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Exposition:

As a little kid, I always thought of DNA as being a description of how to build an organism. For example a human DNA would have "Add two legs and two arms", a dogs DNA would have something like "put a tail here". Now, at school, I have learned that DNA codes for proteins, for structural proteins, enzymes etc. But how does a growing fetus actually know where to put the different parts of the body?

Examples:

For example, why don't I have retinal cells growing on my feet? Why is my cerebral cortex not in my mouth? And where is the information stored that humans do not have tails, or that elephants have trunks?

Summary:

What determines where different cells should be located, and how is that information stored?

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  • $\begingroup$ I have edited your question to remove the anthropomorphic implications. Cells do not ‘know’ anything — they are not sentinent beings, and it encourages sloppy thinking to use this term, even in quotation marks. Otherwise, the scope of your question is huge — it is not my field but it would seem to cover the whole area of embryology and determination of cell fate, which is only partly understood. Perhaps someone else can point you to the chapter of a basic biology text where this is covered, but I doubt whether this question can be answered here. $\endgroup$ – David May 14 '18 at 12:40
  • $\begingroup$ Which organisms? There are several very different answer across life. nematodes and houseflies use very very different methods. For humans and houseflies you may want to look into hox genes or just embryology in general. $\endgroup$ – John May 15 '18 at 21:38
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Cool question. As the other answer mentions, the process is very complex, and we are still learning the relevant mechanisms in organisms other than the fruit fly. But it is considerably well described in the fruit fly which merits a brief summary.

Since a lot of asymmetric (A-P axis, for our purposes) development occurs pretty early in embryonic growth, whatever drives this pole-specific differentiation must act early. As it happens, it begins as early as maternal ovum (Bicoid mRNA). Using cellular machinery (microtubules, motor proteins), these are concentrated towards one end of the egg and subsequently of the early embryo. Once such an asymmetry in the concentration is achieved, further development genes can take advantage of this patterning by being influenced by downstream signalling. Hence there is a cascade of gene activation downstream, which involve Gap genes, Pair-rule genes and several homeotic genes (see Hox genes) which are also differentially expressed along the A-P axis. They directly control patterns of the organs formed from there. Using a gradient of these genes, further patterning of organs can be similarly achieved (the retina gene would be activated only at a concentration of these genes which is found only at the top and so on).

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Developmental biology is a huge field, and we are still learning a lot.

But a basic principle would be "The cells in the developing embryo develop differently depending on where they are".

We understand fairly well how fruit fly embryos figure out their head-to-tail axis; it starts with the fly ova having an asymmetrical distribution of maternal mRNAs

https://en.wikipedia.org/wiki/Drosophila_embryogenesis

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