About Spencer

Selfie at Great Wall

About me- Spencer A. Shorkey

I am a synthetic biologist interested in fundamental studies of molecular machines, namely protein-ligand or enzyme-substrate interactions, and developing nano-biotechnology techniques to study them. Molecular machines are really interesting, and our understanding of the wiggling and jiggling of these machines is relatively limited, compared to our understanding of machines closer to our own size. To give an idea of the relative scale of molecular machines, compare a single human of ~70 kilogram mass and ~1 meter dimension to an average molecular machine (a string of ~10,000 atoms), which would be ~1 x 10-22 kilogram (0.1 zeptogram) mass and ~3 x 10-9 meter (3 nanometer) dimension. The difference between our scale and these nanometer-scale objects is enormous, about the same as the size difference between the Earth and a single human, as illustrated below. We humans are largely composed of various types of molecular structures and machines (~20,000 possible blueprints exist in our DNA), and the materials they manufacture. In interrogating our own composition, we find that a single human is composed of ~1 x 1013 (10 trillion) cells, with each cell containing ~1 x 109 (1 billion) molecular structures and machines. The point is, as humans, we are an agglomeration of these molecular machines, and it is thus really interesting and important to understand them as well as possible!

Nanopore Scale

These molecular machines are too small to see by human eye, though some specialized fluorescence techniques and magnetic-field manipulations have worked out and the wiggles and jiggles of their atoms (which scientists as conformation dynamics) can occur from 1 second to less than 1 microsecond (1 millionth of a second). This is where my research studies come into play; I am working on using nanopores to take measurements of molecules and molecular machines in order to precisely analyze the timescales of their wiggles and jiggles in relationship with their binding and chemical reactions. I am using electrophysiology, a technique with very high temporal precision (down to 10 microseconds), with extremely small nanopore-tweezers, together enabling controllable capture and measurement of individual molecular machines.

Nanopore Analysis

Being able to control and observe molecules over twenty orders of magnitude smaller than myself, even observing atomic-scale interactions and reactivities in real-time, is something that has never gotten old (and I suspect never will). I hope I have convinced you that it is as awesome as I think it is, if so feel free to click the image above or here to learn more about what I do!

Outside of academia, I have a large focus in sustainability. In 2018, myself and another PhD student put our grad stipends together and were able to get a loan on a house. We rented some of the rooms to generate cash flow, and in 2019 we were able to install rooftop solar panels with the help of a MassCEC grant. In 2020, we made an even bigger big leap in retrofitting our oil-burning heating system with a geothermal heating and cooling system, again with the help of another MassCEC grant and MassSave loan. I love all that Massachusetts has done with clean-energy initiatives, and I will be discussing the important steps and economic considerations involved in making these clean energy retrofits happen in an upcoming workshop titled Achieving Affordability with Clean Energy on May 19th 2021. I have also owned 2 EVs (Chevy Volt and Bolt), built a couple of off-grid and portable power systems, and I have a decent gardening operation including chickens.

Solar panel array Geothermal Heating System

Left- Solar array, grid connected. Right- Geothermal for home heating. More info here.

Wealth inequality is also really important to me, although it could be reframed as a sort of sustainability concern of the societal scale. I have been seeing charts like this since a young age, and lived to watch these problems keep getting worse. Growning up on a small family farm, I've witnessed to how some of the hardest working people in society have been crushed by the unfettered capitalism of our age. I hope to be an active and engaged citizen in promoting solutions to help the people suffering the most in society as a result of current economic trends. Though I have not begun any projects yet, one area where I believe I could make an impact is in promoting equity in clean energy adoption. I intend to work with volunteer organizations, such as Greening Greenfield, to encourage the adoption of economically beneficial clean-energy technologies in nearby low-income communities.

Fun facts:

-I am mildly addicted to Craigslist and eBay shopping

-I love a good sensor.

-I am probably way too deep into smart-home tech and automation.

-I have a lot of tools, let me know if you ever need to borrow something because I probably have it.

-My favorite blog is In the Pipeline by Derek Lowe. One awesome quote: We’re surrounded by moving, energy-shifting self-directed hunks of insanely complex nanotechnology, performing functions we don’t completely understand in ways we don’t completely understand. I’m talking about your cat, or your houseplant in the window. We ourselves are more of the same: a pile of ridiculously complicated interlocking systems that we absolutely don’t really understand

-I love to cook (never trust a chemist who can’t cook). Linked here are some of my recipes.

-My brother is in the army and my sister is studying art.

-I love reading

-I love protein structure so much that I took up 3D printing to more completely appreciate them.

-I like to write poetry. You might find them Easter-egged throughout my site.

-My favorite author is Isaac Asimov. My favorite book is The Dark Forest by Cixin Lui.

-Kae Tempest, Kid Cudi, and Linkin Park are probably my favorite musicians

-This is my favorite painting, Summer Prelude by Rhea Costello

-I have a do-it-yourself mentality, which has led to numerous successes (and failures).

-I have travelled to East Africa, China, France, and a few other places, though I have recently given up flying

-I designed and taught a course titled Molecular Metropolis: Imagine a Cell the Size of a Campus

-Ben Franklin is kind of like my ideal role model, in particularly I really enjoy his aphorisms

-I enjoy playing rugby, basketball, hiking, and finding new waterfalls.

-I hang all of my t-shirts, but my sock drawer is chaos.

-My chicken's names are Galleon, Tarkelton, Pharoh, Red, and (chicken)Nugget

-My garden currently consists of strawberries, blueberries, raspberries, spinach, carrots, snap-peas, and tomatoes. I’m planning on adding some herbs, grapes, and pear and/or apple trees in the future.