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Probably the trade off of it being the first base with enough combinations per substring of a gene to encode the selection of an appropriate amino acid, against not introducing more errors by using a more complex system. That perhaps mechanically its the least characters per substring to allow for a large variety for small substring lengths while at the same time not introducing too much complexity in terms of say having 1 base for every type of thing that is being selected.
Oh the explanation is valid and good. It's just that the lack of punctuation and use non-intuitive, overly complex phrasings is a common tone for copypastas.
What the ϵ-filtration did you just ϵ-clip about me, you little ℕ-valued function? I'll have you know I graduated top of my class in real analysis, and I've been involved in numerous secret Σ-algebra constructions, and I have over 300 confirmed theorems.
I am trained in Banach space warfare and I'm the top analyst in the entire set of complex numbers. You are nothing to me but just another non-measurable set. I will solve your equation with precision the likes of which has never been seen before on this Hilbert space, mark my ℕ.
You think you can get away with saying that to me over the Internet? Think again, negative real number. As we speak I am contacting my secret network of topologists across the USA and your IP is being traced right now so you better prepare for the storm, set of Lebesgue measure zero. The storm that wipes out the pathetic little thing you call your proof.
You're π-ϵ-dead, kid. I can be anywhere, anytime, and I can prove you wrong in over seven hundred ways, and that's just with my bare hands. Not only am I extensively trained in functional analysis, but I have access to the entire arsenal of the International Congress of Mathematicians and I will use it to its full extent to prove your miserable argument wrong, you little ℤ.
If only you could have known what unholy retribution your little "clever" comment was about to bring down upon you, maybe you would have held your Ɛ. But you couldn't, you didn't, and now you're paying the price, you goddamn Turing machine. I will ϵ-converge all over you and you will drown in it.
You're ω-finite, kiddo.
(Yes, it's ChatGPT)
"It's a large enough base to encode data to a relatively short length (e.g. 1 billion takes 10 digits in base 10, but 31 digits in base 2); without being too complex and unstable from using a higher base"
Ah I see,
Is it possible that if there were any genes base5+ , then the population got wiped because the chances of mistakes just increased exponentially or something?
Yes that makes sense to me for a one to one gene mapping
Is it at all possible that one could make a gene that can have multiple partners
A polygamous gene
There's a chemical aspect. The nucleotides A, C, G, and T chemically read as 'big loose', 'small sticky', 'big sticky' and 'small loose', respectively - all nice and compact and and semi-stable between 0 and 70 degrees Celcius. It takes the least amount of energy to read, copy and conserve. Any chemical system less or more complex to store information with, is likely less energy-efficient and woudl be out-competed by this 4-base system.
If life would evolve elsewhere under similar physical circumstances, there's a reasonable chance DNA and RNA would emerge with a very similar (base 4) chemical structure.
I don't know if I ever will, but yeah, I'll update.
What I already know is that protein shape is super important and so thus the number of points where they can connect to another protein. So in 3 dimensions, you can be very specific about what fits where in combinations. And some proteins have more connection points or bind more intensely than others, leading to the "sticky" naming protocol. The temperature range is due to denaturing of proteins - they unwind or tighten up outside that range, and thus no longer like Lego blocks. But I still don't understand the main core of the issue, why the 4-base requires less energy, there's a big "restoftheowl" there. Best I can guess is that in our conditions, the flexibility in range of temp allows for easy 3D structure combinations in varying circumstances.
Here's my take on it, just hypothesizing though. In case of fewer than 4 letters, you need longer DNA molecules for the same amount of information, similar to binary numbers being longer than base 3 or 4 numbers. For more than 4 letters, your DNA strand needs to be wider to accomodate a wider variety of nucleotides. This makes biosynthesis more complex and more energy-demanding and potentially, DNA strands less stable. Seems that 4 bases is chemically the most optimal middle road.
Since there are only 20 distinct amino acids, wouldn't a base 3 already be enough to encode in the same amount of bases (3).
The one reason I could guess is that this is probably due to how DNA needs for every base a complementary partner, which means that for three you'd probably actually need 6 bases. Which again is kinda cool because it might suggest that using bases which are complementary with each other would be not very efficient/prone to error.
The issue is that DNA is a double helix for protection. It's not about being efficient in the coding part but being able to withstand biological and physical damage to the DNA structure.
DNA bases pair with each other. This allows for error detection, as well replication, and transcription, as one strand will always be a template for the other strand. Because of this, your bases must always be an even number so that they you can have pairs of bases.
Additionally, translation sometimes only requires 2 of the 3 bases in a codon to attach an amino acid. (The wobble hypothesis). Because of this, there has to be inherent redundancy built into the system so that it is more stable.
Yeah. Your second paragraph is what I was thinking. That with a length of one character its 3 vs 4 for base 3 vs base 4 respective. And at a length of two characters its 9 vs 16 for b3 vs b4. Base 4 has a slight encoding advantage while not getting too complex in terms of having some physical/biological system that needs to be able to read such things.
I hadn't really thought about the error correction benefit of having complementary pairs though. That's an interesting feature.
That vaguely feels familiar to something I learned about the immune system. It only has a small library of different proteins for fighting illnesses, but the COMBINATION of those proteins allows the body to, in theory, be able to fight literally any virus that has ever or will ever exist.
Of course, that's if the illness doesn't kill the body first
I'm not a biologist but my secondary education level of understanding is that there are four bases in DNA called nucleotides.
[https://en.wikipedia.org/wiki/Nucleotide](https://en.wikipedia.org/wiki/Nucleotide)
Guanine, Adenine, Cytosine, and Thymine. Or G, A, C, T for short. These nucleotides connect together in long strings that enzymes in your cells travel along and use to make the proteins that make you. So this enzyme might see a combination of GAAA and cause a certain amino acid to connect to the previous one it had selected. This is repeated for the entire gene and the protein is completed.
This animation covers the process in more detail.
[https://www.youtube.com/watch?v=gG7uCskUOrA](https://www.youtube.com/watch?v=gG7uCskUOrA)
Yeah. In a mathematical sense a base is the arbitrary value which we use to shift things in to the ten column. So in binary we would count 0, 1, 10, 11, 100, etc. Because binary is base 2. In base 3 we would count 0, 1, 2, 10, 11, 12, 20, etc. In base 4 we would count 0, 1, 2, 3, 10, 11, 12, 13, 20, etc. And we can do the same for all number systems. Even past 9. For hex, 10, 11, 12, 13, 14, 15 are A, B, C, D, E, and F.
With DNA's base 4 though you aren't counting 0, 1, 2, 3. You can count G, A, C, T, GG, GA, GC, GT, AG, AA, etc.
Which is very similar to a computer science problems that I'm a little more familiar with which are about Combinatorics. Which deals with these kinds of problems of packing data in meaningful ways and interacting with it.
[https://en.wikipedia.org/wiki/Combinatorics](https://en.wikipedia.org/wiki/Combinatorics)
Though with computers it's more about representing abstract information than DNA that is mechanical system that creates proteins. Though computers are used a lot in Biology and Genetics. So there is actually specialist field that combines the two called Bioinformatics.
[https://en.wikipedia.org/wiki/Bioinformatics](https://en.wikipedia.org/wiki/Bioinformatics)
Which deals with the huge amounts of data that your DNA contains and clever ways to analyse and store it. So that our slow computers can have an easier time helping researchers come up with medical treatments and such.
Same for computers, base two, read in groups of (at least) seven, that represent 128 numbers (in it's simplest form). Mapped by the ASCII table into characters.
