Shapes

Photo Credit: MagicPattern

The basic building blocks of life, the biochemistry that gives rise to cells, to tissues, to organs, to organisms, are shapes and charges. The first portion of this, shapes, are intuitive as modern life is dependent on tangible interactions with geometry on a daily basis. Whether it is arranging shelves in the refrigerator, finding clothes that fit, using a lock and key, parking in a parking lot, or loading a car, there is an intuitive sense regarding the geometry of objects and how things may or may not fit together. This three-dimensional spatial reasoning may come more naturally for some than others, however, it is also rapidly learned. 

The most rudimentary iteration of the geometry exercise is the childhood game wherein wood or plastic shapes such as a star, circle, square, or triangle, must be fitted through their correspondingly shaped holes. The initial efforts at this exercise are simple trial and error, attempting to push each shape one by one through each hole and seeing which fits. Subsequently, a thought process develops, the visual identification of a shape and then the attempt to match that shape with the corresponding hole prior to the attempt to push the shape through. Once mastery of the visual identification of shapes and holes is accomplished there is yet another aspect to the game which must be mastered, that of orientation. With the exception of the circle, every shape can only be placed through the hole in a particular configuration. On an unrelated note, the interview question of the rationale behind why manhole covers round utilizes a similar logic. A round manhole cover does not need to be oriented to a particular configuration to fit in the hole, a round manhole cover cannot fall through the hole no matter what configuration in which it is placed, and the manhole cover can be rolled on its side such that a single person does not have to lift the weight of the manhole cover to maneuver it. Returning to the shape game, all other shapes must be placed in very specific configurations in order to pass through. 

Yet in playing this game, one realizes that there is a linked proximity and probability problem. That is that if the shape is brought in close proximity to the hole and multiple attempts slightly differing from one another are utilized to attempt to pass the shape through, the odds of the shape finding the correct configuration go significantly up. Likewise, decrease or remove either the proximity and probability and any likelihood of success disappears. If the shape is separated from the hole by distance there is no possibility of passing. Likewise if only a single configuration is utilized, there is an extremely low likelihood of the shape passing through the corresponding hole. Both proximity and probability must be present for success. 

Yet the idea of shapes as the building blocks of life becomes even more complicated as neither the shapes nor the holes are static, both are changing in small and large ways many times every second. This adds on the third aspect- both sides must be in an acceptable conformation for the interaction to occur. Imagine a key and a lock. Instead of requiring simply that the correct key be inserted into the correct lock, imagine that both the lock and the key were changing conformations continuously. One would immediately be reduced to the first step of the children’s games with rudimentary shapes as they were forced to resort to trial and error, pushing the key into the lock many times hoping that at one point the conformations were correct. In such a way interactions of shapes are one of the fundamental building blocks of biology and thus life. These random interactions of shapes occur millions of times every second in every cell of the human body. The way in which shapes interact affects subsequent interactions changing the conformation of both shape and hole such that the passage of additional shapes through their corresponding holes may become more likely to the point where a subsequent binding event is a near certainty, or less likely, such that the possibility of a subsequent binding event is vanishingly small. The sum of these interactions between shapes at the molecular level defines biological reactions which determines the phenotypes of organs and organisms. 

This butterfly effect, as shapes interact and change one another, defines biology and is also the building block for how nearly every medication works from small molecule inhibitors which activate or inactivate specific enzymes or receptors, to targeted monoclonal antibodies which bind and activate or inactivate specific signaling molecular or cellular targets, to chemotherapeutic agents which intercalate, or insert themselves between DNA strands, to change cellular biology. All rely upon cascade started by the interactions of the smallest of shapes.

Shapes define life. 

Published by JR Stanley

I am an MD, PhD student, training to be a physician scientist, with a deep interest in science, faith, and living life as an adventure. Join me as I entertain ideas from new findings in science, evolving interpretations of faith, and experience life one day and one adventure at a time.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: