Pipes and Moving Staircases

One of the challenges of embarking on a novel research project is trying to clarify what exactly I’m trying to accomplish as I delve into the details. I know the big picture: My goal is to understand how proto-metabolic systems self-assemble from chemical mixtures of simpler organic molecules. The approach I’m exploring is to first learn some new methodology, but not use it in the way it was originally developed. Instead, I plan to combine it in a novel way with familiar-to-me methodology, and hopefully (fingers crossed) come up with some models to test.

That’s still very broad. Too broad. My collaborator challenged me to try and articulate more clearly what I thought the model needed, how I planned to use it, and what I hoped it would be able to predict more concretely.

I’d been mulling it over for several days while haphazardly typing down seemingly random thoughts in the hope that some catalytic mechanism would crystallize into a model. Ha! That sounds like the actual problem I’m trying to solve chemically.

Then two images came to my mind.

The first was the word “PIPES”. In fact, I was picturing a scrawled piece of paper dug out from the hand of Hermione when she had been petrified in Harry Potter and the Chamber of Secrets. Not quite the image below, which I think is from the movie prop; I couldn’t find anything on the Internet that came close to matching the image in my mind.

That led me to envision a complex network of pipes with many intersections and meeting points, converging and diverging, going up and down, snaking left and right. A spigot began the flow of water at the input, and the water flowed into many streams – the flux of water molecules changing over time as the complex network was traversed. Some pipe locations eventually ran dry while other flows grew into larger torrents, even widening the pipes as molecules rushed by. At the crux of metabolism is the throughput of the molecules of life – flowing through chains and cycles of biochemical transformations.

But this picture was missing a crucial piece needed to allow such systems to evolve.

A day later I was catching up with friends and I was telling them how I got lost in a part of campus I was unfamiliar with. One of them remarked that she had also found it confusing and was ‘convinced’ that the staircases moved, a la Hogwarts. (We’d had a number of amusing Harry Potter related discussions in years past!)

One more day passed before it hit me that some of the pipes in my network should be allowed to move over time as the system evolves. Thus, the second image was ‘moving-staircase’ pipes. New connections made and old connections broken! As new molecules are made, some of which can catalyze prior chemical reactions, they can alter the flows by providing alternate pathways.

I now have a model in mind, though I need to flesh out more details. The model may prove less than ideal as I flesh things out – all models are wrong, some are useful – but it’s a good start. Who would have thought that pipes and moving staircases from the Harry Potter books would come in handy; you might say it was magical!