

  • Reply llPro Playerll September 1, 2019 at 1:58 pm

    I don’t understand lol

  • Reply WhileImWaiting September 2, 2019 at 12:28 am

    It wasn’t a random process. The magnets were designed and then you, a person, put them in a cup and shook them so they would do what they were designed to do. Nope… not random

  • Reply Markus More September 2, 2019 at 3:44 am

    Where can i get my hands on one of those magnetic Virus models

  • Reply oldcowbb September 2, 2019 at 6:17 am

    ribosome sounds like a turing machine

  • Reply Carmen September 2, 2019 at 9:48 am

    I have found ImAllexx's Dad.

  • Reply Joseph McEvoy September 2, 2019 at 11:48 am

    Outstanding

  • Reply Ryan Stallard September 2, 2019 at 3:47 pm

    There are so many creationist videos this obliterates. Especially 4:18.

  • Reply Gina Disantis September 2, 2019 at 8:52 pm

    Just like a hive mind. We are a virus.

  • Reply exactspace September 4, 2019 at 2:31 am

    I kinda doubt bacteriophage crawl with their legs like that. Can anyone explain if they do or not?

  • Reply Baltazar Razatlab September 4, 2019 at 4:56 pm

    your eyes

  • Reply TheyCalledMeT September 6, 2019 at 7:42 am

    absolutely fascinating .. but one question doesn't let me rest …
    why do those copy machines do that .. and how did the come into existance the first place …

  • Reply Gary Hawkins September 7, 2019 at 10:19 am

    Blown away by:
    1. It works like a magic machine
    2. We figured it out
    3. Can be modeled

  • Reply Hellefleur September 16, 2019 at 2:58 am

    Furiously washes hands with a flamethrower

  • Reply Hellefleur September 16, 2019 at 3:03 am

    This product looks similar but it's freaking $90!! This is why 3D printing is great. Buy some mini magnets and you could make your own.

    http://www.sciencewithinreach.com/product/self-assembly-virus-kit/

  • Reply Paradoxically Excellent September 17, 2019 at 6:44 pm

    This video is awesome. I would have liked an explanation of how the viral RNA replicates.

  • Reply The Unboxing Experience September 18, 2019 at 11:45 am

    Very cool topic! Thank you so much

  • Reply Flishry September 19, 2019 at 2:02 am

    At 7:52 the bacterial virus is walking like a hexapod. Can some viruses walk?

  • Reply Fabio Fernandez September 19, 2019 at 11:03 am

    So I can be stored in a fricken thumb drive

  • Reply crazygame crafter September 21, 2019 at 2:55 am

    DNA is base 5

  • Reply SDS 777 September 22, 2019 at 10:33 pm

    In mathematics, the manifestation of an ordered structure of disordered information is called a strange attractor. On the macrocosm, this process of virus building emulates planet formations. Its as if things already exist and we are traveling through time backwards. Seeing the act of their dissolution as an act of coagulation.

  • Reply MattMonago September 26, 2019 at 10:58 pm

    Where can I buy one of those

  • Reply Tim Bomb September 28, 2019 at 2:10 am

    That virus is cool, i want a virus!

  • Reply Jack Dog September 29, 2019 at 9:30 pm

    who'd have thought proteins are programmed in base-4?

  • Reply Krishna Priya October 2, 2019 at 6:07 pm

    Where can i get such self assembly magnets ?

  • Reply Quinn 78 October 2, 2019 at 8:27 pm

    I have geomags just like the ones 6:30!

  • Reply Q Werty October 7, 2019 at 2:55 am

    Have you just proven that entropy does not always increase?
    Your other video on vibrating ball bearings forming a lattice structure would also be considered.

  • Reply Nebuchadnezzar Quellcris October 13, 2019 at 4:19 pm

    HOLY SHEEEEEEET

  • Reply TomtheMagician21 October 17, 2019 at 7:02 am

    Dodecahedron!!! Yay

  • Reply TomtheMagician21 October 17, 2019 at 7:12 am

    What’s RNA

  • Reply Samudra JS October 17, 2019 at 2:06 pm

    MAN!!! WHY THE HECK IS THIS GUY SO UNDERRATED!?!?!?!????? YOU ARE GREEEEAAAAAAT

  • Reply Peter Trast October 22, 2019 at 6:59 pm

    And you probably believe that this amazing complexity just "accidentally" occurred regardless of the possible number of combinations? I might be willing to grant you this random process given enough time… but a couple billion years to stumble onto all of the variety of life we see today?? LOL

  • Reply Peter Trast October 22, 2019 at 7:03 pm

    "Randomly floating in fluid"? Yes, just like the Greeks who believed in "aether" and the "four main elements". So you still think that any part of biology is still random and not part of the biological machine in function? Look at the explanation of "cells" from the 60s and realize how little we knew then, how little we still know and understand that it is far more complex STILL than you might guess…

  • Reply Peter Trast October 22, 2019 at 7:04 pm

    "Directed. Deliberate." Now you're catching on…

  • Reply Peter Trast October 22, 2019 at 7:05 pm

    "Molecules swimming around in solution". Excuse me, but that is way past the starting point 😉

  • Reply Charlie Angkor October 26, 2019 at 12:38 pm

    so is the ribosome ticking as regularly as in the animatio ? or does it sometimes do a step faster or slower depending on how long it takes for the right molecule to accidentally snap in?

