The Surprisingly Deep Connection of Math and Biology (TMEB #0)
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- Опубліковано 1 жов 2022
- There is a deep root of mathematics within biology. How this came to be, you’ll have to watch the video to find out
Biological oscillator:
www.nature.com/articles/35002125
Biological Flash memory:
www.nature.com/articles/35002131
Books referenced:
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DNA being read into mRNA which then gets turned into proteins was _extremely_ familiar. It's the first two stages of a pipelined CPU: fetch and decode. The instruction (mRNA) is *fetched* from memory (DNA), and then fed into a *decoder* to extract the information needed to actually execute it (protein). The main difference seems to be that the decoded instruction is then sent to a separate unit to actually execute it, where as the chemical protein seems capable of executing itself.
The entire process noted in the chemistry is just a fetch. Decode in a CPU is the process of taking in the previously read in instructions as a series of bits then using those bits to set the state of the CPU to allow for the proper flow from input registers to output register(s), which is the execute. If you have no execute you fundamentally have no decode as they are linked by the inherent state of the CPU. That is to say, decode is a setting of state and execute is the flow through that state. If you are not flowing through the state then setting the state is meaningless. This is the inherent problem with this line of thinking, these are chemical systems which mean they react in different ways, the "AND gate" he suggests earlier would not resemble, in any meaningful capacity, an AND gate build from transistors as one would have to wait for enough of the chemical reactants to combine together to become significantly detectable. Chemicals essentially "free float" while the electrons of a transistor "flow." This difference allows chemical system to be highly parallelizable but has the draw back of being slow on direct comparisons as suggested in this video. Much research has been done into this branch of Natural Computing and the limitations of theses chemical systems far exceeds the current benefits (Molecular Computation of Solutions to Combinatorial Problems, Adleman 1994). This, for a lack of a better analogy, comes from the lacking of a precise decode and execute, the proteins aren't shoved into registers as the output of an ALU might be but instead most perform whatever function, with whatever counterpart on "their own" which loses both precision and accuracy in terms of the time of a cycle from a computational standpoint. To sum up, this entire way of thinking just cannot apply without either heavy modification of either the DNA or the way of thinking itself.
@@dbob132 You have separate parts to turn the DNA into RNA and another to turn the RNA into a protein. You'd be blurring the like between decode and execute, but the first part acts like the fetch while the second acts like the decode. From what I can tell, the decoding almost seems literal as it decodes the RNA into a protein. The RNA can't do anything on its own other than move the information elsewhere, while the protein can actually do stuff, but needs to be constructed from the RNA first.
Actually, in bio there is a separate entity that performs the decode - author just didnt mention it in video. once u have the mRNA, there is the ribosome that reads the mRNA's instructions and creates the specific protein from it
@@eldwinc1546 you should mention that there are different tRNAs each with specific three "bits" (DNA also RNA carries quaternary code) and each tRNA transfers (that's marked by the "t" in the name) a specific aminoacid to make the protein. So each aminoacid is encoded by three bits, called a triplet (in quaternary code it enables 64 combinations, but only 22 aminoacids, some triplets are redundant).
Of note: an apparatus of enormous structure, called RIBOSOME is inevitable for the production of proteins
You cannot even imagine how much i needed something like this :D. I'm a programmer interested in molecular biology and would maybe like to study it in the future.
That’s very cool, I study software engineering and biochemistry
This channel is going to blow up!!! I LOVE YOU! You have quality like 3blue1brown!
I was just thinking about 3blue1brown, too!!
I think your channel could cut out a really cool niche in systems bio - great work
The first biology classes I took I immediately understood DNA as an analogue computer.
This is so cool! I've been thinking about majoring in biochem and this has definitely helped seal the deal!
I'm so excited for the next videos 😁 a unique topic indeed!
See you in around a month or so for the next one! I’ve got midterms to write while doing this too💀
The logic here comes from assignment. In other words, you assign True's and False's where it's convenient. It's a very interesting idea, and I look forward to watching more of this series.
