How I Defeated My Arch Nemesis

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  • เผยแพร่เมื่อ 16 พ.ย. 2024

ความคิดเห็น • 1.5K

  • @ExplosionsAndFire
    @ExplosionsAndFire 3 ปีที่แล้ว +6563

    Science is temporary, grudges are forever xx

    • @dangernoodle8813
      @dangernoodle8813 3 ปีที่แล้ว +165

      yellow bad.

    • @captainchicky3744
      @captainchicky3744 3 ปีที่แล้ว +119

      YOOOOOOOOOOOOO i love how all the science chanels are inteconencted

    • @ieatdirtwasntavailable
      @ieatdirtwasntavailable 3 ปีที่แล้ว +41

      DO NOT DO BIOLOGY

    • @jessepinkman1471
      @jessepinkman1471 3 ปีที่แล้ว +16

      Yellow

    • @utsuhoreiuji6155
      @utsuhoreiuji6155 3 ปีที่แล้ว +35

      Hi Tom, nice to see you here;
      As a greeting, here is the obligatory yellow chem bad (especially in a precipitation tittation)
      Good luck to your PhD!

  • @alexbenavidez4500
    @alexbenavidez4500 3 ปีที่แล้ว +1041

    "You can fart DNA in their general direction and they'll take it in"
    That's a great fucking line of a biochemist.

    • @MarkusAldawn
      @MarkusAldawn 2 ปีที่แล้ว +52

      The DNA equivalent of "yeah, I'll incorporate that into my belief system"

    • @user-pr6ed3ri2k
      @user-pr6ed3ri2k 11 หลายเดือนก่อน +1

      👍

    • @OldManRogers
      @OldManRogers 6 หลายเดือนก่อน

      2 days later "FATHER WHY DID YOU CREATE MEEEEeeee? WHYYY DO I SMELL OF CURRY FARTS?!"

  • @waterunderthebridge7950
    @waterunderthebridge7950 3 ปีที่แล้ว +640

    6:06 It still surprises me how a lot of times in biology/medicine it’s just
    “We don’t care _how_ it works exactly. If it works consistently, we don’t question the process. Don’t anger the science gods with your impious insolence!”

    • @knuckle12356
      @knuckle12356 ปีที่แล้ว +90

      Read up on mechanism of action for most every medication used today.
      The number of times that section begins with "while the _exact_ mechanism is unknown, it is suspected..."
      Translated: well, people used to slather this and smoke that, after which more survived than within the "control" tribe, which had neither poultice nor herb.
      So we refined the alkaloids. The health effects compounded. Then we changed a few methyl groups. People died. But THEN we changed these other methyl groups, and shit started popping off! Leading us to conclude that this shape is more gooder than these shapes. So we stuck with this one.
      Other than the copyrights, the basic drug remains unchanged after 300 years. Or 3000, etc. Kinda scary. Same with surgery and medicine. It looks like so much nonsense and butchery, but it takes a few decades to specialize this organ or that system, and lives are saved by these procedures. Babies are even operated on in utero!!! But it still looks like a kid searching a piñata for their favorite candies when they remove your intestines and just pile them up in a heap beside you...
      So much knowledge, so much history we build upon... but sometimes it sure doesn't look like it.

    • @cristianruske2875
      @cristianruske2875 ปีที่แล้ว +5

      I asked the same for my radio tech relative and he just said doesn't matter

    • @thaumatomane
      @thaumatomane ปีที่แล้ว +14

      @@knuckle12356 So, I am doing my PhD in the history of magic in the premodern world (I specialize in a sub-variety of European ritual magic). Anyway, one thing I always think is crazy is how confidently so many people say "I only believe in science." Which is ridiculous, science is a method of inquiry, not a belief system. When people say that they only believe in science, what they mean is that they believe in materialism - a historically constructed modern inheritance from enlightenment era philosophy. It is a cosmological system, just like Catholic theology, neoplatonic philosophy, or astrological theory (the 5000 year old complex stuff, not the silly tabloid/tiktok rubbish). One thing I think is valuable is to realize that materialism is not the baseline objective reality when all "beliefs" have been stripped away. It is just one of the many cosmographies by which people interpret the world.
      Edit: typos.

    • @aragocz727
      @aragocz727 ปีที่แล้ว +13

      Same goes for coding, if it works you don't question it, that's why programmers keep the 20 years old legacy code

    • @mariomario1462
      @mariomario1462 ปีที่แล้ว +15

      ​@@thaumatomaneuh no. Nothing you said Is remotely true. believing in science means you get results in life. Theology Is literal make believe. Maybe you should major in logic classes first before you talk nonsense

  • @bryby216
    @bryby216 3 ปีที่แล้ว +349

    I'm a molecular biologist in an academic lab, and dude, I'm so thankful for your videos. It's easy to forget how cool what we do is, and instead just treat it like a grind. Thanks for making these videos, and thanks for sharing your protocol. It's refreshing

    • @quote.d
      @quote.d 3 ปีที่แล้ว +1

      This

    • @thersten
      @thersten 3 ปีที่แล้ว +1

      Yes. Very true 👍

  • @Pyriphlegeton
    @Pyriphlegeton 3 ปีที่แล้ว +2132

    4:26
    "Sort of like Bioshock but less shooting Spiders and Lightning"
    *...for now.*

    • @Drankoii
      @Drankoii 3 ปีที่แล้ว +35

      Exactly my thought, lol. I hope to live to see bacteria that shoot fire and lightning.

    • @sharpfang
      @sharpfang 3 ปีที่แล้ว +20

      Electric Eel DNA will take care of lightning. Spiders - TRIVIAL.

    • @beezmanit2683
      @beezmanit2683 3 ปีที่แล้ว +6

      @@Drankoii hopefully it isn't sentient

    • @Usual_User
      @Usual_User 3 ปีที่แล้ว +1

      @@beezmanit2683 😂

    • @Waluigi_Time778
      @Waluigi_Time778 3 ปีที่แล้ว +6

      If the petri dish exploded with baby spiders I would be burning down the lab

  • @stijn2472
    @stijn2472 3 ปีที่แล้ว +198

    This is one of the things I like about you. When you discover something, instead of patenting it or trying to sell a method you came up with to a company, you make it available to the public and I appreciate that. Thank you

    • @thersten
      @thersten 3 ปีที่แล้ว

      Bill gates says hello.

