Many biologists will say that studying evolution and development is the key to understanding how phenotypes arise. I agree. Watching the development of an organism- say, a tardigrade egg that grows over a few days and then hatches- is remarkably edifying.

You can see individual cells growing and moving around and then look at another tardigrade egg and see exactly the same cells growing and moving around to the same exact places (this is a feature called eutely- they have a predetermined lineage of cells all arising in the same tree structure from the same original egg cell, which (in many tardigrade species) is in fact a clone of its mother (no fathers rrequired- known as parthenogenesis).

I think many people would see that, along wiht other observations, and easily come to the conclusion that specific behaviors were encoded for by individual genes, or that genes act like an architectural blueprint, exactly specifying either intermediate or final states.

Instead, in each of those cells is a blob of jelly filled with the genome, which is decorated with all sorts of proteins that are flying around, binding to vairous specific sites, activating and deactivating other sites, which then get turned into RNA and ultimately specific proteins. These proteins execute a plan encoded in the genome, but they do so probabilistically, with noise immunity, following physical behaviors that can be understood rationally (although in most cases, the number of actual variables is far too large to work with). And that encoding is extremely complex, more like a collection of weakly linked PDEs (a lot of weakly linked PDEs).

There is massive feedback, both positive and negative, that contributes to automatic regulation of components so that the plan proceeds normally. Many of these regulations lead to extremely non-linear, complex behaviors. Yet, for all this complexity, fairly straightforward actions that are similar to tardigrades happen in nearly all life. A sphere forms from an egg. The egg splits in two cells, then four, then many, retaining the spherical shape. At some point one of the split cells develops a polarity- one side grows more actively than the other. This leads to a body development plan (https://en.wikipedia.org/wiki/Blastulation) that self-generates with mostly local interactions (IE, there's no central controlling cell, it's more that the cells are just pushing against each other and the result is the right shape).

Understanding how genotypes lead to phenotypes has been a massive journey and I have had to unlearn much of what I was originally told, as new data has subsumed previous ones. That mendelian model of peas with discrete characteristics that segregate on different chromosomes is useful, and does show up in biology, but from what I can tell, it's just an easy, special case that we saw early, then geneticists overfit new data on that model.

When viewed through evolution as well as development- we start to see how complex phenotypes begin, then evolve to become far more complex. Early eyes and wings had utility, similar to modern eyes, but far less capable. Through mutation and selection, the organisms whose eyes worked slightly better were more likely to generate offspring that inherited those properties,leading to even more radiation (into many different types of organisms that all share similar eye properties).

I used to think that by this time in my career (I'm 51), we'd have been able to address a simple question I asked when I was 18: why is my nose this funny shape that doesn't look like other people's noses? What genes "encode" the "blueprint"? And to be honest, we're still really far from answering questions like that, but through a combination of data collection and machine learning, scientists actually are beginning to understand the complex process that leads to funny nose shapes.

For those who made it this far, here's your prize. A video of a tardigrade being born while its two younger siblings continue to prepare for life. https://www.youtube.com/watch?v=snUQTOCHito