How does DNA encode 3d space/information?

Submitted by Rit2Strong t3_105jhch in askscience

For example, let's say someone inherited their father's nose. How does this work exactly? Like, how does DNA encode what a nose is and how it's shaped? Does DNA say where every cell should be or does it convey an algorithm/blueprint for nose construction. If it says where every cell should be, how does it convey this information? Like does it use some coordinate system relative to some point in the body? If it's an algorithm, how does it work? Or is it something else? Thanks in advanced!

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[deleted] t1_j3dlsam wrote

A lot of the answers here are long. The tl;dr is that DNA doesn’t encode information like “put the jugular at this position in the neck,” it encodes a bunch of molecular machines that together represent instructions that are more like “if you are an endothelial cell, contribute to vein construction when you encounter the hormone VEGF-A.”

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Boring_Ad_3065 t1_j3ep1ot wrote

I believe the OP is looking for evolutionary developmental biology. If so, there’s an amusing video done to “despacito” that is also highly informative (given its format) by A Capella Science.

https://m.youtube.com/watch?v=ydqReeTV_vk

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I4Vhagar t1_j3ftven wrote

Lex Friedman had an evolutionary biologist on his podcast, sometime in the last few months. The way he explained it was that the accumulation of simple mechanisms trend towards the more complex mechanisms via gradients, electron affinity, etc. I believe it was with Michael Levin, but I can’t play the audio to confirm right now.

I’ve had the opportunity to work with quite a few patients that were born with anatomical structures where they shouldn’t be or oriented abnormally (e.g. Apert syndrome and dextrocardia). It’s fascinating stuff from a biological standpoint.

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Sinemetu9 t1_j3duxzv wrote

So how does cancer work? In my mind, the cells’ programming goes AWOL and they just keep replicating and acting, regardless of procedure protocols. How true is that?

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CrateDane t1_j3dx1jp wrote

Your cells have, for example, some "programs" that tell them to grow and divide, and some programs that tell them to commit suicide. Those programs are normally only turned on when appropriate.

In a cancer cell, mutations cause one or more programs telling the cell to grow and divide to be constantly turned on, and the suicide programs to be broken (so even if it would be appropriate, they will not commit suicide).

There are some other programs that tend to be broken in cancer cells too, but those are two of the main ones.

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Sinemetu9 t1_j3dy6pe wrote

What can reprogram them?

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YandyTheGnome t1_j3dzips wrote

Usually it's damage to the pathway that activates this cell suicide. The body signals for it to die off but it doesn't respond to the signal. This can happen in numerous different ways, as evidenced by the multitude of types of cancers.

Edit: as an example, damage from ultraviolet light causes many cells to die off, in the form of sunburn and the blistering that follows. Some cells get mutated but don't die, and can become skin cancer.

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CrateDane t1_j3dzd0g wrote

Mutations. Those can be caused by many things, most often either DNA damage from the cell's own metabolic byproducts or mistakes made when growing/dividing cells replicate their DNA.

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artlabman t1_j3ec1nk wrote

Is cell death still called apoptosis??

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CrateDane t1_j3egc41 wrote

It used to be we thought of just apoptosis and necrosis, with apoptosis being a clean and deliberate suicide, while necrosis was a messy and uncontrolled cell death.

While those are still very valid, it's turning out that there are a lot more ways for cells to die.

There's necroptosis which is controlled like apoptosis, but messy like necrosis. There's ferroptosis which is iron-reliant and happens in response to excessive oxidation. There's anoikis, which is very similar to apoptosis but initiated by lack of contact to extracellular matrix. There's NETosis, where a type of immune cell called neutrophils eject their DNA as a sticky net to capture pathogens. There's pyroptosis which is triggered by the inflammasome and strongly stimulates inflammation to combat mainly intracellular pathogens.

There are a few more I've left out, probably a few more I haven't heard of, and then all the ones we might not have discovered/characterized yet.

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artlabman t1_j3eheht wrote

Thanks it’s been almost 30years since I was in college….

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provocative_bear t1_j3edpp2 wrote

Apoptosis is a "planned" cell death, where either the body commands the cell to kill itself because it's no longer useful or the cell is mortally wounded and dies a tidy death by suicide for the good of the body.

In contrast, cell necrosis is sudden, "messy" cell death that is not considered apoptosis. It can cause problems for surrounding cells as debris, signaling molecules, and even digestive enzymes get released uncontrolled from the dying cell.

Cancer cells are damaged (usually genetically) in a way that causes them to ignore the body's signals to commit apoptosis, but also to ignore signals to not divide and to stay where they are.

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Yitram t1_j3ei7t8 wrote

You're not wrong. Think of cells as a factory making a product. In cancer, not only is the product wrong but you can't shut off the factory. Also why cancer is so awful if you get it younger. To go back to the factory analogy, in a young person, the factory is shiny and new and efficient, so it makes the cancer really fast. Whereas in an older person, the factory already isn't in the greatest of shape, even before the cancer.