This channel is absolutely amazing. I'm an organic chemist who recently transitioned into software, and these videos are pure magic for me. Please keep doing what you're doing. Fantastic content.
That set of equations reminds me of the Lotka-Voltetra ones used to model prey-predator population relationship.
They are definitely surprisingly similar!
Oh God it's the Logarithmic Fractal inside the Mandelbrot set that predicts faucet drips... please no
Soooo exciting ! You doing a great job man. I'm sure this series will catch a much wider audience soon ! I always wondered if there was a kind of "programming language" for biological machines
Hell yea, keep it coming, this stuff is so good. Thanks for the time and effort.
This is exciting! The math of biology is just as important as figuring out the mathematical representation of the brain's activity.
Hi NanoRooms, I'm loving your content. I wanted to point out that your audio output level seems a lot lower than other channels, so I'm wondering if you might be able to change that in editing.
Keep it up! Congrats on the new vid getting picked up by the algorithm! Edit to just say, I am really excited to see people with your sort of passion and mindset in the realm of biology. And a talent for education to! Thanks for sharing.
I’m so excited I found your channel
Super great job with this. Keep going!
Hell yeah another biology channel and an incredibly interesting and creative one to binge
This is a throwback to my cell circuitry class doing stochastic differential equations. Ah, good times. Thank you!
Very inspiring video!!
First time here, and instant sub. I am just through high school and I did not have bio as a subject so let us see how much I can understand with the math (I am a math person XD)
I hope you do a video on Hopf Bifurcations; I strongly believe molecular biology are inherently oscillatory dynamical systems
Oh boy, that’s a few episodes down the line when we start dealing with oscillations. That’s definitely a topic I’m super excited to cover!
@@Nanorooms That's brilliant to hear m8, I do research in systems biology myself! I'm looking forward to watching this channel grow, similar to how the field is taking off!
If you ever wanted a second pair of eyes for some of these topics hmu!
I'm definitely down for that! I can't find any contacts that I can DM you with. So here's my channel's email: nanoroomsatbottom@gmail.com hmu!
Awesome approach
That is really interesting!
This is the beginning of something great
I find it very strange to say biological life has 'logic embedded' in it.
Wouldn't it be far more on point to say biology/biological chemistry behaves or interacts logically?
"You now understood how information flows in living things"
Ah, uhh... _actually..._
It's still very appreciated if he manages to inspire tech people to investigate in biochemistry...
Can you do a booklist video so that we can go in depth
WOW! How do you even do this🤩😍
💚💚💚
* learns about boolean logic in compsci 101 *
"yeah, I know chemistry, why?"
Can you make biology playlist?
Sure
Yooooooooooo this is fuckin sick dude
The Genetic Protocol, Message generation and Message decoding.
Sick vid, whats the circuit simulator you show near the beginning?
EveryCircuit
What causes the decay of mRNA and proteins? I assume proteins will be used by other processes, which happen faster at higher concentration. But what if proteins are not used, for example because the other part of the AND operator has low concentration. Does the decay rate then still depend on its concentration or mainly on the concentration of another protein?
Hey man! May I ask what software you used to produce this video?
i think it's made using 3b1b's manim library, it's the one he uses for making his videos and he open sourced it. The videos have that certain look to them.
Please make tmeb -10, so i caj understand
Los fisicos y matematicos precisamente conocen muy poco de bioquimica y termodinamica. Por eso aun intentan descifrar la flecha del tiempo y la ILUSION del pasar del tiempo. Cuando en realidad nada esta "sucediendo" y tal cosa como "la flecha del tiempo" no existe en consecuencia. Sigan por el buen camino...
This was an amazing video! Out of curiosity, did you use 3b1b’s `manim` library to produce it?
And a few other softwares, yes. All of it in the desc
@nanorooms9696 I’m not sure if I’m just being stupid but I can’t seem to find any production resources in the description, just the nature papers, textbook, and backing music tracks ):
Oh I meant in my newest video. YT studio sometimes doesn’t show which video the comment is from.
Gotcha gotcha, thanks! Also I’m curious is there a reason you chose the first edition of the systems bio textbook over the second?
Oh there’s no real reason. I think I just quickly found a link to it and pasted it there just for someone who’s interested.
Nice work !
Could you please explain why the rate of production of proteins is much higher than the rate of production of mRNA ?
PS: I don't have a background in biology
One mRNA can be used as "template" for the production of corresponding protein several times (even in a row of several ribosomes, production facilities)
What is the name of this discipline?
Mathematical biology or what?
I want to study it academically
🎉
I personally believe that we are highly engineered human having great machines living within machine. Just like a loop of any array of java.
What's crazy is that this ISN'T intelligent design!
Yo hurry up drop the next one
I got some midterms to take care of😂. Will def upload before 15th Nov!
🎵 a dot isn't the best way to try to sum up how electrons come and go, 🎵
They are the states of a matter field that follows an equation that Dirac wrote~
Chemical computer
Don’t you dare upload this and leave it without more videos
Have you ever tired Julia? My signal processing prof said it's much better for mathy stuff than python
Yikes! I hate to sound negative at such an avideowesome video but MAN!!! If this couldn't do .well with some audio remasfefh her 4
Lysenko was right.
right about what?
bruh
Based
RNA reverse transcriptase enters the chat.
RT enzymes are overhyped 😋
Keep your math out of my biology!
You are trying to say too much with too few minutes. There are a lot of non-sequiturers in your explanation. While I agree with your premise you are jumping around a bit too much and making big claims based on weak explanations. Here are some solutions you can use:
1. Don't just use random graphics that make sense to you when you use them but are rather just based disconnections. You are trying to be fancy but without much substance. This is mainly because you are trying to get the most flash for the least time... but you are doing too much of one(if you scale one back you'll be able to end up with a better result because you'll either have put in more time in to the graphics to make the logic in them flow better or you'll have more time to spend on explanations rather than "wasting" it on graphics).
2. Try not to make grandiose claims that sound obtuse and haven't been fully explained and is broken in flow by, say, the end of the video. Your claim that the mathematical equations are the flow of information in living things and once you know those equations you know how the flow works is a bit absurd. It sounds like something I would say. I get what you mean but I think you are trying to squeeze too much time out of your videos and it's not giving you enough room to be more detailed. The way you cut it off at the end though makes me feel like you pulled the rug out.
3. If you just slow down and say more it will be a lot better. I'd rather here you say 30 minutes worth of relevant and connected things rather than 8 minutes of disconnected things.
The deep connection is much deeper than 8 minutes. I do realize you are doing multiple parts. But each part will be just like the next because that is what parts do usually. Of course if this is an introduction and is meant to be short then it should say it and it should be more of a big picture idea. I think you tried to do that because you intended this as more of an intro but it went a little awry.
I know graphics are all the rage now days but it's mostly all flash(they generally are overused or used somewhat incorrectly). I know this is the "style" everything is headed but for such deep topics about the universe there should be some more "civility". By this, more of a conversational style(which I know, again, things change and most people are used to communicating with their monitors) provides the ability to say more.
Revolutionary ideas are best said with words. Some men's ears are not meant to hear. The way something is said is just as important as what is said... they are, in fact, one and the same.
I will up the ante and say ALL of the universe, not just biology, is mathematical. Everything that one does, at the very least, has mathematics in it. E.g., all space-time movement is governed in the ideas of physics which is just applied math. So, at the very least everything is a dynamical system. (Life, as we know it, can be describe as a dynamical system, at least to a significant degree) It goes deeper though. If everything is mathematical, groups, categories, polymorphic functions, Sobolev spaces, Dirichlet series, and much more are all things that also show up in life. Of course if you call my bluff I will up the ante and say ALL of the universe is also musical.... and so it goes.
God is amazing
Indian 🇮🇳knows it from million of years ago
So the aliens have a patent on our DNA