AFAIK the only output of DNA transcription are proteins but how are things like skeletal structure encoded? I mean things that are not functional specialization like the shape of my nose or the size of my forehead or the length of my legs.
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Because the DNA contains instructions for what the cells should do *from conception* (from the moment when it’s a single-cell egg with some DNA from the sperm). Instructions for how to go from [a cell](https://biologydictionary.net/wp-content/uploads/2018/03/Embryonic-Stem-Cell.jpg) to the millions of cells in the fully grown YOU (as opposed to a fully grown other animal). Meat is meat, bone is bone, more or less (that’s why we can eat the stuff and USE the digested “components” that are inside the cells, proteins, fats, sugars, etc.), but “form” depends on how the cells divide and which organs and shapes they “grow” into as you develop.
DNA doesn’t encode “how” as much as it encodes “when” cells should begin to specialize or begin to show certain traits. This timing depends both on the number of divisions that occur before a gene is expressed, and on hormonal signals that trigger groups of responsive cells to change expression in subsequent divisions.
They aren’t. There’s nothing in DNA that explicitly encodes “your leg bone is this long.” DNA is a program that needs to be run on a very specific set of hardware (a fertilized egg) in a very specific enviroment in a very specific order. It’s the combination of the cell, the timing, the environment, and the DNA that all comes together to make a human (or a banana or a lizard or…).
If you just dump human DNA into the nucleus of a random cell and grow it in a petri dish you don’t get a human.
But *if* you take a fertilized egg and implant it in a functioning womb (or identical chemical equivalent) and let it grow with the right nutrients a whole series of chemical reactions will happen that will eventually end up with a leg bone of a particular length.
Have you ever played with a cellular automaton like Conway’s Game of Life? Each individual cell works on its own and doesn’t really know where it is. Rather they run on rules like “if you see this chemical and this chemical then you are now a bone cell so make this chemical.” During early fetal development cells figure out where they are and make an approximately human-shaped blob; then they basically grow according to their cell type and the cells directly touching them in the blob.
Getting this right is really hard which is why there are so few basic body plans for animals. They all have four limbs and a head and possibly a tail – because evolution figured that out and stuck to it. All the changes, like tail/no tail, or front legs/arms, are just minor variations on this. Instead of coming up with new signals to make arms instead of front legs, evolution found it easier to just convert the front legs into arms, or make the tail convert into something else or not grow.
Making the legs longer is relatively easy as you just make the chemical that makes legs grow last a little longer so they grow more, but adding another leg is difficult because it fundamentally changes how the legs figure out that they’re legs. It’s probably more likely that humans evolve a tail that works a little bit like a leg, than that they evolve a third actual leg.
Check out the experiments of Michael Levin concerning the modulation of charge and termination of anatomical limbs. Most double stranded DNA is non coding and regulatory. Non coding means not a gene or coding for a protein.
Levin asks the question in his papers and talks how do cells know when to STOP growing? Where is the plan and how might it be shared across great distances between cells? The answer is sometimes via charge or electric potential.
We usually think of nerves using charge in action potentials but he suggests that ion gates are prolific throughout other cell types and might be part of a simple communication network.
He also investigates Basal Cognition.
Basically the cells in your body are like little factories that build stuff. However, they also have “antenna” on the outside to pick up signals from the surrounding cells/outside the cell. Some of these signals will tell you cells to do all sorts of stuff (stop, go, go faster, die, etc). The cells themselves can also make these signals, it’s a whole network (like, your entire body’s billions of cells). Anyway, some things like bones will basically stop growing once the cells in a certain part of the bone receives enough “stop” signals.
There’s been lots of developmental biology experiments performed to basically see, “Hey, what happens if we turn this gene on so that it never stops?? Or what if we turn it off completely? What if we gave them extra copies?!” For example, many cats have extra toes because of a mutation in a gene called sonic hedgehog, which plays a role in limb patterning (like how your fingers and toes are organized). When the gene is expressed when it’s not supposed to be, this signal tells the cells to create an entirely new toe, so then your cat ends up with more toes.
While having an extra toe is mostly harmless, but things can go totally, horrifically wrong depending on what signals get released when they shouldn’t have been (or conversely, when there should’ve been a signal but it wasn’t there). Cyclopia is a birth defect where the fetus most notably has 1 eye. The same gene we just talked about (sonic hedgehog) is also responsible for this. If not expressed properly, the eye doesn’t get the signals required up divide into two, so you just get this mega eye in the middle.
TL;DR: cells talk to each other. Usually works out, sometimes miscommunication happens.
To over simplify it; the features are not fully contained in DNA.
Again over simplified but DNA synthesizes proteins and amino acids etc, those in turn influence, along with other factors, what set of proteins etc are built next, which influences what happens next. There are a lot of feedback loops and external checks. Some features like bone length can be a simple “continue until you are told to stop,” your DNA has a default stop point if no external forces and early or late termination then you get whatever you inherited.
You could think of it like DNA being the blueprints and building blocks for every human, complete with a whole ton of custom options (wether they are used or not). A lot of inherited traits like face size and shape are portions of DNA directly and indirectly what other portions of the DNA will be used as a kind of “instruction set”
Even then the DNA isn’t always going to match up with what the end result is. If your sex chromosome is XY, you have something like 99.93% of being born with a male anatomy… But not always
TLDR; it’s a labyrinth of cause and effect and it’s not limited to just the DNA itself.
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