  • Reply Charlie Angkor October 26, 2019 at 12:41 pm

    according to law of thermodynamics, the capsid should fall apart, not self-assemble. UNIVERSE ERROR.

  • Reply Willy Illuminatoz November 2, 2019 at 7:27 pm

    It is not chaotic but Reason exploits chaotic environment to create something

  • Reply A.Tag90 November 4, 2019 at 2:10 pm

    Where can I buy those magnets though?

  • Reply Johnny Symons November 6, 2019 at 11:34 am

    I came here to watch magnets connect, not a fucking science lesson

  • Reply austin fernando November 7, 2019 at 5:42 am

    a turing machine (or billions of them) made alan turing, thus proving him right about ai

  • Reply I. George November 7, 2019 at 4:46 pm

    whaaaaat? the tiny human DNA is 700mb? then forget SSDs, bio storage is the way to go

  • Reply R d November 7, 2019 at 8:55 pm

    7:26 When you realise you fit in a cheap USB stick

  • Reply Don Espoleto November 7, 2019 at 11:40 pm

    The DNA and RNA alone are enough to prove the existence of God.

  • Reply Khardellen November 8, 2019 at 4:41 am

    It would’ve been good to mention that ribosomes font bring it per say, but it’s rather transport to the ribosomes by tRNA (transport RNA) molecule.

  • Reply Ben Brooks November 8, 2019 at 7:09 am

    This really helps as it is one of the hardest things to understand about genetics but it really is our entire life

  • Reply Arto _ November 8, 2019 at 3:10 pm

    Wow, I actually learnt something

  • Reply RickRogers November 8, 2019 at 3:56 pm

    Ah yes, "actually". The word that best defines a scientific education through the years

  • Reply Ora Ora! November 8, 2019 at 8:02 pm

    It seems like that random process of parts floating around and self assemble like magnets is the key to creating replicating machines. Because it allows you to bypass building a very complex machinery that will position parts like we do in human-made devices (while at the same it must have ability to create copies of itself). And thus it significantly simplifies the task of making something that can self replicate.

  • Reply BlankPicketSign November 8, 2019 at 8:10 pm

    Some Creationist: "If a tornado blew through a junkyard, what are the odds it would build a perfect 747? Evolution is nonsense"

    Steve Mould: "I'm about to ruin this fool's whole career"

  • Reply master shooter64 November 9, 2019 at 5:47 am

    dayum molecular biology is amazingly complicated

  • Reply keo kawasaki November 9, 2019 at 7:39 am

    programmers must have got so hyped when they learned about this.

  • Reply Rob Card November 9, 2019 at 1:08 pm

    when you said clever.
    i said accidental.
    chance would perhaps be most fitting.

  • Reply Vorname. Nachname. November 9, 2019 at 4:12 pm

    You could have made it 10 Mina

  • Reply Knives323 November 9, 2019 at 7:13 pm

    I wonder if there's a way we could put a lock on our ribosomes. Like a gene would always need to start a certain way for the ribosome to read it, otherwise it clogs up the ribosome. This way foriegn material could be caught

  • Reply Meph24 November 9, 2019 at 10:00 pm

    Wish these kinds of illustrations existed when I was in school.

  • Reply Cleric775 November 9, 2019 at 10:06 pm

    07:51
    Why on Earth is it crawling?
    Viruses are not Living Things.

  • Reply Preston Garvey November 10, 2019 at 8:05 am

    2:53
    That Guy Is Flyin' Along The DNA
    GO BUDDY GO!

  • Reply h0len November 10, 2019 at 9:11 am

    A great way to show how randomness becomes organised is through AI say ant colony optimization. As each ant starts walking randomly, it is not until there have been a large amount of ants walking in random directions that the AI part starts taking shape, that is when the randomness becomes ordered

  • Reply glen foord November 10, 2019 at 10:29 am

    the same something from randomness can be used to visualise formation of protons in the morass of a birthing universe.

  • Reply Sam Bacon November 11, 2019 at 12:09 am

    DNA isn’t actually a code, it’s just that referring to it as a code is the best way for the layperson to conceptualize it.

