Hacking Bacteria Programming Using Control Theory & Math
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- čas přidán 20. 06. 2023
- Why does a Bacteria come built in with a PID controller?
Books:
- An Introduction to Systems Biology Design Principles of Biological Circuits by Uri Alon
- Chapter 9
Papers Cited:
Alon et al., 1999: www.nature.com/articles/16483
Müller et al., 2021: pubs.acs.org/doi/abs/10.1021/...
Music
City life - Artificial Music
• City Life - Artificial...
Pure Water by Meydän
Link: • Meydän - Pure Water [C...
Softwares used:
Manim CE
Keynote
Can't wait to look back on these videos when you're getting views in the millions rather than thousands.
Lol. Leaving my mark here today
I honestly think he’s the best CZcams channel I’m subscribed to. Valuable videos and quality content. Thanks @NanoRoom
As an electrical engineer that has done a lot of software development and control systems, and has made some biomedical instrumentation, this does not surprise me at all. PIDs, specifically P only, I only or PI loops are so incredibly common thay even when you try to make something fancy, you realize later that what you made simplifies to either 1 PI loop, 2 parallel PI loops or 2 nested PI loops or any similar combinations, sometimes cascading a whole bunch. A P controller being just an error detector, amplifier and actuator, and an I controller being just that but with an accumulator (amount of charge in a capacitor, amount of "number" in a sum, amount of chemical in a liquid, pressure in a tank, distance in a lever) you can so easily accidentally make one.
So many problems can be solved by just adding more and more PI controllers until it works, even if the shear amount of them causes an incredible amount of cross-interaction. Another super interesting thing about P and I controllers is, you don't really need to know that much about the system to tune their gains. You can just randomly set them, then tune them until they work, no matter how many there are in the system, and if their gains are set too low for P and I, it still works, it is just sluggish. Too high gains and it oscillates, which actually is sometimes the desired behavior for your randomly iterated system, or it oscillates and quickly blows up or dies, in which case, no offspring.
incredible video, i am a mechanical engineering student, and being able to see topics i have learnt such as a control of dynamic systems being applied in such different fields of science, in such a digestible format is brilliant! thank you very much
Man these videos are so complex and in depth. I’m considering going in synthetic biology but it’s still a very recent field!
As someone that got into very old fields, go for it, that is a good thing!
the more the reason to go in to it, and pioneer it!
I'm so glad this was recommended to me, super cool and well put together! As a bachelors in engineering and not biology, I'm also curious to know if some more aspects of PID controllers translate to the bacteria here:
- the tumbling frequency responses that you visualize look "critically damped". I'm wondering if bacteria in real life all act like this, or if some act "underdamped", where their tumbling frequency responses overshoot back and forth before settling on the steady state? Intuitively, I might imagine that bacteria with "perfectly tuned" ratios of R and B activation, which I guess can be analogous to being critically damped, may survive the best, so by natural selection bacteria all tend towards one specific tuning
- Is there another protein response chain/biological equivalent to the derivative block in this analogy, or is it just this one?
Well… I have a video on full on applying control theory to biology in the works right now.
As for the derivative path in the bacterial controller, I don’t think it exists for this mechanism. And as for the overshooting, I don’t think it’s possible in this case since there is only one steady state X value it can reach… but I’ll have to look into it more to get a proper answer.
I really love these videos even though I never got a chance to study biology in high school and university, since I did math and computer science I can understand your explanations really well.
This channel is such a hiddem gem! Please, keep posting.
another great video! Have you read Biological Modeling by Phillip Compeau?
I read his biocomp book for uni, but modeling is an interest that led me to your channel. I'm an interdisp molbio/CS and moved to a mosquito lab to model piRNA processing against transposons, Compeau's content and your videos have been really inspirational.
Very interesting! I’ll give it a look
@@Nanorooms Hey, I love your vids, I was wondering what if the same process we use to "understand" things, which is observe and question. Can we figure out mechanistic workings of our thoughts, psychological processes, brain algorithms and even at neurological level in the way we did with biology here?
Maybe… but I’m not enough of an expert on those fields to say so.
Quality content, these videos are amazing. Thanks for sharing, and I will definitely look out for more.