    • @2ue
      @2ue 8 หลายเดือนก่อน +1

      Cant patent a simple change in methodology unless it was made proprietary anyway.

  • @ace-kz9id
    @ace-kz9id 3 ปีที่แล้ว +3600

    I might not understand this stuff at all but it is super intresting

  • @KateeAngel
    @KateeAngel 3 ปีที่แล้ว +1403

    "Everything in biology is yellow".
    Me, a cyanobacteriologist: "Cool story, bro!"

    • @DancingRain
      @DancingRain 3 ปีที่แล้ว +173

      I see some very confused botanists and mycologists in the room too 😀

    • @wormguts5950
      @wormguts5950 3 ปีที่แล้ว +78

      epic cyanobacteriologist meme

    • @carsonfujita-turnbull4549
      @carsonfujita-turnbull4549 3 ปีที่แล้ว +47

      Yeah, someone is gonna have to translate this into common speech in order for anyone but biologist to know what the joke is. If anyone could explain to me, I would appreciate it.

    • @Actvontact
      @Actvontact 3 ปีที่แล้ว +52

      @@carsonfujita-turnbull4549 the cell watching mfers are mad coz light vibes at the worng wavelangth n shit

    • @inciteinsight2331
      @inciteinsight2331 3 ปีที่แล้ว +94

      @@carsonfujita-turnbull4549 Cyanobacteria are all blue. Their name means “blue bacteria”.

  • @VincentGroenewold
    @VincentGroenewold 3 ปีที่แล้ว +713

    I worked in science and doing things like this for over 10 years and 1 thing I learned is how everyone always copies protocols to the T. It may make sense of course, but it's never really a thing people think hard about it seems. I once started research on an entire new species for our work, got a protocol from another lab full of alternative approaches and no real explanation as to why. Turned out they had 1 step I recognized to likely be extremely in-efficient. So I just did it my way and presto, totally worked. That was when I concluded this probably happens a lot in labs. That protocol was in use for years as well.

    • @calamariaxo
      @calamariaxo 3 ปีที่แล้ว +92

      Yeah, seen this myself in our lab, but it's not just in labs.. This happens everywhere. Humans are surprisingly happy to just follow instructions without thinking about what we're actually doing most of the time. Engineers and scientists might be somewhat better trained to notice these things, it's often the kind of magical *zing* that somehow improves your project or furthers science in some way, but we're still all human.

    • @paavobergmann4920
      @paavobergmann4920 3 ปีที่แล้ว +34

      Yeah. In EM work, also. I think, usually your margins of error are unknown, or tight, and you have so many variables at play that systematically trying the parameter space to find the optimal protocol is not feasible (an EM fixation & embedding can stretch longer than a week, and you haven´t even started sectioning). Also, lab protocols tend to evolve like software code: stitched together from subroutines that used to work somehow for similar problems. So if it happens to work for you, or did work at least once for whoever published it, you stick with it, however inefficient or counterintuitive or downright weird it might seem. Better get "kind of ok-ish" results consistently than burning your PhD grant on optimization. You can start doing that once things stop working altogether. And you will, eventually.

    • @kendarr
      @kendarr 3 ปีที่แล้ว +9

      @@calamariaxo agree I've seen some stuff in wood working that people just don't seem to know why it is the way it, and don't seem to try in change it

    • @Max-cj8vm
      @Max-cj8vm 3 ปีที่แล้ว +3

      I used to work under a grad student who insisted that all steps of a Western blot must be kept protected from light

    • @thersten
      @thersten 3 ปีที่แล้ว +7

      That's pretty much how the peak of human technology is reached. It's a conglomeration of individual pieces of knowledge and technology.
      Ask how it works and very few people really know.

  • @afroninjaman1
    @afroninjaman1 3 ปีที่แล้ว +86

    The superstition comment got me. I've always said genetics is half black magic. In my capstone project lab the grad students had special P10 pipettes labelled "Golden Child" and "Vampire" because respectively the former made reactions generally and PCR specifically work like magic, and the latter drained the life out of your experiments.

  • @moonface550
    @moonface550 3 ปีที่แล้ว +2553

    Obligatory "yellow chem bad"

    • @TurboFryer1337
      @TurboFryer1337 3 ปีที่แล้ว +107

      ah, a fellow "piss chemistry bad" enthusiast

    • @Dinnye01
      @Dinnye01 3 ปีที่แล้ว +43

      @@TurboFryer1337 and they are actually friends with the piss chemist

    • @explosiverift2037
      @explosiverift2037 3 ปีที่แล้ว +30

      @@Dinnye01 Nile Red?

    • @22Mycraft
      @22Mycraft 3 ปีที่แล้ว +27

      @@explosiverift2037 explosions and fire, extractions and ire. Get chemist, highly recommend

    • @TheRealDescartes
      @TheRealDescartes 3 ปีที่แล้ว +10

      *Y E L L O W*

  • @NicRobertsNerd
    @NicRobertsNerd 3 ปีที่แล้ว +75

    What an amazing thing to be living in a time when credible science procedural tutorials are available for free on TH-cam. Thank you so much for posting this.

  • @karigucio
    @karigucio 3 ปีที่แล้ว +202

    the advert i got before this vid was about getting rid of ecoli from the water. Quite on point

    • @Amipotsophspond
      @Amipotsophspond 3 ปีที่แล้ว +26

      yeah the word detecting advert is funny sometimes.
      Video Title:why the new kia is a death trap!
      Advert: buy the new kia!

    • @junigearx7452
      @junigearx7452 3 ปีที่แล้ว +2

      Ahh.. Foreshadowing i like that.

  • @Quroe_
    @Quroe_ 3 ปีที่แล้ว +32

    You've made bioengineering somewhat understandable to me, a mechanical engineer. I hope I get to collaborate and effectively communicate with a bioengineer well enough later in my life and make something cool because of you.