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Mr_HandSmall t1_j3e3j6k wrote

Cells are always having a few mutations in their DNA, but there are systems in the cell that will recognize excess mutations and kill the cell before it can cause problems.

Things can really start to get out of hand when you get mutations in those proofreading systems themselves. Then you get a set of cells that can start mutating freely. Eventually natural selection takes over and the mutant cells keep accumulating more and more mutations that help them replicate and spread, leading to cancer.

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mpinnegar t1_j3e99t2 wrote

Cells have a variety of processes going on inside of them to do things like maintain homeostasis, replicate, fix DNA errors, produce power, etc. They even have machinery to self terminate when something goes wrong.

In a cancer cell one of the processes has broken down and the self termination process has ALSO broken down. Once that's happened you essentially have a rogue cellular factory inside of your body that can hijack the resources you need to survive and can replicate itself going from one cell to enough to kill you by any number of factors. The cancer could just physically put pressure on organs like the brain. It could produce a wild amount of signaling hormones therefore causing secondary non-cancerous cells to follow erroneous instructions. It could also take over resources that other parts of your body need to survive.

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Trips-Over-Tail t1_j3dve7w wrote

Pretty much. They don't do much normal stuff beyong replication and releasing hormones that stimulate capillary growth to keep them fed.

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Sinemetu9 t1_j3dxqlc wrote

Ok thank you. So the procedure protocols can be disrupted by environmental influences eg. radiation poisoning, and by genetic, inheritable weaknesses in coding checking procedures? Why don’t the surrounding cells say ‘hey, you’re going crazy, stop!’?

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Mr_HandSmall t1_j3e4y20 wrote

> Why don’t the surrounding cells say ‘hey, you’re going crazy, stop!’?

A cancerous cell might develop a mutation that would reduce the amount of a protein on it's surface that would normally be recognized by immune cells trying to kill cancerous cells.

No two cancers are exactly alike on a genetic level, even though may have the same medical label. Each is a unique collection of many mutations that lead to a cell population that can replicate, invade, evade immune detection, etc.

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Trips-Over-Tail t1_j3e2fje wrote

They do. Our immune system works very hard to suppress cancerous and pre-cancerous cells all over our body. The ones that become deadly tumours are the ones that by chance are able to fly under the radar of the immune system. Natural selection.

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pzzia02 t1_j3e3ah3 wrote

Thats about it they stop listening to the "cyclins" that regulates cell replication. This is usually quite common and the body can destroy the cells as long as theyre recognised. When they arent recognised and grow out of control it can get out of hand.

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Greyswandir t1_j3clakl wrote

You’re both over and under thinking this lol. So, your DNA encode a ton of information that ultimately determines a lot about your body’s morphology. But that information isn’t a “picture” of what you’ll look like. There’s no coordinate system and your DNA doesn’t “know” where the tip of your nose will be or what your eye color is, etc. Generally speaking your DNA doesn’t know anything about macroscopic space or encode any information about it. DNA directly encodes tiny little parts and machines, and those parts and machines work together in a way that is vastly more complex than the DNA “knows” about.

To give a simple view: DNA codes for proteins in units called codons. Each codon is three bases of the DNA chain (the A, C, G, and T letters you’ve probably seen) and which of those bases appear in what order defines the meaning of the codon. Through a process called transcription and translation, the codon is used to pick a chemical called an amino acid. There are 20 possible amino acids (in humans). The DNA tells the cell which amino acids to assemble in what order. The chain of assembled amino acids folds into a protein (often along with other chains) based on what amino acids go in what order. The proteins do all kinds of things but they’re not smart, they’re structural building blocks or simple machines. But the interplay of simple machines can lead to extremely complex behaviors (like “grow a nose”).

Imagine we have a first protein that sits on the surface of the cell. It bends one way if it’s touching something and bends another if it’s not. We have a second protein that checks the bend of those first proteins and triggers a signal to grow if it’s bent touching something. Now we have a simple little system which means that the cells will grow across an object (like the bottom of a Petri dish) but stop when they run out of room for each cell to be touching the dish. A relatively complex spatial behavior from two simple parts*

And cells are way, way, way more complicated than this, with tons and tons of interlocking signal pathways.

*to be clear: I made the parts and their functions up for my example to just illustrate how the proteins can lead to a spatial behavior without the DNA knowing anything about space. Growing to confluence is a real behavior in many cells, but frankly it’s been a long time since I took cell bio and I don’t remember the exact mechanism.

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Xilon-Diguus t1_j3dfooz wrote

Space can be somewhat inferred by cells through hormone and signaling molecule gradients. So if a central group of cells can start releasing some sort of signaling molecule, and as cells get more distant from that central packet of cells they get less of that molecule, changing their behavior (ie gene expression).