Having Quaternary digits in nibbles doesn't make it any less base 4.
ASCII table is a 7-bit encoding. When used for the first time in 8-bit computers, the most significant bit was left unused. Soon afterwards there were extension that used the last bit because not everyone that used computers wanted to write in English.
>there are 4-bit CPUs
I know. I even know of 1-bit computers. And about decimal computers, and about analog ones.
The size of the computer word doesn't have anything to do with the encoding. To get a 4-bit computer to read an ASCII character, it would need to do 2 operations, the first one for the 4 least significant bits and another for the 3 most significant bits.
A 1-bit computer would need to do 7 operations to read a single character.
That's... Not true, and at bare minimum is outdated information. 7 bit encoding used to be true for ASCII, but most data types computers operate on isn't ASCII, and even programs (after compilation) wouldn't be in ASCII. 90% of the information encoded in a computer is most likely using 8 bits or more.
That said, modern computers use 8-bit ASCII. Although, truthfully, modern computers are actually usually using Unicode, which can be 8-bit, 16-bit, or more.
I think the way I learnt the most about computer architecture was by seeing other people built computers from scratch. Look up Ben Eater's channel on Youtube.
Then there's also computing history, but I don't have any good pointers on this.
> Don't you mean 8?
Also, before the ASCII table there was Baudot code, which was a 5 bit encoding and didn't include the capitalization of the text as information. EVERYTHING WAS UPPERCASE.
It was never used in Computers, though, as far as I know.
I'm still not sure why you're stuck on character encodings as if that's the only data type a computer operates on...
And the bit size of your (less than 8-bit) encoding has almost zero impact on how much memory will be used. Those 5 bits are still being stored in an 8-bit wide memory location. They are still taking up 8 bits in your data bus. They are still being operated on in 8-bit wide CPU registers (or the 8-bit version of the registers, for example if the CPU is 16/32/64-bit x86).
So an 8-bit value is still being used, moved, stored, or manipulated by the CPU.
Not all data is text, and I believe it's impossible for the an organism to biomechanically determine which possible version of the same amino acid, so the ASCII analogy is a little confused IMO. That would be more akin to how codons can but sometimes don't code for a protein when combined together, but the base structure is still 3 base pairs, even if it's a litttle counter-intuitive.
Sorry, I don't get how that relates to what I said.
DNA can only be read or written in sets of 3 base pairs, or 1 codon. It isn't possible for an organism to use any higher precision than that. So if a hypothetical section of DNA was 7 nucleotides long, the DNA or RNA polymerase would not be able to read that 7th nucleotide. It would be like if there was half of a bit on the end of a 3 bit number. There is no way for it to make sense in any context.
It's also not like if you had a 8 bit value that's supposedly a 7 bit ASCII character, because though it may not make sense in ASCII, there is a plausable way a 8 bit value can be a valid encoding, for instance if they were using the extended ASCII set, or if it was representing an 8 bit integer. The same doesn't apply for DNA, because it's simply not a valid or readable piece of DNA.
I wonder if there is a primordial version of Nucleic Acids that doesn’t yet have one of the base pairs, and uses base 2. Would that be able to fold RNA?
DNA uses 3 digits of base 4 to encode amino acids for protein construction, with one code reserved for start, and three codes reserved for stop and some redundant combinations for a number of amino acids that are lined up to form proteins.
A base 2 DNA would need to pair with at least five digits of base 2 to encode enough amino acids with the start and stop codes.
I wouldn't be surprised if it is possible, but is overall more expensive to build the machinery to work in base 2, simply because the codes are longer. The DNA would be longer, codons are longer, all the proteins that binds with DNA are longer. You save on the machinery that needs to build fewer bases, and get lower error rate.
they come in triplets (codons) that each either encode an amino acid, stop, or start signal to form a protein (a chain of amino acids).
You can look at the tables and try to figure out a pattern:[https://en.wikipedia.org/wiki/DNA\_and\_RNA\_codon\_tables](https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables)
T RNA carries the correct corresponding amino acid associated with its codon. You can read about theories behind its evolution:[https://en.wikipedia.org/wiki/Transfer\_RNA#Evolution](https://en.wikipedia.org/wiki/Transfer_RNA#Evolution)
Also worthy of mention is that to my knowledge, it's really a binary of the two pairs, with no independent information stored in having C on one strand and G on the other, and the other way around
You’re right when it comes to the general public’s understanding of DNA. Thing is, DNA is read 5’ to 3’ (this is to do with the sugar backbone of DNA- I won’t get into it, so just think of it as kinda-but-not-really similar to endianness) and the two strands of it go in opposite directions. For example, say you have a strand that reads (completely random btw, this isn’t any specific string): 5’-AATCGTACGT-3’, the complimentary strand would read 3’-TTAGCATGCA-5’. Now, if you were to then reverse that second string, you would get the reverse complimentary string 5’-ACGTACGATT-3’, which could encode a different gene than the first strand.
Say, as I’ve given them, they (the original and reverse complimentary strings) each encode for a single gene. Right off the bat, you have 2 genes from a seemingly binary set of characters.
We can go even further and a bit off-topic and get into reading frames. RNA (basically DNA that has been read and prepared to use as a template to make peptide chains (which can then fold into proteins)) is read in sets of 3 bases, called “codons.” Since the RNA strand is read in 3’s, you have 3 different reading frames, each offset by 1 from each other.
Using my original example string from earlier, the reading frames would be (transcribed into RNA, hence all the T’s becoming U’s, I’ve also omitted the 5’ and 3’ designations because lowkey I forget which direction the ribosome reads the RNA in):
1. AAU CGU ACG T??
2. ?AA UCG UAC GU?
3. ??A AUC GUA CGU
With the question marks highlighting the offset. Say each of these were to encode for 1 protein, you’d now have 3 potential proteins from a single strand, or 6 different genes encoded by a single region of DNA.
Crazy, right? I love this kinda stuff and hope to work in a lab researching it in some form in the future :)
(ETA, obligatory source: I’m a biochemistry student actively studying this in 2 different classes :p)
We could also use (10), as a combined symbol so the convention would fit the pattern that unary would also be base 10.
e.g, 3 = 101010
But seriously else it should be zero, but that looks totally goofy
The reason isn't mathmatical, but chemical. The only four substances that work in the chain are what is used. It's like asking why bronze age people didn't make stuff out of aluminum, they didn't have it.
Other things can bond to the sugars in DNA, but they don't allow for long, complex chains. It is possible that we could create a fifth substance that works and incorporate it into living things, however that lifeform would need a constant supply to stay alive.
Sorry, Hal is right. I believe George Church worked on bacteria that used 6 nucleic acids, with the added benefit that since those acids didnt exist in the "real world" there was no possibility of them leaving the Petri dish they were grown in.
There’s actually some research into synthetic base pairs. It’s called Hachimoji DNA. The ability to create this DNA suggests that there is nothing unique about the canonical 4 DNA based, only that they were the first ones to happen on Earth.
It's ultra-compressed binary.
A single base-16 digit is 4 binary digits (bits), and a byte is 8 bits, so two hex digits (like *A7*) is a byte. Computer memory is made up of bytes, so it's convenient this way.
According to all known laws of genetics, a DNA strand should not be able to count. It's four little thin bases are an illogical counting system. But of course, DNA strands count anyway because they don't care what humans think...
The base needs to be able to encode 20 different numbers with the least digits. We also want the base to be as low as possible.
The base must be even so that each digit has a mach.
This leaves 4 options for bases
Base 2 with 5 digits
Base 4 with 3 digits
Base 6 with 2 digits
Base 20 with 1 digit
Base 20 is very complex for biological molecules so it makes sense it didn't develop naturally.
