Michael Clarke-Whittet

PhD student in quantum biology tackling molecular noise and quantum decoherence.
I like playing music, hiking, and the rule of three in lists.

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Teaching life science to quantum physicists

Recently I had a great but unusual opportunity: leading an introduction on life science (biology and biochemistry) to a group of people who were young scientists like myself, but happened to be quantum mechanics graduate students. In my previous blog I discussed what the potential benefits of this could be, and the conversations that have been generated have not disappointed. This is part of our ongoing quantum biology doctoral training venture.


Selling the science - life scientists know everything


The first thing I wanted to do with the introduction was implant the child-like wonder at the concept of life that I think every life scientist must have, to understand that at some point nature isn’t just particles and stars which are interesting in their own right. We needed to understand that life is a property of nature that requires this testing method we call evolution. While drawing out a taxonomic tree of life based around Carl Woese’s three-domain system that begins: Bacteria, Archaea and Eukarya, our conversation turned to what the point of these three domains are. Which, as a life scientist, I found intriguing. Why have these different flavours of cellular life?

So while sketching out generalised structures of prokaryotes and eukaryotes I encouraged my peers to think about the function of every structure. How does a cellular membrane give diffusive control? What are the benefits of having more than one membrane? What could life even look like without membranes? Why do prokaryotes tend to have much more protection from their environment than eukaryotes, what might this say about their evolutionary niche?


Life scientists don’t know everything (despite what they tell you)


I also introduced the challenges in life sciences and the type of language we use to discuss a world teeming with species that one-by-one defy generalisation. General questions were answered as I met the anxious eyes of my life scientist peers in the back of the room “… of course, there are exceptions to this.” Of course plants also have cell walls even though they are eukaryotes, of course prokaryotes can and often do thrive by working together, of course, of course.

Another common response to questions about unusual cellar interactions that, which aren’t commonly in the forefront of scientists minds: ‘If mitochondria are thought to originally be invasive prokaryotes that became mutualists, and invasive prokaryotes can integrate their own genes into the host genome, did mitochondria exchange DNA with eukaryotes?’

I don’t know the answer to that, but the speed at which my physicist colleagues started to formulate interesting and relevant hypotheses gave me confidence in the value of our co-operation. My typical answer for something that seems technically possible but unlikely is 'it might have happened once'.


Life scientists know a bit about biopolymers


I then took us in the direction of polymers and their relevance to life: lipids, proteins, nucleic acids in particular. Having explained the concept of a polymer in general (which did not take long), I proceeded to show the ribozyme-free reaction between two generalised amino acids. While working through the reaction we discussed how a protein is a polymer that has a sequence and, unlike sequences of letters or numbers that informaticians are familiar with, the sequence defines its chemical properties and shape.

A colleague asked ‘How do all of these proteins exist in the cell? What do they float in, how do they move?’ The understanding that proteins were not like fish swimming in a sea that can easily miss one another but are more like a barrel completely full of fish with some water in between them caused an upset in the same theme as before: the task of understanding life is so much more complicated than expected. Physicists like to deconstruct a system by simplifying it, supposing the existence of free particles in the absence of any forces and formulating neat models of motion but this approach is irrelevant in life; interactions are so convoluted and dependent that empiricism has proven necessary. A recent estimate of protein content in yeast put the average at 42 million molecules per cell*.

I sketched out the DNA-polymerase catalysed synthesis of ds-DNA without even making the structure of the polymerase explicit, instead just leaving it as a big lump that interacts with the nucleotide domain and the magnesium ions that stabilise the second and third phosphate to allow reaction between the 3’ hydroxyl group and the 5’ phosphoester of the incoming nucleotide. This made some heads spin, the sheer scale and diversity of matter and reactions inside something as tiny as a single cell is a tough concept especially for a reductionist approach. Somehow, life exists as a result of this structured anarchy that needs no invisible hand to move it or no requirement to be set in motion. As Iain Johnstone’s fascinating writing on The Noise Within [cells] puts it: Cellular biology is “a brewery in a bouncy castle**.

Teaching some fundamentals of evolutionary and cellular taxonomy. What have I left out in the left hand diagram?

* Ho B, Baryshnikova A, Brown GW. Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. Cell Syst. 2018;6(2):192–205.e3.

** Johnston I. The chaos within. Significance. 2012;8(2010):17–21.

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©2019 by Michael Clarke-Whittet, all views expressed here are my own.