    • @kdevlogs5550
      @kdevlogs5550 11 หลายเดือนก่อน +1

      I've always been interested in all types of engineering, and biology has always been mind blowing to me from the dumbest mechanical perspective because, by some miracle, a tiny protein made some mechanism and those mechanisms became bacteria, and now we're here. crazy how complicated even the tiniest little organism is

  • @LagnajeetPradhan
    @LagnajeetPradhan 3 ปีที่แล้ว +103

    This was my protocol for transforming BL21s when I was doing protein engineering and crystallography. I believe I also used to add MgCl2 besides the CaCl2 for making the cells competent. I guess there's no need to do that since ur protocol clearly works very well. I worked with BL21s for a long time. Never knew that it could be someone's arch nemesis. 😊

    • @yeduprasad
      @yeduprasad 3 ปีที่แล้ว +11

      I think it's a bit of a sensationalist take on the differences between various E. coli strains. I agree with you, BL21 is a perfectly uncomplicated strain to work with.

    • @ekaterinaburakova8629
      @ekaterinaburakova8629 3 ปีที่แล้ว +8

      That's what he's doing here: just regaining cell competence that is lost upon storage or just over time. This is indeed never a problem when you work in a well equipped lab.

    • @skegfod51
      @skegfod51 3 ปีที่แล้ว +5

      I was just about to type this up, but yeah Ive always added MgCl2 when making compitent cell. Ive never had a problem making compitent BL21 with a high transformation efficency. BL21 is very well behaved compaired to some of the other strains i have had to work with!

    • @cybersentient4758
      @cybersentient4758 3 ปีที่แล้ว +1

      I like your funny words magicman up

    • @cybersentient4758
      @cybersentient4758 3 ปีที่แล้ว

      I like your funny words magicman

  • @lucashuttebraucker6255
    @lucashuttebraucker6255 3 ปีที่แล้ว +20

    Hey there, just a few tipps:
    When you prepare your cells fresh every time you have a big margin of error.
    I would suggest to prepare competent cells in advance supplement the buffer with 15% glycerol and freeze them. There are lots of viable protocols available. Important is just to work on ice the whole time, and keep the cells always cold.
    Best at -80c but -20 is sufficient for a week or two.
    Also I recommend to transform one prepared aliqout with a standardized plasmid and calculate the theoretical transformation efficiency.
    Then you can transform cells within 2 h.
    Also for plating the cells I personally prepare always 2 plates, one with 100 ul of the cells in soc media and one with the rest one with the rest.
    Finally if you can't or don't want to prepare cells ahead, you can use TSS transformation, it is fast, simple and idiot proof. You can use e coil directly from the plate. Just the efficiency is not that great.

  • @blackychan7335
    @blackychan7335 3 ปีที่แล้ว +537

    I understood almost nothing but still enjoyed every minute

    • @jonathanodude6660
      @jonathanodude6660 3 ปีที่แล้ว +13

      @Niculae George his bacteria wasnt getting genetically modified so the step that kills unmodified cells killed everything. this is how you make the GM bacteria survive

    • @LordSniggles
      @LordSniggles 3 ปีที่แล้ว +6

      @@PeterohPeter this guy gets it. Ignorance does not equal lack of intelligence.

    • @thersten
      @thersten 3 ปีที่แล้ว

      I don't really know why anyone who hasn't studied biology would watch this..... But just study biology and you'll get it. 🤷👍

    • @GetBonked
      @GetBonked 3 ปีที่แล้ว +1

      @@thersten the same reason people watch any other educational video. To learn lmao. You dont know things until you introduce yourself to them. The more you watch, the more you understand.

    • @thersten
      @thersten 3 ปีที่แล้ว

      @@GetBonked he literally said he understood almost nothing. That's not how educational videos work and that's not how courses work either. If you didn't understand like him then you're missing more than a few prerequisites. LMAO

  • @NachozMan
    @NachozMan 3 ปีที่แล้ว +36

    I've been learning Micro Biology for college this semester and I'm starting to understand what you talk about a bit more in your videos now! Really cool!

  • @-w-.
    @-w-. 3 ปีที่แล้ว +537

    Now that E&F is taking a break, I'm glad that someone decided to take his place.

    • @pas.
      @pas. 3 ปีที่แล้ว +8

      What's E&F? Asking for a friend of a friend.

    • @-w-.
      @-w-. 3 ปีที่แล้ว +31

      @@pas. Explosion & Fire, the mad chemist TTE mentioned at the start

    • @kamilag2791
      @kamilag2791 3 ปีที่แล้ว +5

      Bold of you to assume there's only 1 position

    • @twothreebravo
      @twothreebravo 3 ปีที่แล้ว

      My thought exactly.

    • @bur1t0
      @bur1t0 3 ปีที่แล้ว +3

      Is it a one year break? Or is it just his usual upload schedule?

  • @zenzetsu
    @zenzetsu 3 ปีที่แล้ว +84

    Me: subscribes to The Thought Emporium for his physics videos with little knowledge or interest in biology
    The Thought Emporium: releases biology video
    Me watching the biology video anyway: I like your funny words magic man

    • @nmraven-gx9gt
      @nmraven-gx9gt 2 ปีที่แล้ว

      Opposite direction for me lol

  • @janrace6466
    @janrace6466 3 ปีที่แล้ว +676

    3:35 Ooooooh, so THAT's why the university of biology in my country keeps a herd of sheep!

    • @andrewseung2692
      @andrewseung2692 3 ปีที่แล้ว +3

      Lol

    • @noahhuffstutler2686
      @noahhuffstutler2686 3 ปีที่แล้ว +111

      As a computer scientist, can confirm that fresh sheep blood helps make our programs work.

    • @firestorm5371
      @firestorm5371 3 ปีที่แล้ว +37

      @@noahhuffstutler2686 child sacrifice also work

    • @noahhuffstutler2686
      @noahhuffstutler2686 3 ปีที่แล้ว +58

      @@firestorm5371 I've tried it before, but the Devil is sick of my shit. IIRC his last words to me were "You are putting me through hell."

    • @janrace6466
      @janrace6466 3 ปีที่แล้ว +26

      @@noahhuffstutler2686 And that explains why the university of computer science is right next door.

  • @AdalizMColon
    @AdalizMColon ปีที่แล้ว +3

    This was fascinating! Thank you for giving me an inkling again of why I loved and studied microbiology. I never got to work in the profession but still love it. Also, the last note, where it read "Use loop, not swab," brought back how much I hated using a loop in my college lab courses. I was so bad, I always broke the agar. Again, this was great!

  • @jafizzle95
    @jafizzle95 3 ปีที่แล้ว +101

    This is my favorite channel where I don't know what the hell is going on.

  • @davidgrigoryan6207
    @davidgrigoryan6207 3 ปีที่แล้ว +87

    Me an Electronic Engineer: Ah yes, E. coli

    • @shadowghost-lk1sg
      @shadowghost-lk1sg 3 ปีที่แล้ว +9

      If anything electrical engineering is pretty close. Lots of theory and terminology in genetic engineering are taken from electrical engineering; the engineered sequences are called circuits and a lot of the papers even use IEEE formatting. Its actually really interesting stuff.

    • @meltossmedia
      @meltossmedia 3 ปีที่แล้ว +5

      @@shadowghost-lk1sg first them, now neuroscientists. It's the ultimate "You can copy off me, just change it a little"

    • @jacky9575
      @jacky9575 3 ปีที่แล้ว +4

      @@meltossmedia as a neuroscientist, I confirm, literally we have biostatistics, advanced mathematics and bioelectricity as subjects

    • @_-_-Sipita-_-_
      @_-_-Sipita-_-_ 3 ปีที่แล้ว +2

      Electronic coil

  • @Reddotzebra
    @Reddotzebra 3 ปีที่แล้ว +7

    Like we used to say back when I was in molecular diagnostics "The definition of insanity is attempting the same thing over and over and expect different results. In this lab that's Tuesday."

  • @Tommy-pv1vh
    @Tommy-pv1vh 3 ปีที่แล้ว +36

    6:10 just like a cadillac northstar v8 nobody knows for sure how or why the engine is running but as long as you don't look too closely at it it will work

    • @TheAechBomb
      @TheAechBomb 3 ปีที่แล้ว +4

      until it just doesn't for no reason

    • @Dinnye01
      @Dinnye01 3 ปีที่แล้ว +5

      @@TheAechBomb superposition. It both works and doesn't, until you start checking explicitly.
      Macro wuantum phenomena.

    • @SoI_Badguy
      @SoI_Badguy 3 ปีที่แล้ว +1

      Just keep putting oil in it lmao

  • @seannoe750
    @seannoe750 3 ปีที่แล้ว +4

    I love troubleshooting that goes like this. Something that seems daunting at first becomes obvious when you perfect your protocol.

  • @skublicsimre8047
    @skublicsimre8047 3 ปีที่แล้ว +137

    ah yes explosions and fire my favorite crackhead chemist

    • @hugovandenhoek1032
      @hugovandenhoek1032 3 ปีที่แล้ว +13

      He now works with state secrets. I'm not sure if this is ridiculously good, bad, or both.

    • @ExplosionsAndFire
      @ExplosionsAndFire 3 ปีที่แล้ว +20

      @@hugovandenhoek1032 look, it's either good, or bad, or both, and I also haven't figured it out yet

    • @05Matz
      @05Matz 3 ปีที่แล้ว +10

      @@hugovandenhoek1032 Wait, really? That sucks. Secret "science" isn't real science. It's why I always have such mixed feelings when cool new technology is announced and then I find out it's a publicity stunt from somebody like DARPA and won't actually be used for non-war purposes for decades, if ever -- an organization officially dedicated to world domination (OK, technically "maintaining USA global dominance") is a bad poster child for science, no matter how much people try to conflate the two (perhaps they watch too many James Bond movies?). Governments will use new technology only to undermine each other or otherwise play zero-sum or negative-sum games until it is eventually independently discovered by too many people to keep it secret, rather than allowing it to be developed on and benefit all of humanity.* Only in the openness of daylight and peer review can true science exist. Open Access is the only true scientific publishing, though for the other 'non-proprietary' stuff, at least there's Sci-Hub to make the best of a bad situation that shouldn't exist in the first place.
      *(Not that monopolistic corporations are any different in that regard -- they just borrow the state's apparatus for violence and have a time limit on how long they can be dicks about it due to patent expiry [unless it's considered a pharmaceutical in the USA, in which case it never expires as long as you keep up on the "change of process" paperwork]. DIGRESSION ON PATENTS FOLLOWS:
      In my opinion, patents should be a central registry that is automatically licenced by the government on the holder's behalf for a fixed maximum royalty rate, and you can negotiate with the holder [if they can be contacted] for a better deal if you want. Nobody should ever hold a true monopoly, or be unable to use something because they can't figure out who owns the rights or if they even still exist. It would also help small inventors get money out of patents without the need for a legal team, marketing, negotiations and the like, as well; and discourage the filing of large, intentionally vague, over-broad patents in favour of a greater number of specific, clear, well-documented ones relating to different parts of a process -- becoming a money-making building-block for other companies' processes, rather than 'area denial' to prevent competition. You might even WANT to publish guides helping other companies implement your patents, as it makes them more likely to use them rather than find a way around them or buy from someone else.
      Patent enforcement, royalties collection from users and receipt of funds by patent-holders would all be easier, more transparent, and more efficient if a single centralized government body (rather than hordes of legal contractors and sub(sub(sub))contractors backed up by the overworked court systems) handled it -- as would taxation of patent income (such as to fund more research), which is probably another reason why incumbents would be against such reforms.
      From what I've heard, both Intel and AMD can only exist today by violating each other's patents flagrantly (as you can't build a modern X86 CPU without technology from both companies) and settling the inevitable lawsuits out of court by 'trading' dropping lawsuits against each other over and over again. This is silly, and prevents any third company from competing in that space because they don't have the patent arsenal to 'trade' settlements and the big two aren't licensing their patents at any price. I'm sure this goes on in other fields as well. Mandatory licencing changes that to a monetary barrier to entry that can be easily quantified (such as to potential investors) even if all negotiations break down -- they'd end up with a significant amount of their profit siphoned off to the big two in royalties depending on how many patents they need to use, but if their own technology is revolutionary enough, they can get a shot at trying it out and might still end up profitable (and/or used in turn BY the big 2 after the independent offering fails, still granting the new inventor a revenue stream). If a technology is truly world-changing, the barriers to implementing it need to be as low as possible, and if we're determined to give the first-to-file on a new technology a cut of revenue from all products even vaguely related to that invention (instead of, eg. funding R&D through government prize programs or commissioned research), this is the least damaging way to do it.