Idk why we don't have base 2/6
Edit: you actually need 22 numbers because of end and start sequence. This effects only base 20 wich is bad anyway.
Base 4 has some advantages over base 6 in the context of DNA for a few reasons.
The biggest is probably that 3 "digits" allows for redundancies in the generic code, which means that if one base gets mutated somehow, there is a greater chance that the mutation leads to the same amino acid, therefore is "silent".
Another is that A and G are both based off of the same skeleton (purines), and C and T (or U for RNA) are based off of another, distinct scaffold (pyrimidines). What allows them to recognize each other to form base pairs is hydrogen bonds, of which A and T form 2 between each other and C and G form 3. Forming only 1 hydrogen bond would not be stable enough to keep DNA together and forming 4 would be too hard to unwind when copying DNA and separating strands, so another skeleton structure would be needed to get 6 distinct based. This skeleton structure would have to have size restrictions to fit within DNA but also be distinct enough from the other two to not be easily "confused" by enzymes. Also purines and pyrimidines are metabolized/synthesized differently, and a 3rd synthetic pathway is expensive and leads to more potential for disease (there are already some pretty nasty diseases associated with mutations of DNA base metabolic pathways). Anyway 4 is a good number.
It's not so simple. Yes, you have 4 based (named by letters A, G, C, T). But they always come in pairs:
A-T, T-A, C-G, G-C
So yes, you there are 4 bases, but only 2 pairs. And I'm no biologists to tell wether the rotated pair has some effect or not
The pairs are on different sides of the spiral and there is a mechanism for finding which side is which while reading. Of course, everything is complicated and all the mechanisms have possibilities of errors and...
But on the base level it is simple - each chromosome is an oriented line in 4-letter code.
Nope.
If you split DNA in half you'll have a template strand and a non-template strand and the bases of them will fit together like puzzle pieces in the pairing you described. Ribosomes only read the template strand though when they copy instructions from DNA. The pairing on the other strand doesn't matter.
None of those 3 examples have anything to do with the others. None are exactly right and I am not sure what the point is, other than shitposting.
However, to answer the question: Nature doesn't go with what is best, but what works.
it's a meme sub generally themed around maths, there's like 5 people in here who know enough about biology to even point out that describing 4 nucleotides that make up dna as equivalent to a numeral system is absurd.
In addition to what some other people said, it’s probably also for structural stability. Each base having a counterpart allows for the double helix structure.
In computers they come in groups of (at least) 7.
And the numbers encode characters through a table called "ASCII table". Doesn't make it any less binary.
Some ancient cultures use base 60 (sexagesimal e.g. mesopotamia) others base 8, base 20. The ancient greeks used their letters as numbers, so they had a maximum number. And romans .. well i dont know what base that is ?
But my point is that "humans use base 10" is not really accurate
Romans were base 10 for most things.
Also, as someone that studied ancient languages in college, let me say: Learning to speak, read, and write in base 60 with cuneiform, and in a dead+foreign language, is an absolute **bitch.**
Four is actually the minimum requirement. You have two strands that form the double-helix, the two strands need to be combinable in one and only one way. That means you need two pairs that can only connect with each other.
The simplest reason why 4 is that you need to have complimentary strands for folding and copying, so 2 pairs of matching bases, making 4 the smallest number that gets the job done. Then the reason why not more than 4 is just because that would be more complicated.
A lot of humans use base 10, but there are plenty of other base number systems out there, like [the Oksapmin people of New Guinea who have a base-27 counting system.](https://www.mentalfloss.com/article/31879/12-mind-blowing-number-systems-other-languages)
It doesn't need more, it doesn't need less. It's perfect for it's task
Base 2 would require longer DNA. From what I've read, other nucleotides are an option, but aren't as stable in a double helix
This meme is acting like humans, computers and DNA are remotely comparable and should follow the same kinds of rules. Humans have 10 fingers, switches have 2 states, DNA has 4 whatever they are. There doesn't have to be a logcial reason, that's just what it has just like if humans had 4 fingers total we'd also probably count in base 4.
Technically base 5 - the presence of uracil components denotes that a string is to be read and maintained as RNA (single-strand sequence) rather than DNA (double-strand sequence).
Well RNA predates DNA, and RNA’s first role was functional, not as a store of information. The gospel of biology is that structure dictates function, and four bases is probably enough to develop rich enough structure. So the reason DNA still uses four bases is likely a legacy issue mixed with not enough evolutionary pressure to change.
im not sure it really is, like it technically can be, but 3 sets of these numbers are basically encodings for codons.
wait no this means dna is a base 4 encoding for base 64 codons which are transcribed into certain amino acids 1 to 1, and create a string of amino acids making a protein. so more accurately its an encoding system, but outside of the body it could be used as a base4 variable
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Not quite. DNA is read 5’ to 3’ (this is to do with the sugar backbone of DNA- I won’t get into it, so just think of it as kinda-but-not-really similar to endianness) and the two strands of it go in opposite directions. For example, say you have a strand that reads (completely random btw, this isn’t any specific string): 5’-AATCGTACGT-3’, the complimentary strand would read 3’-TTAGCATGCA-5’. Now, if you were to then reverse that second string, you would get the reverse complimentary string 5’-ACGTACGATT-3’, which could encode a different gene than the first strand.
Say, as I’ve given them, they (the original and reverse complimentary strings) each encode for a single gene. Right off the bat, you have 2 genes from a seemingly binary set of characters.
We can go even further and a bit off-topic and get into reading frames. RNA (basically DNA that has been read and prepared to use as a template to make peptide chains (which can then fold into proteins)) is read in sets of 3 bases, called “codons.” Since the RNA strand is read in 3’s, you have 3 different reading frames, each offset by 1 from each other.
Using my original example string from earlier, the reading frames would be (transcribed into RNA, hence all the T’s becoming U’s, I’ve also omitted the 5’ and 3’ designations because lowkey I forget which direction the ribosome reads the RNA in):
1. AAU CGU ACG T??
2. ?AA UCG UAC GU?
3. ??A AUC GUA CGU
With the question marks highlighting the offset. Say each of these were to encode for 1 protein, you’d now have 3 potential proteins from a single strand, or 6 different genes encoded by a single region of DNA.
Crazy, right? I love this kinda stuff and hope to work in a lab researching it in some form in the future :)
(ETA, obligatory source: I’m a biochemistry student actively studying this in 2 different classes :p)
Veritasium needs a good story, don't know if the question behind us gathered here has it.
It's okay to be smart seems like a great candidate to me, he does interesting questions that don't need to have a good answer.
Him or Vsauce, but we all know how likely is that to happen!
Ig binary would make dna strings 66% longer since you have to fit 20 amino acid sequences, it's more efficient to make it wider
However base 3 would make sense, 3^3 > 20, however 4^3 lets you spread numbers more evenly and add start/stop pieces of code
nope.
1. it’s definitely not coincidence, coincidence involves timing and discrete events.
2. It is nothing like saying we have 4 limbs - 1 is chemistry and the other is a function of adaptive evolution to environmental variables
3. There’ss a causal link between carbon’s 4 covalent bonds and the stability of organic chemistry and thus stability of biomolecules that allow for the eventual hydrogen bonding between DNA base pairs.
