I can tell you that the three dimensional visual imagery in the post to which Stephanie refers was a replacement for the actual visual imagery I had in mind when I wrote it. But I couldn't use that because ...
... because it was too narrowly defined, topically, focusing on protein function in the intracellular environment. But I can tell you how that image would look.
In the ultra tiny world of proteins, inside cells, there is little difference between form and function. Form is function. Its like putting a hammer and a pile of nails in your garage. If that was a cell and not a garage, the hammer would just hammer on the nails, and the nails would penetrate something, because they are shaped as hammers and nails and thus will act as hammers and nails.
If this is a little too Fantasia for you, don't worry, it is not the main point. The main point is that if you can visualize it, you can understand what it does (in the ultra tiny world of inside a cell). You might not know everything until you can also visualize the other molecules with which your molecule will interact, but ultimately, visualization is a large part of knowledge about the intercourse among biological molecules.
So, I imagine a tiny scientist. She is smaller than a chromatid. Small enough to get stuck in an ion pump. When she looks around inside a cell, she recognizes a lot of the shapes and her recognition of these shapes corresponds almost perfectly to her knowledge of what each shape is for. But there are also shapeless translucent nearly colorless forms that come and go in her field of vision. Some hover near the objects she recognizes, and she can barely perceive what part of such objects might look like, because she can imagine them fitting hand in glove with those parts she does understand.
Over time, she designs a series of experiments that cause the shapeless forms to be tested. If calcium flows past the sarcoplasmic reticulum, will the molecule she barely understands bind with another molecule? If she replaces a piece of one of the molecules she fully sees and understands with a device that lets her measure its movement, and causes some large scale activity in the cell, will that measuring device trace out the relationship between that part and one of the shapeless forms?
Have you ever tried to read the date on a really really old coin, like one that just came out of an archaeological site? You look at where the date should be, where a certain number should be, and you imagine it is a 1. And you realize it can't be a 1. So you imagine it to be a 2. Then a 3. And so on. Eventually, you come to a set of numbers that you can't really disprove, and you hand the coin to a colleague and say "What's the date on this thing" while you are thinking "1639" ... and if your colleague says ""1639, I think" then you can now see the date. Your mind allows your eyes to settle down with that idea.
In a similar way, the tiny scientist I imagine tries different ideas of what these other molecules are up to, what they do, how they are shaped, and how that shape interacts with other molecules, and how the molecule moves when it changes its energy state or is challenged with contact with water or calcium ions or something.
And over time, like the date on the coin, the shapeless colorless form becomes part of the known universe of this cell, recognizable by subset of experts starting with our tiny scientist. Eventually the molecule, characterized now more formerly, becomes known to those who read technical journals. By and by, if the molecule is part of a story with good pedagogical potential, a very cleanly full color three dimensional looking characterization of the molecule will make its way into the textbooks.
And if the molecule is amazing enough, it might even make the centerfold.
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