I've just discovered your channel! Youre' making such great content! 🤩
You have the best content. Thank you.
Thanks for amazing video!
the speech at the end sounded like you're an evil necromancer
anyway, i like your funny words, magic man
I’ve always wondered what control theory was about
Thank you so much for your videos ! Is it possible to make the (automatic) subtitles available?
Thanks!
pretty cool ideas!
I could see the Manim. Beautiful.
I just finished programming for sensor fusion, and I just want to take a detour, and here it is youtube, recommending me, a fucking PID control in Bio (great vids btw)
woah, maybe i won't have to wait for video 1000 for you to start programming your own living beings
amazing video❤
The Bacteria knows where it is because it isn't.
The Bacteriumn't
By subtracting where it isn't from where it isn't, it obtains food.
Can you like do a book list video so that we can know more
Great video. You should look into the book Nature of technology ny Brian Arthur. Where he covers a lot of other similar projects. It changed my view on technology as being something humans invented. To being all there is. PID was not invented by humans, they where discovered.
I mean.. by that logic nothing can be invented. You just discover states you can put matter into for stuff to happen.
@@MaakaSakuranbo Exactly. And when things are in the right sequence you form memory.
And the compute layer
ur channel is really beautiful
humans always act so amazed at how elegant nature is , yet we ourselves are products of nature , and ofc nevermind the fact that nature has had BILLIONS of years to figure this stuff out while we humans have only had a few million-ish
Trying to prove life began with feedback, the ability to control outcome? It needs help, any suggestions?
Man can only copy what a greater one has already created. There is nothing new under the sun.😊
I love your videos so much literally marry me
Lolll
@@Nanorooms seriously though man tysm for making these videos I'm marinating in nanoscale mechanics before college so I can achieve goals keep it up it's excellent 🙏🙏🙏
lgbt Lol
4:42 .... this was a bit of a shock, thought that the step response would lead to overshoot with oscillations and eventually stopping when distance to source because too small but the system appears naturally critically damped .... the how is rather easy (bit of math) but WHY ???
I feel like scientists who study systems biology watch all of these, so hello Emily Ackerman and Leonidas Bleris! 😛
which application did u use for animation?
If it looks like deliberate engineering, if it works reliably like deliberate engineering, if it elegantly handles a variety of inputs like deliberate engineering, then it's probably e- .... "nature"?! 11:12 🤔😆
14:58 "Devise - verb [ T ] /dɪˈvaɪz/ - plan or invent (a complex procedure, system, or mechanism) by careful thought"
It's either devised or it's the product of evolution by unguided natural selection but you can't have both, they are mutually exclusive.
Nc, I pid control in my line followers
I don't understand anything but nice video lmao
You are Morpheus from the Matrix
It's not that PID appear in biology it's just that we impose the schema on biology. Remember how that guy who only has a hammer sees every problem as a nail to be hit? It's almost like that. Lol
Thanks for the comment!
Yes, I agree. What I was trying to say in the video is that the mechanism for the chemotaxis control just works like a PID controller. But it certainly helps that we can see these sort of control structures in nature. We can learn a lot from nature’s evolution-optimized design. That’s what I was trying to communicate with the video!
@@Nanorooms true, it's kind of unsettling and wonderful at the same time.
@@lorenzomizushal3980 Wrong.
You clearly don’t understand what a PID is and are just quoting generic wisdoms at us 🤣🤣🤣🤣
@@maalikserebryakov true, you're very clever. I'm impressed by your smartness.
@@lorenzomizushal3980 You’re welcome.
I’m your teacher boy. 💪🏾
Its a geomitry
Awesome video
Why do man-made controllers appear in biology?
Because someone really did make them.
This actually proves God doesn’t design biological systems
Because if all wise God designed something it would no doubt be a mechanism beyond human understanding, the fact we can understand it means it was not designed by GOD.
@@maalikserebryakovstop limiting God bruh
God can do whatever he wants. Whether we understand or not
And one more thing
We still don't understand the full nature of particles
i prefer videos where the person talks in a normal voice but that's just me and sorry for the ignorant comment
11:12 *God
Which one?
math has invaded biology
I was like "man this video looks awesome" then I seen math, downvote, 0/10.