    • @sharadthecurioustardigrade1533
      @sharadthecurioustardigrade1533 3 ปีที่แล้ว +1

      @@ExplosionsAndFire it's in a superposition of all of them (quantum shit)

    • @theowainwright7406
      @theowainwright7406 3 ปีที่แล้ว

      ok

  • @Eterrath
    @Eterrath 3 ปีที่แล้ว +3

    It's the first time in highschool that I learned about DNA, Escherichia Coli and this mythical field called genetic engineering. I was looking up on TH-cam about DNA and stuff to prepare my notes better and oh well, here I am now. But I really like your sense of humor and how you were so open minded about sharing your recipe with everyone. So, liked and subscribed! Best of luck.

  • @latitzouri
    @latitzouri 3 ปีที่แล้ว +231

    The problem is that you're too interesting, each time you publish something I redo a marathon

  • @FantomZap
    @FantomZap 3 ปีที่แล้ว +4

    I really can't tell you enough how much I love your videos. Every single one is immensely informative and relaxed. Thank you so much.
    Also as per your question, I'd like to see a multicellular organism modified in a unique way. That would be so cool although I know its much more expensive and labor intensive.

  • @129chrisseb
    @129chrisseb 3 ปีที่แล้ว +31

    Avoid like the plague, says the biochemist with several petri dishes before him. . .

  • @TotallyNotJoe_
    @TotallyNotJoe_ 3 ปีที่แล้ว +6

    This honestly gives off the same vibes as a relaxing cooking channel

  • @morkovija
    @morkovija 3 ปีที่แล้ว +48

    Oh boy!The wait is over! Smother us with delicious bacteria comrade!

    • @heh2393
      @heh2393 3 ปีที่แล้ว +8

      Uhhh, mom! The neighbour's kid is behaving weirdly... again!

  • @CamStLouis
    @CamStLouis 3 ปีที่แล้ว +6

    Man I wish I had known this approach back in my college days (2010-14). My old bio prof will love this, I'm going to get in touch and see if we can't amp up that disappointing glow gene demo with this method.

  • @dominicsurette2890
    @dominicsurette2890 3 ปีที่แล้ว +122

    EXPLOSIONS AND FIRE, YEESSSSSS

  • @yeduprasad
    @yeduprasad 3 ปีที่แล้ว +1

    CaCl2 transformation is the standard chemical transformation protocol for BL21 cells. You could use a bit of MgCl2 too to enhance the process. You can do it on a larger scale and freeze the cells in liquid nitrogen, and then store it in a freezer for long periods of time. I find it very strange that you find BL21 cells so frustrating. I think they are brilliant to work with as long as you don't have to use them for DNA isolation. The key is to use RecA negative strains like DH5alpha for all DNA manipulations, and once you have your clones sorted and confirmed, switch to BL21 strains for protein expression.

  • @haydenclaussen7155
    @haydenclaussen7155 3 ปีที่แล้ว +75

    BL21 E. Coli: *nooo u cant just spin me to get me to accept DNA easier*
    ThoughtEmporium: *hehe spin go brrr*
    bro you should get an award for this, bc this is incredibly smart

    • @SouthernHerdsman
      @SouthernHerdsman 3 ปีที่แล้ว +2

      this comment should be pinned ;)

    • @ReapingMiner
      @ReapingMiner 3 ปีที่แล้ว +3

      This is common practise in molecular biology labs across the world. ;)

    • @Relatablename
      @Relatablename 3 ปีที่แล้ว +3

      @@ReapingMiner I really liked how he plated the entire cell pellet though. I haven't seen that done during my time in the lab (as an intern).

    • @ReapingMiner
      @ReapingMiner 3 ปีที่แล้ว

      @@Relatablename yeah, i usually grow a liter to OD 0.45, wash, and then ultimately resuspend the pellet in like 20 ml transformation buffer or so; with a little DMSO and make ~60 tubes of 300 ul aliquots. Easily enough for 540 transformations and will last me 2-3 years. Unless my colleagues "borrow" my cells or if i come across many difficult transformations.

    • @Relatablename
      @Relatablename 3 ปีที่แล้ว

      @@ReapingMiner Sounds pretty efficient. We were in a medical research lab so cultured stuff was a minority of our work. Our trials were mouse based, so lots of BALF samples, RNA extraction from lungs, qPCR and western blotting. Maybe that explains why I hadn't seen it before? Idk, but the mouses were pretty cute.

  • @sirgareth87
    @sirgareth87 3 ปีที่แล้ว +30

    TH-cam: Are you interested in microbiology?
    Me: No
    TH-cam: Well here's a video on bacteria. Enjoy!
    Me: But I....
    TH-cam: I SAID ENJOY!!!

  • @PancakeInvaders
    @PancakeInvaders 3 ปีที่แล้ว +5

    Thanks to your videos, I've been motivated to follow biology and chemistry courses on MIT open courseware, and I now understand way better the things you talk about in your videos and streams about genetical engineering (plasmids, promoters, etc)

  • @Lorentari
    @Lorentari 3 ปีที่แล้ว +2

    I have a possible improvement to your plating technique to avoid having only a big smudge of cells that you talked about around 12:45
    - On a single plate, plate your bacterial in one quarter of the dish.
    - Take a new inoculation loop and drag a sine-like wavy line from the inoculated quarter an adjacent quarter.
    - Take another inoculation loop and drag a new wavy line from quarter 2 to quarter 3 - repeat for 3 to 4.
    This way you will have made a natural dilution of your culture, and assuming you had enough for the first quarter, one of the quarters should have an appropriate amount of cells for your continued work.

  • @mmcharchuta
    @mmcharchuta 3 ปีที่แล้ว +14

    My internet's low, but i just have to set the quality to the highest to appreciate your nice shots!