  • Reply Malcolm Forbes November 11, 2019 at 1:38 am

    Cool. So cells are Turing Complete. Head? Check. Tape? Check. Availability to make any new thing? Check.

  • Reply Caleb Walker November 11, 2019 at 4:10 am

    Great video!

  • Reply Son of Ode November 11, 2019 at 6:32 am

    You shaking it with purpose, is that random?

    Is it possible that it is not random.
    Sure I am looking for a random woman to take as wife (mate), but the intention was not random, and the criteria also not random.

    Pardon me often I find dificult to understand which is random.

    Gin,

  • Reply Matt G November 11, 2019 at 8:38 am

    This dude is like the pbs kids version of science.

  • Reply Andy Solomons November 11, 2019 at 9:42 am

    People speak as if these atoms KNOW which atom to "grab" next. These atoms have to be "programmed" from somewhere!!.

  • Reply A wYm November 11, 2019 at 9:53 am

    Ty YouTube for that video and thank you Steve

  • Reply MaxChronos November 11, 2019 at 12:26 pm

    So.. my DNA is about 700 megabytes.

    Can I store myself into my flashdrive?

  • Reply macro deth November 11, 2019 at 2:58 pm

    Just say it is molecular programming.

  • Reply eyeam9key November 11, 2019 at 5:43 pm

    All I know.. from a 1970s education.
    Viruses don't have metabolism…
    It's like.. a toxin hidden in a perfect shell, to run wild in organisms that do..

  • Reply David Noll November 11, 2019 at 7:44 pm

    Wow!

  • Reply Xkaku xkaku November 11, 2019 at 10:01 pm

    Your voice sounds like another ryoutuber

  • Reply Kael Griffis November 12, 2019 at 3:56 am

    The process isn't random, it's encoded. That's like saying randomly typing in a sequence of numbers, letters & special characters can, eventually, produce a complex computer program. I agree with your science but it's hard to accept your conclusion of random processes producing complex & meaningful codes that are essential for life. If any one thing goes wrong, depending on what it is, can have devastating results in regards to the genetics.

  • Reply Bloodstar123 November 12, 2019 at 8:03 am

    moar plz

  • Reply Seth Catalano November 12, 2019 at 9:11 am

    Awesome

  • Reply CrryBaaby24 Uzerschwits November 13, 2019 at 6:03 am

    I can’t believe that I know most of this damn, Thanks Biology class lmao

  • Reply Aswin November 14, 2019 at 7:58 am

    He missed the 10 minute Mark by a second
    Honesty level 100?

  • Reply Chris Heichel November 14, 2019 at 3:35 pm

    7:53 I swear that reminds me of replicaters from Stargate

  • Reply Chris Heichel November 14, 2019 at 4:04 pm

    Simple is seriously deceptive….. Compared to other life say human, tree, and pretty much any other life it's very simple but when you take a look at all of the different amino acids all left-handed and nature they don't form that way you still need DNA there for the RNA to reproduce so no virus reproduction without DNA already being involved along with it

  • Reply Emilio Sánchez Rdz November 14, 2019 at 8:30 pm

    Viruses are the irrefutable proof of evolution

  • Reply John Snow November 15, 2019 at 11:42 am

    if random shake of molecule can create a arranged structure, is the chaos decreasing in this process?

  • Reply Ghryst VanGhod November 16, 2019 at 6:54 am

    this is incorrect. the kinesin travels along fibres within the cell and takes the various molecules exactly where they need to be, they are not randomly "jumbling around in solution".

    https://youtu.be/gbycQf1TbM0

  • Reply Ran Charted November 20, 2019 at 8:32 am

    Meaningful structure can arise from molecules swimming around in solution. It is the truth about life. Any order stems from randomness.

  • Reply Ran Charted November 20, 2019 at 8:40 am

    He did not mention how the virus protein helps to replicate the virus itself. sad

  • Reply Sam Sung November 22, 2019 at 9:27 am

    Nice job dragging this video out to the 10 minute mark, according to Dumbtube guidlines.

  • Reply Danielle Wilson December 1, 2019 at 4:52 pm

    This video made me think about how what we call life is really a set of processes that make itself and replicates

  • Reply Silvio Francisco December 8, 2019 at 12:27 pm

    Hi Steve. Very nice video. But explain please how do the DNA or the RNA of the virus get inside the shell of twelve proteins that are produced by the ribosome. Is this also a random process? It means some viruses don't contain any RNA at all? And viruses that contain other kinds of RNA, that are not the viruses' RNA? Oh, wait. You have already answered my questions. Thanks.

  • Reply Erfan Imankhani December 19, 2019 at 7:38 pm

    Actually ribosome translates codes of RNA to different Proteins not codes of DNA
    and RNA is a copy of parts of DNA

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