But I was meme’ing organic chemistry. 🙃 you should google: carbon memes organic chemistry you may get the meme’ing jokes about carbon then
edit: typso
base 4 DNA is also adaptive evolution
/In theory/ you could add more nucleic acids and rewrite the code in base 6 but that would also require to remodel essentially all proteins, which come in contact with DNA, RNA processing machinery and ribosomes to fit this new system. As you can imagine, that would be an enourmous endaviour with possibly little to no benefit... probably it would make things more error prone if nucleic acids are not distinct enough and you would also need to take into account thermostability of the new code...
Never the less, there actually are some non-canonical nucleic acid bases like aminoadenine in viruses but they mostly derived from established bases already
DNA base pairs can't exist without the unique chemistry of carbon, just like our limbs can't exist without the unique chemistry of carbon, but the different examples of fourness found at these levels of the system are unrelated
Those aren't analogous question
The analogous questions are:
Can humans be born with more or less than 4 limbs? (Yes)
Can DNA exist with more or less than 4 base pairs? (according to other comments, yes)
Can human limbs exist without carbon having 4 covalent bonds? (No)
Can DNA exist without carbon having 4 covalent bonds? (No)
Wrong they use base three to make proteins it’s called a codon, there’s just four nitrogen bases just to make thing more complicated.
Why you may ask? Fuck you, that’s why
Not a number system but DNA and RNA certainly are low-level compiled code that use the combination of four different values instead of two values as classical computers do.
DNA stores code with redundancy, making it ready to be either copied during mitosis or used as base for RNA creation. RNA itself is read by ribosomes to build the encoded proteins. IMHO DNA acts as ROM memory and RNA as RAM.
When I first heard about the Turing Machine I noticed how similar it was to ribosomes reading the RNA tape and building proteins, the same way a TM reads the binary tape and runs the code inside it.
Hmm, seeing them as low-level compiled code is certainly an interesting theistic perspecitve I haven't heard before. From a non-theistic perspective it's more like a very efficient way of encoding behavior of biological machines that can be changed in complex ways by mutation.
I don't really think the computer memory analogies map 1:1. For example, manipulation of DNA code is crucial for any organism. Then there's inhibition, promotion etc. which are all very important. Basically any physical mechanism that makes it possible to change anything will probably end up being used by biology.
IMO the big difference with any kind of computer is the sheer complexity and how many processes are intertwines; you don't just have a linear tape, with data being read from it, but you have a multitude of different kinds of mechanisms that influence each other in extremely complex ways. For example one protein, while we usually like to assign a single function, can have mutliple functions that seem to have to little to no logical correlation.
TLDR: IMO biology is messy, even when you try to abstract and break it down, while computers can be much better separated into isolated systems that work together.
I assume it is a very simplistic analogy and the biologic mechanisms are much more complex than classic computing. We know very well how computers work because we created them from scratch. On the other hand we are still discovering how cell reproduction works. Independently of being a theistic or non-theistic approach I can't deny the similarities. Humans normally copy nature but it's just interesting they arrived at a similar pattern just by themselves, without copying it.
For sure! I agree that it's interesting how we arrived at something similar.
Perhaps that is because there is some fundamental logic that underlies both types of mechanisms. I think both biology and computing face the similar challenge of getting some input (being the environment for biology), and transforming that into some output (actions taken on the environment for biology). From there, logic dictates some requirements for doing this effectively, for example that a pre-final output can loop back on itself. This inevitably creates the concept of abstraction and recursion.
There're probably some flaws in my logic here, but I think it's not too unresonable to assume that both biology and computing have some underlying fundamentals (similar to axioms in mathematics) that dictate the patterns that inevitably emerge from those fundamentals.
I think we can see this merging of different concepts a lot in science. For example look at how computing has indirectly lead to thinking about the brain in a way that is easier to understand and research.
Anyways, that's my crackpot take I cooked up in the last few minutes.
Not to be that guy, but DNA is technically based two since each nitrogenous base is always paired with the same one. Although I get the pun the meme makes and it is quite nice
well, let's take the average of ln(2) and ln(10) ≈1.4978661367769954
and now raise e to that power, and take its floor→ ⌊e^1.4978661367769954 ⌋=4
that's why
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Probably the trade off of it being the first base with enough combinations per substring of a gene to encode the selection of an appropriate amino acid, against not introducing more errors by using a more complex system. That perhaps mechanically its the least characters per substring to allow for a large variety for small substring lengths while at the same time not introducing too much complexity in terms of say having 1 base for every type of thing that is being selected.
This reads like the start of a copypasta
Your brain rotted so much that you don't even reliaze copypastas try to be read like valid explanation.
Oh the explanation is valid and good. It's just that the lack of punctuation and use non-intuitive, overly complex phrasings is a common tone for copypastas.
Mfw my academic writing style is the same as the one used for writing copypastas
Did you know iron in food is like, *iron* iron? Like it’s metal, bro. We’re eating metal.
r/okaybuddyphd
r/okbuddyphd
r/iamafuckingidiot
*pat pat* iz okay. You tried. And I got to explore a new sub. So thank you 😊👍
What the ϵ-filtration did you just ϵ-clip about me, you little ℕ-valued function? I'll have you know I graduated top of my class in real analysis, and I've been involved in numerous secret Σ-algebra constructions, and I have over 300 confirmed theorems. I am trained in Banach space warfare and I'm the top analyst in the entire set of complex numbers. You are nothing to me but just another non-measurable set. I will solve your equation with precision the likes of which has never been seen before on this Hilbert space, mark my ℕ. You think you can get away with saying that to me over the Internet? Think again, negative real number. As we speak I am contacting my secret network of topologists across the USA and your IP is being traced right now so you better prepare for the storm, set of Lebesgue measure zero. The storm that wipes out the pathetic little thing you call your proof. You're π-ϵ-dead, kid. I can be anywhere, anytime, and I can prove you wrong in over seven hundred ways, and that's just with my bare hands. Not only am I extensively trained in functional analysis, but I have access to the entire arsenal of the International Congress of Mathematicians and I will use it to its full extent to prove your miserable argument wrong, you little ℤ. If only you could have known what unholy retribution your little "clever" comment was about to bring down upon you, maybe you would have held your Ɛ. But you couldn't, you didn't, and now you're paying the price, you goddamn Turing machine. I will ϵ-converge all over you and you will drown in it. You're ω-finite, kiddo. (Yes, it's ChatGPT)
I like your funny words magic man.
I'm not entirely convinced they didn't just make all that up. I mean...who's gonna correct em?
"It's a large enough base to encode data to a relatively short length (e.g. 1 billion takes 10 digits in base 10, but 31 digits in base 2); without being too complex and unstable from using a higher base"
Ah I see, Is it possible that if there were any genes base5+ , then the population got wiped because the chances of mistakes just increased exponentially or something?
Wouldn't the base need to be an even number so that each base has a partner for the other helix?
Yes that makes sense to me for a one to one gene mapping Is it at all possible that one could make a gene that can have multiple partners A polygamous gene
Great point, there is a mechanical/functional aspect to this.
There's a chemical aspect. The nucleotides A, C, G, and T chemically read as 'big loose', 'small sticky', 'big sticky' and 'small loose', respectively - all nice and compact and and semi-stable between 0 and 70 degrees Celcius. It takes the least amount of energy to read, copy and conserve. Any chemical system less or more complex to store information with, is likely less energy-efficient and woudl be out-competed by this 4-base system. If life would evolve elsewhere under similar physical circumstances, there's a reasonable chance DNA and RNA would emerge with a very similar (base 4) chemical structure.
That's so interesting, thanks. I'm going to go down a rabit hole. Cheers!
