The Math Behind Evo Devo (TMEB #3)
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- čas přidán 4. 02. 2023
- The math behind Evo-devo~
Uri Alon's Book:
www.amazon.ca/Introduction-Sy...
Jim Collins paper:
www.researchgate.net/publicat...
www.nature.com/articles/s4146...
The math behind fly development:
journals.plos.org/plosone/art...
Music:
City Life - Artificial.Music (No Copyright Music)
Link: www.youtube.com/watch?v=caT3j...
Pure Water by Meydän
Link: • Meydän - Pure Water [C...
Forever Sunrise - by Jonny Easton
Link: • Forever Sunrise - Soft...
Softwares used:
Manim CE
Keynote
Bruh, Were you inspired by the Science Music Video, Evo Devo A Capella Science?
Yes 100%
@@Nanorooms understandable. Evo Devo is the reason I'm watching this video :)
Hi. Another evo-dvo fan here. Whenever you said "signal" in this video, my brain automatically ran 1.5-sec voice of Tim saying "signal! signal!signal!" in evo-dvo song. Brilliant video btw. Science is awesome and you're too
@@Nanorooms, so these are the switches and the subprogrammes
Exactly
In 1 year from June I'll graduate from med school and until now I've just begun to really understand the logics of celular biology. Since first semester I'll always ask myself how genes know which side is cephalic or caudal or which organs need to be placed medial or lateral or even the deepness of the organs, and thanks to your series now I am capable of understanding them a little more and now I am really sold for pursuing a biomedical engineering career after I accomplish my medical career. Thank you for your videos I really love and share them among my folks :)
Genes don't know, and a gene first approach fails utterly at allowing us to make any actual predictions regarding morphology. Genes produce proteins, the hardware of cells. Morphology is one of the greatest mysteries of modern biology.
This approach is like modeling the trajectory of an F-35 and, and solving differential equation of forces, and then claiming you know everything about the plane, which is just absurd
It is creating an illusion of understanding, making certain humans think they understand far more than what is actually going on
@@pyropulseIXXI yeah, that's why I actually love this video because it can put a model that I can understan and it doesn't feel like it's magic or something, just a model about genes and the logic behind them. It's not trying to say "hey this is how exactly happens and behaves in this exact manner", it's just explaining a model of genetics c:
@@noctisumbra4656 I love the video too, but it is so far from the reality that we should remain humble.
It obviously helps with understanding, but life is magic from the perspective of our human brains.
We cannot build life from scratch, and if we could, that would prove we actually do understand it
@@pyropulseIXXI Yeah, that's why it's called a model, because it's not reality, just a platonic state of it. And he clarifies this in his other videos, like in TMEB #2
I'm a software engineer with some interest in biology, and CZcams just recommended this video for me. This is all very mindblowing!
You just earned yourself a subscriber (with notifications turned on for future videos)! :)
Hey even I have the same interest can u tell me some careers that combines the both
Going deeper into DNA's and initial biomes' creation and the evolution of species and perceptions will be ABSOLUTELY AMAZING
@@luffymonkey4232 I guess bioinformatics?
Some years ago, the MIT Technology Review organized a call where everybody were invited to define what will be XXI st century grand challenges.
I came with the idea of "general embryology" i.e. a synthetic way of manufacturing goods patterned after what biology is realizing for the birth of every organism.
Thanks to your video (I just came across by pure CZcams serendipity), I have now a firmer ground to articulate my too vague insight. THANK YOU SO MUCH.
Of course I liked and subscribed. Keep up the good work!
As a junior professor in synthetic biology, thanks for the channel and keep it up!!!
You've created some incredibly high quality videos - please keep it up! Super impressive stuff; really looking forward to seeing (and learning) more.
Mate whatever your doing, don't stop.
It's informative, because to know stuff like this i have to get myself deep into books and papers Ya know?
Your video is so refreshing in its presentation of the ideas and attracting user engagement, ontop of having awesome and intriguing subject matter too!
Man this channel is incredibly amazing and should be way bigger than it is now
Another great video!! I don't know if this channel's concept is ever going to be mainstream enough to make you as popular as you deserve, but I am so glad that I subscribed.
This video answers so many questions I've had about biology for years.