  • @RonakDhakan
    @RonakDhakan 3 ปีที่แล้ว +14

    Biologists getting their fun by naming bacteria 'Turbo".

    • @paavobergmann4920
      @paavobergmann4920 3 ปีที่แล้ว +3

      biology is nickname heaven

    • @michaelclark4876
      @michaelclark4876 3 ปีที่แล้ว

      @@paavobergmann4920 Joke nickname heaven even. Especially the names or mutant phenotypes and the genes producing them in many model organisms. Rutabega and Dunce mutants for memory defect mutants, cheapdate for ethanol sensitivity, ether-a-go-go for making flies shake and dance from ether. The gene gets named after the mutant. So dunce encodes a
      serious, stoodforcan probably guess what the name for the cell cycle regulatory kinase called YAK means. We kept pulling kinase after kinase out of screens for a while. It got old.

  • @Broetchen98
    @Broetchen98 3 ปีที่แล้ว +12

    The comparisson with the goat reminds me on a Lab at my university, where you shouldn't wear a hat. Because everytime someone wears a hat, the experiment did not work.

    • @lewan1905
      @lewan1905 3 ปีที่แล้ว +3

      These are the kind of things that I love about working in a lab. These completely absurd and random rules that get established because something went wrong one to many times or something worked once and nobody wants to change it.

  • @michaelhicks8603
    @michaelhicks8603 3 ปีที่แล้ว +5

    Thankyou for referencing possibly the greatest chemistry channel on TH-cam!

  • @ttld678
    @ttld678 3 ปีที่แล้ว +19

    I can’t believe we have a scientists such as yourself who’s also willing to share such amazing breakthroughs that’s revolutionize Proteins synthesis processes

  • @dsblocks
    @dsblocks 3 ปีที่แล้ว +3

    "the biggest issue with these is: they were ONLY selected for speed, this means they're terrible at just about everything else" also accurately describes horses.

  • @matterwiz1689
    @matterwiz1689 3 ปีที่แล้ว +44

    3:46 Is it alchemy? Or is it surface plasmon resonance?

    • @PranavViswanathan
      @PranavViswanathan 3 ปีที่แล้ว +8

      all the references in this comments section make me so happy. nah its probably ghosts.

    • @matterwiz1689
      @matterwiz1689 3 ปีที่แล้ว +8

      @@PranavViswanathan the ex&f fanbase is on withdrawal. The last video came out pretty recently but we know it's gonna be a while...

  • @PaulMenden5659
    @PaulMenden5659 10 หลายเดือนก่อน +1

    This is interesting. I haven't had many issues with transformation efficiency of BL21 (I used Origami B)
    My trafo protocol is:
    200uL chemically competent cells + 1uL Plasmid (from a miniprep)
    Incubate on ice for 30 minutes
    Incubate at 42°C for 1 minute
    Add 800uL LB medium
    Plate 100uL on agar containing an antibiotic (I used Amp).
    I didn't incubate the cells in LB before plating on antibiotic, but it works.
    Variation with more recovery time:
    After the 42°C step
    Transfer all 200uL to 2mL LB
    Incubate at 37°C for 45 minutes (agitated)
    Plate 100uL on agar containing an antibiotic.

  • @Djoodibooti
    @Djoodibooti 3 ปีที่แล้ว +32

    GLOW IN THE DARK BABY, HERE I COME!

  • @theovermuffin1027
    @theovermuffin1027 3 ปีที่แล้ว

    I do a very similiar protocol for quick and dirty E. coli transformation.
    Only differences:
    0,1 M NaCl is already pre-cooled
    No washing of the pellet with NaCl
    Heat shock done at 42 °C for 45 s
    I only add 200 µl of LB0 for recovery, do the same incubation and then plate twice, once 10 µl and once 100 µl (to buffer out too little or too many colonies)
    Rest is stored at 4 °C over night in case I switched up the antibiotic resistance :D
    For spreading I love glas beads, best spread I have ever seen

  • @thorvaldspear
    @thorvaldspear 3 ปีที่แล้ว +7

    14:00 nice Tom Scott reference

  • @stagnantfox3027
    @stagnantfox3027 3 ปีที่แล้ว +1

    I wonder what the ratio of Natural scientists (biology, chemistry, physics) vs average people view this channel. I for one barely understand anything said in this video but I love watching these kinds of things.

  • @o_--
    @o_-- 3 ปีที่แล้ว +72

    14:03 do I spy a tom scott reference?

    • @randomgooy7456
      @randomgooy7456 3 ปีที่แล้ว +3

      Wait how is this comment 3 hours old

    • @Theinatoriinator
      @Theinatoriinator 3 ปีที่แล้ว +5

      @@randomgooy7456 channel member / patreon

    • @randomgooy7456
      @randomgooy7456 3 ปีที่แล้ว

      @@Theinatoriinator oh

    • @sohamsengupta6470
      @sohamsengupta6470 3 ปีที่แล้ว +4

      Yes indeed. I'm just trying to figure out if it's also a covert little jab at the ad itself which he's doing

  • @KeAlHa
    @KeAlHa 3 ปีที่แล้ว +1

    I've worked with BL21 cells a lot and don't seem to have the same issues you're having. There's two main differences I noticed between how we work with cells. One is to keep them on ice for just about all of the steps except for heat shock and 37 C incubations, and two is the length of time to heat shock. 90 seconds seems like a very long time. The protocols I follow it's usually 10 seconds, maybe 30 at the longest. Also, I think pelleting the cells at too high of a speed can damage them, same with pipetting them up and down too much.

  • @namAehT
    @namAehT 3 ปีที่แล้ว +12

    "They all smell like butthole" is probably the best line I've ever heard you utter.
    Ok, "Fart DNA in their general direction" is pretty good too

  • @MegaScienceguru
    @MegaScienceguru 3 ปีที่แล้ว

    To think i started following this guy when i was a teenager and he was making a fuser in the basement with an old vacuum cleaner and now we're here. My hats off to you dude your videos never disappoint

  • @SomeGuy-yl1bx
    @SomeGuy-yl1bx 3 ปีที่แล้ว +8

    *Mentions Explosions&Fire*
    Ah, I see you're a man of culture as well.