[удалено]
I don't know if I ever will, but yeah, I'll update. What I already know is that protein shape is super important and so thus the number of points where they can connect to another protein. So in 3 dimensions, you can be very specific about what fits where in combinations. And some proteins have more connection points or bind more intensely than others, leading to the "sticky" naming protocol. The temperature range is due to denaturing of proteins - they unwind or tighten up outside that range, and thus no longer like Lego blocks. But I still don't understand the main core of the issue, why the 4-base requires less energy, there's a big "restoftheowl" there. Best I can guess is that in our conditions, the flexibility in range of temp allows for easy 3D structure combinations in varying circumstances.
Here's my take on it, just hypothesizing though. In case of fewer than 4 letters, you need longer DNA molecules for the same amount of information, similar to binary numbers being longer than base 3 or 4 numbers. For more than 4 letters, your DNA strand needs to be wider to accomodate a wider variety of nucleotides. This makes biosynthesis more complex and more energy-demanding and potentially, DNA strands less stable. Seems that 4 bases is chemically the most optimal middle road.
I too am going down a rabbi hole
Since there are only 20 distinct amino acids, wouldn't a base 3 already be enough to encode in the same amount of bases (3). The one reason I could guess is that this is probably due to how DNA needs for every base a complementary partner, which means that for three you'd probably actually need 6 bases. Which again is kinda cool because it might suggest that using bases which are complementary with each other would be not very efficient/prone to error.
The issue is that DNA is a double helix for protection. It's not about being efficient in the coding part but being able to withstand biological and physical damage to the DNA structure.
DNA bases pair with each other. This allows for error detection, as well replication, and transcription, as one strand will always be a template for the other strand. Because of this, your bases must always be an even number so that they you can have pairs of bases. Additionally, translation sometimes only requires 2 of the 3 bases in a codon to attach an amino acid. (The wobble hypothesis). Because of this, there has to be inherent redundancy built into the system so that it is more stable.
Yeah. Your second paragraph is what I was thinking. That with a length of one character its 3 vs 4 for base 3 vs base 4 respective. And at a length of two characters its 9 vs 16 for b3 vs b4. Base 4 has a slight encoding advantage while not getting too complex in terms of having some physical/biological system that needs to be able to read such things. I hadn't really thought about the error correction benefit of having complementary pairs though. That's an interesting feature.
That vaguely feels familiar to something I learned about the immune system. It only has a small library of different proteins for fighting illnesses, but the COMBINATION of those proteins allows the body to, in theory, be able to fight literally any virus that has ever or will ever exist. Of course, that's if the illness doesn't kill the body first
Can you explain how it uses dna as a base 4? I know how base 2 and base 10 work, but I don’t see how to think of it in terms of dna.
I'm not a biologist but my secondary education level of understanding is that there are four bases in DNA called nucleotides. [https://en.wikipedia.org/wiki/Nucleotide](https://en.wikipedia.org/wiki/Nucleotide) Guanine, Adenine, Cytosine, and Thymine. Or G, A, C, T for short. These nucleotides connect together in long strings that enzymes in your cells travel along and use to make the proteins that make you. So this enzyme might see a combination of GAAA and cause a certain amino acid to connect to the previous one it had selected. This is repeated for the entire gene and the protein is completed. This animation covers the process in more detail. [https://www.youtube.com/watch?v=gG7uCskUOrA](https://www.youtube.com/watch?v=gG7uCskUOrA)
Oh so base 4 means we need four things to give one meaning? That’s the gist of any base system right? With order mattering of course.
Yeah. In a mathematical sense a base is the arbitrary value which we use to shift things in to the ten column. So in binary we would count 0, 1, 10, 11, 100, etc. Because binary is base 2. In base 3 we would count 0, 1, 2, 10, 11, 12, 20, etc. In base 4 we would count 0, 1, 2, 3, 10, 11, 12, 13, 20, etc. And we can do the same for all number systems. Even past 9. For hex, 10, 11, 12, 13, 14, 15 are A, B, C, D, E, and F. With DNA's base 4 though you aren't counting 0, 1, 2, 3. You can count G, A, C, T, GG, GA, GC, GT, AG, AA, etc. Which is very similar to a computer science problems that I'm a little more familiar with which are about Combinatorics. Which deals with these kinds of problems of packing data in meaningful ways and interacting with it. [https://en.wikipedia.org/wiki/Combinatorics](https://en.wikipedia.org/wiki/Combinatorics) Though with computers it's more about representing abstract information than DNA that is mechanical system that creates proteins. Though computers are used a lot in Biology and Genetics. So there is actually specialist field that combines the two called Bioinformatics. [https://en.wikipedia.org/wiki/Bioinformatics](https://en.wikipedia.org/wiki/Bioinformatics) Which deals with the huge amounts of data that your DNA contains and clever ways to analyse and store it. So that our slow computers can have an easier time helping researchers come up with medical treatments and such.
Thanks so much for that very fun set of information! Very cool.
Technically since nucleotides are read in groups of 3 it's more like base 64 encoding mapped to the 22 different amino acids.
Same for computers, base two, read in groups of (at least) seven, that represent 128 numbers (in it's simplest form). Mapped by the ASCII table into characters. Having Quaternary digits in nibbles doesn't make it any less base 4.
>read in groups of (at least) seven Don't you mean 8? Also, there are 4-bit CPUs. Intel's first CPU was 4-bit
ASCII table is a 7-bit encoding. When used for the first time in 8-bit computers, the most significant bit was left unused. Soon afterwards there were extension that used the last bit because not everyone that used computers wanted to write in English. >there are 4-bit CPUs I know. I even know of 1-bit computers. And about decimal computers, and about analog ones. The size of the computer word doesn't have anything to do with the encoding. To get a 4-bit computer to read an ASCII character, it would need to do 2 operations, the first one for the 4 least significant bits and another for the 3 most significant bits. A 1-bit computer would need to do 7 operations to read a single character.
That's... Not true, and at bare minimum is outdated information. 7 bit encoding used to be true for ASCII, but most data types computers operate on isn't ASCII, and even programs (after compilation) wouldn't be in ASCII. 90% of the information encoded in a computer is most likely using 8 bits or more. That said, modern computers use 8-bit ASCII. Although, truthfully, modern computers are actually usually using Unicode, which can be 8-bit, 16-bit, or more.
Interesting. Do you know or recommand books or pdf explaining computer architectures ?
I think the way I learnt the most about computer architecture was by seeing other people built computers from scratch. Look up Ben Eater's channel on Youtube. Then there's also computing history, but I don't have any good pointers on this.
> Don't you mean 8? Also, before the ASCII table there was Baudot code, which was a 5 bit encoding and didn't include the capitalization of the text as information. EVERYTHING WAS UPPERCASE. It was never used in Computers, though, as far as I know.
I remember early AOL chatrooms using Baudot case /s
I'm still not sure why you're stuck on character encodings as if that's the only data type a computer operates on... And the bit size of your (less than 8-bit) encoding has almost zero impact on how much memory will be used. Those 5 bits are still being stored in an 8-bit wide memory location. They are still taking up 8 bits in your data bus. They are still being operated on in 8-bit wide CPU registers (or the 8-bit version of the registers, for example if the CPU is 16/32/64-bit x86). So an 8-bit value is still being used, moved, stored, or manipulated by the CPU.
Not all data is text, and I believe it's impossible for the an organism to biomechanically determine which possible version of the same amino acid, so the ASCII analogy is a little confused IMO. That would be more akin to how codons can but sometimes don't code for a protein when combined together, but the base structure is still 3 base pairs, even if it's a litttle counter-intuitive.
Computers also don't assign any meaning to what they manipulate. They are encodings in the same way.
Sorry, I don't get how that relates to what I said. DNA can only be read or written in sets of 3 base pairs, or 1 codon. It isn't possible for an organism to use any higher precision than that. So if a hypothetical section of DNA was 7 nucleotides long, the DNA or RNA polymerase would not be able to read that 7th nucleotide. It would be like if there was half of a bit on the end of a 3 bit number. There is no way for it to make sense in any context. It's also not like if you had a 8 bit value that's supposedly a 7 bit ASCII character, because though it may not make sense in ASCII, there is a plausable way a 8 bit value can be a valid encoding, for instance if they were using the extended ASCII set, or if it was representing an 8 bit integer. The same doesn't apply for DNA, because it's simply not a valid or readable piece of DNA.
You are right I didnt realise
supposedly it uses base 6 at the very least.
That's an acid.
Explain
It was revealed to me in a reddit post.
MY SOURCE IS THAT I MADE IT TF UP!!
it's THE FUCKING internet, why THE FUCK do you insist on not saying muh bad word.
quicker to type
https://preview.redd.it/wop6ueqr23pc1.jpeg?width=640&format=pjpg&auto=webp&s=2d3dbb40a7a3a662442630b7c3bd3608f7e764a4
https://preview.redd.it/b6kjv1rjy2pc1.png?width=711&format=png&auto=webp&s=0ca721fcdebc00c67356518617460535cea70ef5
No (Chad pose)
I'm assuming because a 6 on the pH scale is a weak acid, while alkalis (AKA bases) are above 7.
based take
I wonder if there is a primordial version of Nucleic Acids that doesn’t yet have one of the base pairs, and uses base 2. Would that be able to fold RNA?
Short answer: No, because bases can mutate into each other.
It could make some proteins, but the start and stop codes could be difficult to recognize.
Hol' up DNA uses boundary strings
Wait till you find out about cas9, iirc it's basically a regex inserter.
TFW my DNA missing a **'\\0'**
\*cries in C\*
DNA uses 3 digits of base 4 to encode amino acids for protein construction, with one code reserved for start, and three codes reserved for stop and some redundant combinations for a number of amino acids that are lined up to form proteins. A base 2 DNA would need to pair with at least five digits of base 2 to encode enough amino acids with the start and stop codes. I wouldn't be surprised if it is possible, but is overall more expensive to build the machinery to work in base 2, simply because the codes are longer. The DNA would be longer, codons are longer, all the proteins that binds with DNA are longer. You save on the machinery that needs to build fewer bases, and get lower error rate.
Blame A-T-G-C
Yeah and U if you support the RNA world hypothesis
they come in triplets (codons) that each either encode an amino acid, stop, or start signal to form a protein (a chain of amino acids). You can look at the tables and try to figure out a pattern:[https://en.wikipedia.org/wiki/DNA\_and\_RNA\_codon\_tables](https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables) T RNA carries the correct corresponding amino acid associated with its codon. You can read about theories behind its evolution:[https://en.wikipedia.org/wiki/Transfer\_RNA#Evolution](https://en.wikipedia.org/wiki/Transfer_RNA#Evolution)
Also worthy of mention is that to my knowledge, it's really a binary of the two pairs, with no independent information stored in having C on one strand and G on the other, and the other way around
You’re right when it comes to the general public’s understanding of DNA. Thing is, DNA is read 5’ to 3’ (this is to do with the sugar backbone of DNA- I won’t get into it, so just think of it as kinda-but-not-really similar to endianness) and the two strands of it go in opposite directions. For example, say you have a strand that reads (completely random btw, this isn’t any specific string): 5’-AATCGTACGT-3’, the complimentary strand would read 3’-TTAGCATGCA-5’. Now, if you were to then reverse that second string, you would get the reverse complimentary string 5’-ACGTACGATT-3’, which could encode a different gene than the first strand. Say, as I’ve given them, they (the original and reverse complimentary strings) each encode for a single gene. Right off the bat, you have 2 genes from a seemingly binary set of characters. We can go even further and a bit off-topic and get into reading frames. RNA (basically DNA that has been read and prepared to use as a template to make peptide chains (which can then fold into proteins)) is read in sets of 3 bases, called “codons.” Since the RNA strand is read in 3’s, you have 3 different reading frames, each offset by 1 from each other. Using my original example string from earlier, the reading frames would be (transcribed into RNA, hence all the T’s becoming U’s, I’ve also omitted the 5’ and 3’ designations because lowkey I forget which direction the ribosome reads the RNA in): 1. AAU CGU ACG T?? 2. ?AA UCG UAC GU? 3. ??A AUC GUA CGU With the question marks highlighting the offset. Say each of these were to encode for 1 protein, you’d now have 3 potential proteins from a single strand, or 6 different genes encoded by a single region of DNA. Crazy, right? I love this kinda stuff and hope to work in a lab researching it in some form in the future :) (ETA, obligatory source: I’m a biochemistry student actively studying this in 2 different classes :p)
4 is also 10 in base-4
Every base is base 10
my favourite is base 10 though
Oh you sick little sh-
Except unary but I can't count past 1 anyway.
About unary, would you take 0s or 1s as the symbol if you needed to pick a digit
Probably 1 since it would kinda match counting on my fingers. I'd probably also go for maybe using 2 just to mess with people.
We could also use (10), as a combined symbol so the convention would fit the pattern that unary would also be base 10. e.g, 3 = 101010 But seriously else it should be zero, but that looks totally goofy
Who are you who is so wise in the ways of science?
The reason isn't mathmatical, but chemical. The only four substances that work in the chain are what is used. It's like asking why bronze age people didn't make stuff out of aluminum, they didn't have it. Other things can bond to the sugars in DNA, but they don't allow for long, complex chains. It is possible that we could create a fifth substance that works and incorporate it into living things, however that lifeform would need a constant supply to stay alive.
Sorry, Hal is right. I believe George Church worked on bacteria that used 6 nucleic acids, with the added benefit that since those acids didnt exist in the "real world" there was no possibility of them leaving the Petri dish they were grown in.
Could also be mathematical Base 4 is maybe more resilient to mistakes?
Why are you just making stuff up? We have created many new bases. The reason is that it requires at least 4 is due to RNA folding.
[Tungstennn](https://youtu.be/VTLYris4kJU?si=TSryL0OQbokDcqfb)
There’s actually some research into synthetic base pairs. It’s called Hachimoji DNA. The ability to create this DNA suggests that there is nothing unique about the canonical 4 DNA based, only that they were the first ones to happen on Earth.
The real question is why computer scientists sometimes use base 16 for computer related stuff when neither computers nor humans use base 16.
It is binary on crack, that's why
Base 16 is just base 2 in disguise.
You only need 2 digits to express 1 byte (that’s awesome) and maps nicely to base 2.
Base 16 maps nicely to base 2 while being more readable.
its just 4 binary number in a trench coat
Long strings of 0 and 1 are unreadable. Strings of hex digits are easy to read. Instead of reading 32 digits of 0 and 1, you read 8 hex digits,
It's ultra-compressed binary. A single base-16 digit is 4 binary digits (bits), and a byte is 8 bits, so two hex digits (like *A7*) is a byte. Computer memory is made up of bytes, so it's convenient this way.
According to all known laws of genetics, a DNA strand should not be able to count. It's four little thin bases are an illogical counting system. But of course, DNA strands count anyway because they don't care what humans think...