Really well delivered, I found the video very fascinating- I wish you all the best in the future
Really fascinating perspective and incredible presentation! Keep it up!
This is so insanely good I can't believe these videos
I was introduced to Uri's book in 3rd year and I was just fascinated, systems biology is so sick. There is Uri's Course online too on youtube! Thanks for the video, you explained it with colors in each equation just like the book and my professors did, nice throwback!
Really loving this series!
Instant subscription, 99% of educational channels fail to explain much of anything, not this channel, keep at it, love it.
I've thought about this a lot, most educational channels are not experts at communication, or on the subject matter, or both, so they might read off a script without intention. When someone understands what they're talking about or helping produce a video I can see in my mind what they mean beyond just the words, while many educational youtubers aren't actually imagining/visualizing what they're talking about while talking, just talking using their signature anchor voice without correlation to the subject matter. It's like the difference between hearing a chef of 30 years talk about activating the different flavor profiles vs an AI bot voice faking tone of voice.
this was a subject i was pondering on for YEARS. I couldn't find a good source that i could understand with my low level of mental capacity:D THANKS
Your graphic illustration and animation style is stunning!
i have been loving this series. thank you! Id love if you could somehow upload the script as subtitles somehow for more accessibility!
Amazing video. Im currently planning to write a book about a whole lot of concepts in life and genes have been one of the main sources of issues for me to try and decode myself
keep up these videos and i assure you, you are going places! nice work
Fascinating, thank you so much for sharing!
Awesome and informative! Thank you!
great video. You're an excellent communicator
This is gonna be a good channel.
Just wrote my exam for Evo Devo yesterday. Would have been nice to have seen this before then.
Amazing video, amazing explanation!
Appreciate!
Great video. Thank you
This video is incredible man
At 11:40 I don't understand what you mean: what is on the axis? The signal are the dots you place on the plane and they shift towards the nearest stable point, but I don't understand what do you mean by "when I remove the signal the system does not go to (0,0)" and then you place another dot that goes to the other stable point. I'm missing something if you have time to explain ahah
Awesome content, more plz
Bienvenido al grupo del cómo se programa las apariencias para que se hagan realidad por medio de la Topologia, teoría de categorías, análisis matemático y lógica para-consistente...
Thanks!
Thanks!
This is a amazing video, I'm now a subscribed happy fellow creator 🎉
These look a lot like pressure gradients which would lead me to believe that the combination of chemicals with varying densities that change the way the body responds to changes in pressure by creating currents that circulate each compound over time. Although my description may not be accurate or correct it's how I imagine embryonic development.
I was getting intimations of cymatics and vibration stable states
Your youtube chanel is very awesome
great channel,
Can you do one on neurons... From mitosis to their specialisation.
Amazing
this was awesome!
I love this
Just a minute in, and I have to comment before I watch it all. First, glad to see the comment section blowing up with amazement. I felt the same, thinking "whoa, math in biology, this is mid-21st century stuff. Secondm, bro, please get a decent mic for your voice, the audio isn't so great and it's hard to understand. Thanks and looking forward to more video content like this.
I see the singularity is coming along nicely. Soon we'll be 3D printing household pets :] Great video.
😳 well thanks.....the golden ratio thing explains alot
Your videos are amazing. On your recommendation, I got the book on biological circuitry and have been enjoying it so far.
The system is very subtle and nuanced, but the result is incredible complexity.
However, because of that, I may have missed a key point. Your explanations make a ton of sense. One thing, though, that is less clear, is what, specifically prompts the organism to begin producing mRNA copies of specific genes. I get the regulation motifs of the translation aspect of the system- that the various proteins affect the likelihood that specific mRNA segments in the cytoplasm get translated into proteins.
But perhaps I missed, or it was implied but I missed, what prompts the machinery to transcribe the specific sections of the entire DNA so that only those mRNA strands of the desired genes get transcribed and passed into the cytoplasm?
From what i understand, the transcription process of DNA into RNA isnt random. Something is driving that level of the code. Is it those control proteins? Has that aspect been pursued.
On an unrelated note (and I haven't finished your series yet) what really struck me was how very similar all this is to neural networks with their various weights, biases and activation functions. You probably touched in this, but I amazed me to realize that this is an abstracted version of a neural network (given that implementation is just details for the specific medium). I very much get the same feeling here that I do when I look at how neural networks are coded and work.