Cells can also divide non-symmetrically, where one cell stays as one type and the other differentiates into a new cell type, creating shape. Cells can pass on information on what genes to express through chemical marks left on the DNA (and the proteins bound to the DNA) telling the new cell what genes to express and what genes to repress.

In the end, though everything does come back to gene expression, which is regulated by a complex network of gene expression networks generated by where the cell originated and what signals it is getting from where it is in the organism.

Interesting the actual genome in the nucleus does have a conserved 3D shape, which has a big impact on how it regulates its genome.

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[deleted] t1_j3di5iq wrote

[removed]

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aaeme t1_j3e1e20 wrote

It's really hard to explain in words even in a book let alone in a few paragraphs.

Perhaps an analogy:

Langton's Ant is a mathematical curiosity. The idea is an infinite grid. The 'ant' is a marker with position and direction and gets set in motion from anywhere in any direction (the grid is infinite and uniform so it makes no difference). When the ant lands on a cell (a grid square), if the cell is white it turns it black and turns right, if the cell is black it turns it white and turns left. The future behaviour of the ant and the grid is entirely determined by those two rules and the colour-scape of the grid. No other information is present. But the picture it creates is immensely complicated.

Fractals like the Mandelbrot Set and Julia Sets could be another example.

A simple set of iterated rules can produce a very complicated structure and do so repeatedly and reliably. If you don't change the rules you'll always get the same structure.

The degrees of separation between the rules that DNA (combined with all sorts of biochemistry) provide and the physical structures they lead to are as a chasm but they are still pretty reliable and predictable so clones will reliably look almost exactly the same as each other (same rules, same outcome).

Another analogy would be trying to understand how a sequence of zeroes and ones, or the simple rules of machine code, can lead to what we can achieve even just nowadays with AI (outthinking grandmasters at Chess, generating convincing art, etc). It boggles the mind (or should). The rules of DNA (and their interaction with all sorts of biochemistry) are arguably much more complex and varied than machine code so it shouldn't really come as a surprise that it can produce an infinitude of possible biological shapes and yet do so as predictably and consistently as a computer program.

Does that make sense?

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ancientevilvorsoason t1_j3drgxy wrote

Since you get half of your genes from each parent, getting the specific let's say ALIGNMENT of the expression of genes is why your nose looks the same.

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humboldtcash t1_j3f8s7m wrote

There is some degree of spatial information within DNA. There is something called “hox genes” which are arranged on chromosomes in the same order our body parts are arranged (head, neck, thorax, hips, legs, in that order). There have been experiments where fruit flies genomes were edited. Basically the hox genes positions were changed and the flies has feet instead of antenna on their heads.

More precise spatial information such as having 5 fingers that are on the end of your arm is given by cell signaling mostly. During the development of an embryo most things are related to cells releasing certain molecules that cause other cells to move or differentiate. But the actual code for all those things is in our DNA as well. However the exact processes are still being researched and it’s not 100% clear how it works.

Edit: just a thought that occurred to me: I think if we knew the exact mechanisms of how this works, medical science would be creating functioning 3D organs or something close to that

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aggasalk t1_j3dugka wrote

maybe a too-fine point to make here, but nothing is 'encoded' in DNA. DNA is the base level of the biological process - DNA is fed through molecular machines and the result is construction of various proteins and new molecular machines and etc, and you could see this as a process of "decoding" (stretching the information processing metaphor too far, imho). but nothing was ever "encoded" there.

DNA comes to be the way it not by some kind of encoding process (it would if evolution were more like the Lamarckian idea), but by random mutation and natural selection, and is selected for the fact that, when it runs through that machinery, useful stuff is produced that supports the creation of more of that same DNA.

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CrateDane t1_j3dxp6r wrote

On the other hand, we do talk about genes coding for stuff, so that kind of language is useful (but in a more basic manner - a gene codes for a protein, not a gene (or allele) codes for a big nose).

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aaeme t1_j3e3ju8 wrote

Very good point to make.

I think you can make a valid analogy between

DNA, biochemistry, and the physical forms of all animals and plants etc,

with

An encrypted hash (or lossless compression), the encryption/compression algorithm, and the thing that was encrypted/compressed.

The difference as you rightly point out is that we produce the hash from the desired end result 'encode' videos and images etc,

Whereas DNA evolves by the reverse process: with random hashes and if something useful emerges from that then the DNA gets kept and then adapted with more random changes that get kept or discarded.

Nevertheless, the end result is the same: a compressed/encrypted file that, with the application of the correct algorithm, can produce the entity in question. In that sense, 'encoded' is a valid verb for DNA: our physical forms are encoded within our DNA the algorithm is not reversible and never needed to be.

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Hamza-067 t1_j3gvm0f wrote

DNA is a molecule that stores genetic information in the form of a code made up of four nucleotide bases: adenine (A), cytosine (C), guanine (G), and thymine (T). These bases are paired together in a specific way to form a double-stranded helix structure, with adenine pairing with thymine and cytosine pairing with guanine.

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