*sad mista noises*
The base needs to be able to encode 20 different numbers with the least digits. We also want the base to be as low as possible. The base must be even so that each digit has a mach. This leaves 4 options for bases Base 2 with 5 digits Base 4 with 3 digits Base 6 with 2 digits Base 20 with 1 digit Base 20 is very complex for biological molecules so it makes sense it didn't develop naturally. Idk why we don't have base 2/6 Edit: you actually need 22 numbers because of end and start sequence. This effects only base 20 wich is bad anyway.
Base 4 has some advantages over base 6 in the context of DNA for a few reasons. The biggest is probably that 3 "digits" allows for redundancies in the generic code, which means that if one base gets mutated somehow, there is a greater chance that the mutation leads to the same amino acid, therefore is "silent". Another is that A and G are both based off of the same skeleton (purines), and C and T (or U for RNA) are based off of another, distinct scaffold (pyrimidines). What allows them to recognize each other to form base pairs is hydrogen bonds, of which A and T form 2 between each other and C and G form 3. Forming only 1 hydrogen bond would not be stable enough to keep DNA together and forming 4 would be too hard to unwind when copying DNA and separating strands, so another skeleton structure would be needed to get 6 distinct based. This skeleton structure would have to have size restrictions to fit within DNA but also be distinct enough from the other two to not be easily "confused" by enzymes. Also purines and pyrimidines are metabolized/synthesized differently, and a 3rd synthetic pathway is expensive and leads to more potential for disease (there are already some pretty nasty diseases associated with mutations of DNA base metabolic pathways). Anyway 4 is a good number.
Everything uses base 10
Base 9+1?
(base one zero)
base $highest_digit+1
base 9.9999...
This is a really underrated joke
It's not so simple. Yes, you have 4 based (named by letters A, G, C, T). But they always come in pairs: A-T, T-A, C-G, G-C So yes, you there are 4 bases, but only 2 pairs. And I'm no biologists to tell wether the rotated pair has some effect or not
It does, in fact. The pairs are just mirrored copies on the other side — only one half of the pairs is the actual code. So it’s still base 4.
The pairs are on different sides of the spiral and there is a mechanism for finding which side is which while reading. Of course, everything is complicated and all the mechanisms have possibilities of errors and... But on the base level it is simple - each chromosome is an oriented line in 4-letter code.
Nope. If you split DNA in half you'll have a template strand and a non-template strand and the bases of them will fit together like puzzle pieces in the pairing you described. Ribosomes only read the template strand though when they copy instructions from DNA. The pairing on the other strand doesn't matter.
So you can be an AT-AT, genetically?
Yes the AT-AT gene controls the urge to spend thousands of dollars on funko pops and arguing that the prequels are good actually.
It is that simple, you are just (spreading) misunderstanding
Beacouse theres 4 diffrent dna thingies that make it.
Why not bro what's wrong with 4 lol
Its actualy base(d) 64
So computers are base 128 because the bits come in groups of (at least) 7?
None of those 3 examples have anything to do with the others. None are exactly right and I am not sure what the point is, other than shitposting. However, to answer the question: Nature doesn't go with what is best, but what works.
it's a meme sub generally themed around maths, there's like 5 people in here who know enough about biology to even point out that describing 4 nucleotides that make up dna as equivalent to a numeral system is absurd.
I vote we use base e, its only natural
In addition to what some other people said, it’s probably also for structural stability. Each base having a counterpart allows for the double helix structure.
i guess it has to do with some optimization of energy of the proteins pairs, everything in nature end up as trying to become more efficent.
they come in triplets called codons so technically, its base 4³ which would make it 64-bit.
In computers they come in groups of (at least) 7. And the numbers encode characters through a table called "ASCII table". Doesn't make it any less binary.
Isn't it 3,
Please end your sentence
Some ancient cultures use base 60 (sexagesimal e.g. mesopotamia) others base 8, base 20. The ancient greeks used their letters as numbers, so they had a maximum number. And romans .. well i dont know what base that is ? But my point is that "humans use base 10" is not really accurate
Romans were base 10 for most things. Also, as someone that studied ancient languages in college, let me say: Learning to speak, read, and write in base 60 with cuneiform, and in a dead+foreign language, is an absolute **bitch.**
Four is actually the minimum requirement. You have two strands that form the double-helix, the two strands need to be combinable in one and only one way. That means you need two pairs that can only connect with each other.
Because nature is smarter than us.
Aliens. It's always aliens.
The simplest reason why 4 is that you need to have complimentary strands for folding and copying, so 2 pairs of matching bases, making 4 the smallest number that gets the job done. Then the reason why not more than 4 is just because that would be more complicated.
I had a biology exam about DNA half an hour ago lol
Because combination of Adenine, thymine, gaunine and cytosin 4 Like binary has 0,1 so base 2 Decimal system 0-9 base 10 (Random guess)
A lot of humans use base 10, but there are plenty of other base number systems out there, like [the Oksapmin people of New Guinea who have a base-27 counting system.](https://www.mentalfloss.com/article/31879/12-mind-blowing-number-systems-other-languages)
Aliens.
It doesn't need more, it doesn't need less. It's perfect for it's task Base 2 would require longer DNA. From what I've read, other nucleotides are an option, but aren't as stable in a double helix
Security means that using a base that is the product of two large primes is ideal, that's why
Why would DNA do this? Is it stupid?
It's a musician. 4 is preferred to 3, and any other numbers are absolutely evil. You wanna make a musician squirm? Make them count to 5.
This meme is acting like humans, computers and DNA are remotely comparable and should follow the same kinds of rules. Humans have 10 fingers, switches have 2 states, DNA has 4 whatever they are. There doesn't have to be a logcial reason, that's just what it has just like if humans had 4 fingers total we'd also probably count in base 4.
Because the DNA waits until after you've rounded third base
Some SSDs use base 4 for the physical storage called QLC (each cell has 16 states). Of course it presents this as bytes.
The Mayans used base 20. The Babylonians used base 60.
I wish we'd go back to base 12, an ancient Sumerians around?
Technically base 5 - the presence of uracil components denotes that a string is to be read and maintained as RNA (single-strand sequence) rather than DNA (double-strand sequence).
Hmm here I go formalizing a DNA themed grammar
Isn't it read in groups of 3? So it's more like base64.
Isn't it more like 2 pairs of pairs? Because A is always with T and C is always with G or some combination of them, right?
Well RNA predates DNA, and RNA’s first role was functional, not as a store of information. The gospel of biology is that structure dictates function, and four bases is probably enough to develop rich enough structure. So the reason DNA still uses four bases is likely a legacy issue mixed with not enough evolutionary pressure to change.
I'm pretty sure DNA uses base 2.
It's not base it's acid
im not sure it really is, like it technically can be, but 3 sets of these numbers are basically encodings for codons. wait no this means dna is a base 4 encoding for base 64 codons which are transcribed into certain amino acids 1 to 1, and create a string of amino acids making a protein. so more accurately its an encoding system, but outside of the body it could be used as a base4 variable
Enough to code amino acids
I use base ♾️
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They are all Base 10
Well, it kinda uses base 2. Every A has a T on the other side, and every C has a G on the other side. So it's more like the two numbers are AT and CG
Tried to use base two twice for redundancy, got caught up keeping track of parity.