It actually is a great piece of the puzzle that helps explain the complex behavior based on numerous inputs.
But the missing piece, for me, is the controlling mechanism for unwnding the DNA at specific locations to copy the data for the specific genes that will need to be expressed. Do some proteins (more likely combinations behaving as a NN) also control the transcription process?
nanorooms gotta get boosted. dude could train a whole generation on biomechanics if the algorithm recognized the genius. GIVE HIM A CHANCE !
Can you please share some prerequisites to fully understand what you are explaining?
Love your videos. The sound quality can be improved a little bit though
Is there a comprehensive map of these signal pathways as well as the ion pumps like Michael Leven's research...
An encyclopedia if you will, that maps out what is known as well as the majority that isn't ?
so interesting
Very good
This must be all about coupled systems of PDEs!
There exist gradients of particular species, which ultimately can be organized into a matrix. The matrix has a spectrum that tells about concentrations at various places in space time.
I started a multidisciplinary channel a while ago, and It's satisfying to see more multidisciplinary content on youtube. Keep going. Your content is amazing. Also, this video reminded me of one of my videos regarding the signaling gradient with the topic of "How to confuse planarian regeneration" (czcams.com/video/wCA-nwMvLEs/video.html). Your video gave me a lot of new insights. Thanks.
I'm at second 45,I already like it 👍
Hey, I'm a software engineering student who is very interested in the math and logic behind biology. The direction these videos take is really fascinating and I wanted to ask, since I'm probably going to graduate with a degree in SE, where I can find more information about it (maybe a book or something that focuses on the math or computable problems in biology). What do I need to learn so that I can use math and SE to do some projects at home, like genetically modify plants or symulate a cell, etc.?
Welcome to the world of genetics and biochemistry.
can this model explain stem cells? you did not mention the research being done around bioelectricity and it may have more influence than DNA
Can you do a booklist video so that we can go in depth
casual Evo-Devo reference by acapella science
lov u
Reminds me of cppn's in artificial intelligence... For neuroevolution....
Morphology and how stuff forms is actually one of the greatest mystery in biology. Modeling it with math and claiming to know is like modeling an airplanes path through space, the forces acting on it, and claiming you know how an airplane actually works and with literally all of its components. Or better yet, it is studying an F-35 and creating a paper airplane and then saying since your paper airplane flew, you know how the F-35 works in all its intricacies. Life is even more complex than this, and the gap between what we think we understand and what is yet to be understand is the biggest gap in science, next to consciousness
No one knows how a fly forms. Again, this is one of the biggest current mysteries in biology. You can use bioelectricity to cause eyes to form anywhere, or cause an arm to regrow on certain animals, but we just know how to trigger it; we know nothing of what is actually going on
Also, claiming genes are code, or code for behavior, is the worst analogy; genes produce proteins, which are the HARDWARE of cells; they don't program stuff. This is also another great mystery of cellular biology, of how things actually 'know' what to do.
This information structure is most likely an emergent thing that arises from extremely complex interactions; that is, genes alone cannot account for this, and how a cell 'knows' which genes to even turn on and off is another huge mystery.
Okay, first of all I’d like to thank you for taking the time to write this comment. Indeed, I should’ve been more discrete with the fact that the math introduced at the end of the video are simply models of how the system works for very specific cases. The models shown are taken from Uri Alon’s book and “The math behind how a fly develops” paper I cited in the description. I apologize if the way I worded it in the video sounds misleading.
I’ve also addressed the concerns with the analogies in the previous video of this series. In short, they’re simply analogies that aid in non-life science (ie. the majority of my audience) folks into getting a better sense of biology through terms they are familiar with. By no means is the DNA the OS of the living thing, nor proteins just executable functions; biology is definitely more unique and complex than that.
@@Nanorooms I want to add that I believe your videos are amazing and they do add and help our understanding.
I am just in pure awe of life that I felt to comment that, but I also love math (I'm a physics major), so your content is top notch
I hope I didn't come off as rude or negative in my original comment
Noice!
4:20 now i know why most villains are biologist
WOW
8:27.... gaps for producing a pair of something, pair rule for pattern formation and polarities for structure? Just guessing
why is the word crippled or purple banned from the subtitles its a biology/math matter, these subjects introduce new ideas for me through english content, i'm hispanic and i find the subtitles helpful but when some words are missing is kinda hard to be honest. can someone relate?
also I'm procrastinating as shit, wish me luck I've got a test in 27 hours and I'm watching this thing.
2:20 Turing patterns?
Can I rewind and pause or should I just guess now edit: three part triangulation methods?
I would really appreciate it if you included subtitles. I'm autistic, and I can't process rapid speech very well. Ðe Ēnglisc spelling sistem is eſéncaly a logógrafy, sō if yu say a new word ðat I'v never héard befōar, I wōn't knōw how tis spelt, and knōwing ðe spelling will help ðe word stick better.
Then how tf are you typing
@blank3067 Tis difficult for me to process speech, but I can write just fine.
@@jordanschriver4228 then what's all that gibberish you wrote 🤔 to let people you have autism even through writing
@@jordanschriver4228 they are included from youtube
@@WayOfTheCode I don't think I can fully trust auto-generated subtitles, as they aren't fully accurate.
Reminds me of a cnn with each protin being a filter.
so it's like fractals but more complex
What was that echo at 8:21
Despite a couple very minor squabbles about some of the "machine/programming" language used here, this is a really great video on some of the central maths of evo-devo. Great work!
Also the cool thing is that the dynamical regimes can switch between bistable/multistable configurations, dependent on the strengths of interactions with the gene network. This can lead to markedly phenotypic patterns. Johannes Jaeger has a great lecture showing how this can happen here: czcams.com/video/XXE303T-r2M/video.html .
What that ultimately means is that we can't actually reduce down to just the network of gene activation/repression networks a lot of the time and we need to look at the dynamics of the system as a whole. Which means biologists have to do some maths haha. Anyways, cool video :)
Good to see you again
At 2:20 my guess is that you will say there are several gradients and you can locate where something goes by a type of triangulation using some sort of if statement in DNA control regions. Ha ha. Prob waaaay wrong but just having fun.
what is software simulate logic circuit in the start?
Simply cicruit
@@Nanorooms thanks bro
*For a second i thought you were talking about the m€th from breaking bad!* 💀🗿
great vid but please improve the audio, I think you can use free ai apps to do it or get audacity
Biological Lagrange points.
0:25 Diff eq
3:41 differential equations ?
12k views with 17k subscribers is a very good ratio 😶🌫️
The Way produces one.
One produces two.
Two produces three.
Three produces everything.
Everything has polar elements in it
That interact to achieve harmony.
People all hate being isolated, helpless and wicked,
But kings use these words as their titles.
Therefore, things can gain from losses
And can lose because of gainings.
I just teach what I have been taught.
Those who willfully go against the Way
Will die an undue death,
And are fit to be my textbook.
_Tao Te Ching chapter 42_
diffusion dt 5 sec
This video is a weird mix of deep domain info and ELI5.
5:46 fourier..?
you can't just flash up lotka volterra and not expect me to get it
God
CFBR
It's not flash memory!
Now "now" here's the
Is this type of technology used to help with birth defects for humans?
This has scary implications
𐑤𐑲𐑒 𐑢𐑨𐑑?
Damn. What now?
that was like 3 minutes of math
As far as I’m concerned fly is not developed from embryos….
Do you think it would be possible to lab grow and pump a bunch of this stuff into a embryo to grow organs? Or perhaps grow meat, since you can grow certain pieces?
There’s only so far one can go with this before realizing that this, and myriad other ultra-complex, involved systems simply could not have resulted from spontaneous mutation and natural selection.
The probability of the arrival and formation of nucleotide bases, nucleic acids, amino acids, proteins, formation of selectively permeable membranes with favorable bio-energetics, rxn thermodynamics, organelles, countless metabolic pathways, cycles, shunts, and avoiding destruction by water, inhibition by oxygen, having precisely appropriate chirality, and occurring by itself, without intention, and planned engineering, from non living C, H, N, O, S, P present in a pre-biotic world……….is ZERO.
Subhanallah
"Also the fly dies"
Me who fing hate those pesky annoying buzz drones:
I see tis as wIn win!