  • @jim2725
    @jim2725 3 ปีที่แล้ว +13

    Its funny how i watch these video's, while the closest thing to actual lab equipment I have is a $20 microscope.

  • @PoIiwag
    @PoIiwag 3 ปีที่แล้ว +3

    "How do defeat bullies"
    Google: tell an adult
    Bing:

  • @absoluteunit2542
    @absoluteunit2542 3 ปีที่แล้ว +1

    With that transmutation circle, you're gonna bring back a dead person instead of sacrificing a goat.

  • @Ethereal.18
    @Ethereal.18 3 ปีที่แล้ว +57

    Any new updates on synthetic spider silk beverages 😂

    • @teteteteta2548
      @teteteteta2548 3 ปีที่แล้ว +25

      It’s silky smooth

    • @mozkitolife5437
      @mozkitolife5437 3 ปีที่แล้ว

      @@teteteteta2548 Here, take all my likes.

  • @cryptid-king
    @cryptid-king 3 ปีที่แล้ว +1

    I remember doing this as a lab in highschool but I didn't really understand what we were doing- this breaks it down much better

  • @leemon2677
    @leemon2677 3 ปีที่แล้ว +6

    No idea what is going on in the video but youre basically the Half Blood Prince of microbiology

  • @andoan4510
    @andoan4510 2 ปีที่แล้ว +1

    This is both fun contents and helpful stuffs. I am trying to do a similar thing in my undergrad research lab but with a mammalian cell line, though different, there are some pretty helpful stuff to learn here while enjoying the content. Please don't stop making videos :)

  • @devinnelson2504
    @devinnelson2504 3 ปีที่แล้ว +11

    The explosions&fire love is great to see. I’d love to know what advice you’d pick up from crime pays but botany doesn’t lol

  • @tanteidaiko
    @tanteidaiko 3 ปีที่แล้ว

    In my lab we plate it a little differently. Similarly, we pellet down the bacteria. But instead of picking up the pellet, we remove access LB, leaving about 50uL of LB. Then, we resuspend the pellet in the 50 uL LB. The 50 uL suspension is then drawn and plated. I find this method much more effective as we do not leave any pellet inside the tube.

  • @danielnewton2390
    @danielnewton2390 3 ปีที่แล้ว +3

    The frozen peas really caught me off guard!

  • @TseMaverick
    @TseMaverick 3 ปีที่แล้ว +1

    There are a few problems in your protocol:
    1> [IMPORTANT] Duration of sub-culture: should grow until mid-log phase or slightly early. Actual time depends on the growing environment. OD600 should be around 0.2~0.3
    2> Vessel for sub-culture: use a larger vessel to get more aeration and more healthy cells, eg. conical flask/50ml conical tubes
    3> [IMPORTANT] Keep your competent cells on ice ALL the time until transformation!
    Especially with 1 and 3 in mind, you shouldn't need to use all the cells for plating at the end... and get a spreader for the plating pls
    Advice to look into the CaCl2 transformation protocol in "Current protocols in molecular biology" for a complete protocol, and look at comparisons among DH5a, BL21, TOP10 for transformation efficiency provided by science suppliers. Should not be a big difference for well-known plasmid like pUC series.

  • @slowlylosingmysanity9726
    @slowlylosingmysanity9726 3 ปีที่แล้ว +6

    The container and apparatuses you guys use just look amazing am im really curious what are those and what they do, im planning on collecting em for some reason lol

    • @kendarr
      @kendarr 3 ปีที่แล้ว

      Right? They look so cool lol

  • @palliyil
    @palliyil 3 ปีที่แล้ว +1

    Oh! That frozen peas idea is just pure genius!

  • @genericalias2179
    @genericalias2179 3 ปีที่แล้ว +4

    this video: *exists*
    me, an artist who probably won't ever ever do anything with this information: interesting

  • @throughcolouredglasses9300
    @throughcolouredglasses9300 2 ปีที่แล้ว

    I cannot get over how solid the science and protocols are, like this guy is legit - yet all the "I bought this" and "I built this cheaply myself" -equipment gives it the distinct vibe of just some dude in his garage fiddling with a hobby he taught himself from youtube tutorials

  • @BobofWOGGLE
    @BobofWOGGLE 3 ปีที่แล้ว +15

    0:25 "The media is yellow"
    have fun when this line gets taken out of context in a few years

  • @Iwoodlikethat
    @Iwoodlikethat 2 ปีที่แล้ว +1

    I shit you not, in undergrad we lysed the resistant cells with SDS, spun it down, and mixed that pellet with the non resistant cells in a blender. Incubated and plated on antibacterial agar. We were given the same explanation as the heat shock, cell wall opens and DNA goes in.

  • @devilgene7330
    @devilgene7330 3 ปีที่แล้ว +35

    Next video "how I got raided by the FBI because of a thumbnail

  • @damianvdm6527
    @damianvdm6527 3 ปีที่แล้ว +1

    I don't comment much but watching this video I really was blown away by how easily you share such valuable knowledge. Just know that people like you keep the world spinning

  • @hgbugalou
    @hgbugalou 3 ปีที่แล้ว +4

    Explosions and Fire is my favorite youtube chemist, though nurd rage and nile red and close. He is aussie though so advantages.

  • @AbeDillon
    @AbeDillon 3 ปีที่แล้ว

    When you say "the centrifuge will break violently" I imagine that scene from the movie Outbreak where a guy absentmindedly sticks his hand in a centrifuge.

  • @Mchacz8008
    @Mchacz8008 3 ปีที่แล้ว +10

    Amateurs: Ice
    Pros: *PEAS*

  • @ButterBallTheOpossum
    @ButterBallTheOpossum 3 ปีที่แล้ว +1

    This is one of the coolest videos I've ever seen. I wish this video existed when I was a teenager and inspired me to go to school for something like this. Unfortunately I'm too old now.

    • @kellydrodgers8957
      @kellydrodgers8957 3 ปีที่แล้ว

      No, you're never 'to old' as long as you've the ability to learn new things and your mind is sharp.
      TH-cam is a powerful platform for learning just about anything you wish to learn.
      Just 20 years ago, this kind of technology didn't exist to the point it does now.

  • @thingyjim
    @thingyjim 3 ปีที่แล้ว +4

    I LOVE THE PEAS! Gunna try bringing a bag of peas into my lab and see how it goes with health and safety!

  • @louis1001
    @louis1001 3 ปีที่แล้ว +1

    I love your open source approach to science.

  • @TheGroundedCoffee
    @TheGroundedCoffee 3 ปีที่แล้ว +3

    0:56 looks like a delicious batch of fruity sour gummies.

  • @paulpardee
    @paulpardee ปีที่แล้ว +1

    This is the kind of thing that makes me consider changing to a career in microbiology.

  • @AmblesJambles
    @AmblesJambles 3 ปีที่แล้ว +3

    These amounts are super overkill! I used to use a fraction of the DNA and plating up the whole pellet at the end? No wonder it works!

  • @LordOfCookies123
    @LordOfCookies123 3 ปีที่แล้ว

    I have a hearty chuckle every time brilliant scientists or superiors in any way display a handwriting of an elementary school child

  • @bobfrediii2131
    @bobfrediii2131 3 ปีที่แล้ว +15

    Programmers nemesis is the semi colon ;

    • @OkuriLucy
      @OkuriLucy 3 ปีที่แล้ว +1

      Damn you

    • @JGnLAU8OAWF6
      @JGnLAU8OAWF6 3 ปีที่แล้ว

      Not if you write in Python

  • @FilterExel
    @FilterExel 3 ปีที่แล้ว +1

    Ahhh, you've found the ease and magic of the CaCl2 method. I used that to make some Rosetta(DE3)PLysS cells competent to about 1x10^7 cfu back in the day. It really saved me. Before that, my competent cells were all incompetent.

  • @jetfire5380
    @jetfire5380 3 ปีที่แล้ว +4

    Can you modify yeast so that it produces vitamin c? I know you've done it with vitamin a before but vitamin c is very hard to store for long periods so I was wondering if it were possible to just make it so you could eat it in bread while cut off from fruits that make it. Your videos are amazing by the way, keep on keeping on

  • @simonsays5552
    @simonsays5552 3 ปีที่แล้ว +1

    Most of this was over my head, and I’ll probably never use any of this in my day to day. I loved every second of it!

  • @engineer0239
    @engineer0239 3 ปีที่แล้ว +13

    13:13
    Why is melanin so interesting?

    • @minecraftermad
      @minecraftermad 3 ปีที่แล้ว +3

      @@JoshuaNorton HE'S GONNA TURN HIM SELF INTO A N-

    • @chuckcrunch1
      @chuckcrunch1 3 ปีที่แล้ว

      for science !

    • @UNSCPILOT
      @UNSCPILOT 3 ปีที่แล้ว +6

      Melanin is the magic cell-juice that protects us from the more dangerous aspects of the sun, good stuff

    • @niggacockball7995
      @niggacockball7995 3 ปีที่แล้ว

      @@UNSCPILOT and makes us into chocolate

  • @theclipreaper
    @theclipreaper 3 ปีที่แล้ว +2

    I thought that when bacteria are stressed (in harsh conditions), they pick up any random DNA they find (usually plasmids or DNA from other dead bacteria) in order to perhaps stumble across genes that will help them survive (this being a mechanism that they evolved). Steve Mould made a video about the sex pilus in which he explained that (if I recall correctly). I tend to believe that as more likely.

  • @Dinnye01
    @Dinnye01 3 ปีที่แล้ว +5

    Heeey, nice video, and good references. Now only the 'Pyromaniac' Nile Red should mention you and the circle is complete.
    I noticed the "move lab" there. ;)

    • @TheAechBomb
      @TheAechBomb 3 ปีที่แล้ว +1

      he and nile have done at least one video together

    • @TheGreatWolfYT
      @TheGreatWolfYT 3 ปีที่แล้ว

      @@TheAechBomb That's neat! Can you link that please?

    • @TheAechBomb
      @TheAechBomb 3 ปีที่แล้ว

      @@TheGreatWolfYT sure
      th-cam.com/video/YlQT4ptwLKs/w-d-xo.html

    • @Dinnye01
      @Dinnye01 3 ปีที่แล้ว

      @@TheAechBomb Two. Singlet oxygen and opal. If this was normal yputube, I would have to berate you for not being a huge enough fan...
      But since this is a cultured environment, you are welcome for the hint :)
      Also, Ben at Applied Science has been an inspiration for both of them. Maybe... check him out (wink)

    • @Dinnye01
      @Dinnye01 3 ปีที่แล้ว

      @@TheGreatWolfYT check my other answer. It is not a de facto collab vid, as Nigel stays in the background mostly, but ample credit is given.

  • @roborichi2307
    @roborichi2307 3 ปีที่แล้ว

    Happy to see that you got over this hurdle! Hope you get over more soon and fast!

  • @bobdylan6237
    @bobdylan6237 3 ปีที่แล้ว +3

    I just realised at hearing the title "genetic engineer" that I might have kinda wasted my life. But like, let me know if you guys need an app.

    • @kendarr
      @kendarr 3 ปีที่แล้ว

      Hey you want to develop your an app?

  • @Ranger881
    @Ranger881 3 ปีที่แล้ว

    Oh my god thank u for sharing ur protocol with everyone! Also as a student who's done tons of bacterial transformations, I love seeing seeing u work with such mastery on camera :)

  • @GEONEgaming
    @GEONEgaming 3 ปีที่แล้ว +4

    You should update the title to add "BL21" to the end. If your intent is to share this information with other biologists, the current title does not link this video to BL21 in any way. If you were trying to search for BL21, this video would not stand out.

  • @magencrisis1682
    @magencrisis1682 3 ปีที่แล้ว +2

    As a first-year student in a university of biology who just started the career a couple of weeks ago, this video gives me a little bit of fear for what awaits me.

  • @blakebrown1664
    @blakebrown1664 2 ปีที่แล้ว +1

    IT WORKS! I can’t believe I actually managed to follow this protocol It worked perfectly