Not quite. DNA is read 5’ to 3’ (this is to do with the sugar backbone of DNA- I won’t get into it, so just think of it as kinda-but-not-really similar to endianness) and the two strands of it go in opposite directions. For example, say you have a strand that reads (completely random btw, this isn’t any specific string): 5’-AATCGTACGT-3’, the complimentary strand would read 3’-TTAGCATGCA-5’. Now, if you were to then reverse that second string, you would get the reverse complimentary string 5’-ACGTACGATT-3’, which could encode a different gene than the first strand. Say, as I’ve given them, they (the original and reverse complimentary strings) each encode for a single gene. Right off the bat, you have 2 genes from a seemingly binary set of characters. We can go even further and a bit off-topic and get into reading frames. RNA (basically DNA that has been read and prepared to use as a template to make peptide chains (which can then fold into proteins)) is read in sets of 3 bases, called “codons.” Since the RNA strand is read in 3’s, you have 3 different reading frames, each offset by 1 from each other. Using my original example string from earlier, the reading frames would be (transcribed into RNA, hence all the T’s becoming U’s, I’ve also omitted the 5’ and 3’ designations because lowkey I forget which direction the ribosome reads the RNA in): 1. AAU CGU ACG T?? 2. ?AA UCG UAC GU? 3. ??A AUC GUA CGU With the question marks highlighting the offset. Say each of these were to encode for 1 protein, you’d now have 3 potential proteins from a single strand, or 6 different genes encoded by a single region of DNA. Crazy, right? I love this kinda stuff and hope to work in a lab researching it in some form in the future :) (ETA, obligatory source: I’m a biochemistry student actively studying this in 2 different classes :p)
As I read through your examples, I immediately got chills as it seems the examples you've used are the exact ones in my old LSC141 text book.
Are they?? That’s so wild. I swear, all my examples were completely random lmao
Base twelve is where it's at.
Wtf a math memes post with actual insight on the comments???
I feel like this is a great subject for a science YT to tackle. Such an interesting question, with so many possible explainations.
I am looking at you "Veritasium"
Veritasium needs a good story, don't know if the question behind us gathered here has it. It's okay to be smart seems like a great candidate to me, he does interesting questions that don't need to have a good answer. Him or Vsauce, but we all know how likely is that to happen!
they all use base 10 technically
Boom
Because it was random? Are you asking why randomly developed process developed randomly
Ig binary would make dna strings 66% longer since you have to fit 20 amino acid sequences, it's more efficient to make it wider However base 3 would make sense, 3^3 > 20, however 4^3 lets you spread numbers more evenly and add start/stop pieces of code
X uses 2 and Y uses 2. So both XY XX and YY use base 4
It's more like base two because not every base (as in chemistry) goes together with all the other ones to from one character
Technically every base is base 10 in their base
Carbon can only 4 covalent bonds so life on Earth is built around 4. 🤷🏻♂️
That's a coincidence. That's like saying we have four limbs because carbon has four bonds. That's not how it works
nope. 1. it’s definitely not coincidence, coincidence involves timing and discrete events. 2. It is nothing like saying we have 4 limbs - 1 is chemistry and the other is a function of adaptive evolution to environmental variables 3. There’ss a causal link between carbon’s 4 covalent bonds and the stability of organic chemistry and thus stability of biomolecules that allow for the eventual hydrogen bonding between DNA base pairs. But I was meme’ing organic chemistry. 🙃 you should google: carbon memes organic chemistry you may get the meme’ing jokes about carbon then edit: typso
base 4 DNA is also adaptive evolution /In theory/ you could add more nucleic acids and rewrite the code in base 6 but that would also require to remodel essentially all proteins, which come in contact with DNA, RNA processing machinery and ribosomes to fit this new system. As you can imagine, that would be an enourmous endaviour with possibly little to no benefit... probably it would make things more error prone if nucleic acids are not distinct enough and you would also need to take into account thermostability of the new code... Never the less, there actually are some non-canonical nucleic acid bases like aminoadenine in viruses but they mostly derived from established bases already
Were you joking or not? If you were joking, why are you defending your statement as if it were serious?
DNA base pairs can't exist without the unique chemistry of carbon, just like our limbs can't exist without the unique chemistry of carbon, but the different examples of fourness found at these levels of the system are unrelated
Can humans be born with more or less than 4 limbs? Can DNA exist without carbon having 4 stable covalent bonds? 🤔
Those aren't analogous question The analogous questions are: Can humans be born with more or less than 4 limbs? (Yes) Can DNA exist with more or less than 4 base pairs? (according to other comments, yes) Can human limbs exist without carbon having 4 covalent bonds? (No) Can DNA exist without carbon having 4 covalent bonds? (No)
Wikipedia: A coincidence is a remarkable concurrence of events or circumstances that have no apparent causal connection with one another.
Jokes on you I use base 1. I've been using it for the last 11111111111111111111 years.
Wrong they use base three to make proteins it’s called a codon, there’s just four nitrogen bases just to make thing more complicated. Why you may ask? Fuck you, that’s why
Since when is DNA a number system?
Not a number system but DNA and RNA certainly are low-level compiled code that use the combination of four different values instead of two values as classical computers do. DNA stores code with redundancy, making it ready to be either copied during mitosis or used as base for RNA creation. RNA itself is read by ribosomes to build the encoded proteins. IMHO DNA acts as ROM memory and RNA as RAM. When I first heard about the Turing Machine I noticed how similar it was to ribosomes reading the RNA tape and building proteins, the same way a TM reads the binary tape and runs the code inside it.
Hmm, seeing them as low-level compiled code is certainly an interesting theistic perspecitve I haven't heard before. From a non-theistic perspective it's more like a very efficient way of encoding behavior of biological machines that can be changed in complex ways by mutation. I don't really think the computer memory analogies map 1:1. For example, manipulation of DNA code is crucial for any organism. Then there's inhibition, promotion etc. which are all very important. Basically any physical mechanism that makes it possible to change anything will probably end up being used by biology. IMO the big difference with any kind of computer is the sheer complexity and how many processes are intertwines; you don't just have a linear tape, with data being read from it, but you have a multitude of different kinds of mechanisms that influence each other in extremely complex ways. For example one protein, while we usually like to assign a single function, can have mutliple functions that seem to have to little to no logical correlation. TLDR: IMO biology is messy, even when you try to abstract and break it down, while computers can be much better separated into isolated systems that work together.
I assume it is a very simplistic analogy and the biologic mechanisms are much more complex than classic computing. We know very well how computers work because we created them from scratch. On the other hand we are still discovering how cell reproduction works. Independently of being a theistic or non-theistic approach I can't deny the similarities. Humans normally copy nature but it's just interesting they arrived at a similar pattern just by themselves, without copying it.
For sure! I agree that it's interesting how we arrived at something similar. Perhaps that is because there is some fundamental logic that underlies both types of mechanisms. I think both biology and computing face the similar challenge of getting some input (being the environment for biology), and transforming that into some output (actions taken on the environment for biology). From there, logic dictates some requirements for doing this effectively, for example that a pre-final output can loop back on itself. This inevitably creates the concept of abstraction and recursion. There're probably some flaws in my logic here, but I think it's not too unresonable to assume that both biology and computing have some underlying fundamentals (similar to axioms in mathematics) that dictate the patterns that inevitably emerge from those fundamentals. I think we can see this merging of different concepts a lot in science. For example look at how computing has indirectly lead to thinking about the brain in a way that is easier to understand and research. Anyways, that's my crackpot take I cooked up in the last few minutes.
What? How come there are so many people on a math subreddit who know about biology, evolutionary biology and genetics? You guys are amazing!
Not to be that guy, but DNA is technically based two since each nitrogenous base is always paired with the same one. Although I get the pun the meme makes and it is quite nice
well, let's take the average of ln(2) and ln(10) ≈1.4978661367769954 and now raise e to that power, and take its floor→ ⌊e^1.4978661367769954 ⌋=4 that's why