A Software Engineer's Guide to Biotech ================================ This is a list of resources that I've consumed in my journey from traditional software engineering to research engineering in biotech. This doesn't come anywhere close to a complete education, and doesn't include innumerable little resources/articles/blogposts/conversations that educated me, but should hopefully provide some useful starting points for your own exploration. ## "Pop" Biology These are general books that didn't get overly technical but described a general narrative that I found fairly interesting. - The Gene by Siddhartha Mukherjee - Entangled Life by Merlin Sheldrake - A Crack in Creation by Jennifer Doudna - The Billion-Dollar Molecule by Barry Werth ## Microbiology/Biochemistry These are resources to study biology at smaller scales: tiny organisms, macromolecules, and their interactions. Developing a more robust intuition here was one of the more challenging things for me - I found it very tempting to anthropomorphize biology: "How does a protein know where to bind to?", "How can a bacteria decide where to go?", "What does it mean for a protein to be a molecular machine?" Many of these resources helped me develop a better intuition for how biology could achieve effects that seemed "intelligent" to me, and how it was a consequence of more innocent mechanisms such as diffusion, gradients, and how my intuitions for things like the frequency of collisions between molecules were heavily biased due to the scale of the world we live in. - [smart-bio](https://smart-biology.com): I'm a huge fan of the animations here. I did not feel like I understood how a protein really worked until I worked through these (paid) resources. - The Machinery of Life by David Goodsell. This book is a classic for its illustrations, and rightfully so. - Cell Biology by the Numbers by Rob Phillips and Ron Milo. This book is dense with concrete numbers and data that do a lot to help inform your intuitions about what is actually happening in a cell. - [BioNumbers](https://bionumbers.hms.harvard.edu/search.aspx) - The Processes of Life by Lawrence Hunter - Biochemistry by Voet and Voet ## Bioinformatics - [Cal State Lecture Series](https://www.youtube.com/playlist?list=PL17NIL2mko8mOPN9W0e4LOjJ2Dkome7ZH) - [Protein Structure and Design Lecture Series](https://www.youtube.com/playlist?list=PLHn7WmALbthnAwbJ4mWw5gk8dgqsjRL87) ## Physiology These are resources about the human body and various subsystems within the body. I really like books that lie in the sweet spot between pop science and a textbook: I want it to be somewhat technical so that I feel like I actually learned something about the various mechanisms and pathways, but I don't want it to be a dry table of a list of chemical reactions. I'm actively on the lookout for more good books in that sweet spot about other physiological subsystems. - The Body: A Guide for Occupants by Bill Bryson - Vital Circuits: On Pumps, Pipes, and the Workings of Circulatory Systems by Steven Vogel - Immune: A Journey Into the Mysterious System That Keeps You Alive by Philipp Dettmer ## Lab Protocols There are a huge number of different protocols that exist in the lab, but these are a sampling that have pretty good online resources that you can peruse to get a better understanding of what kinds of work lab scientists might engage in. If you can find a community lab where you can do workshops or basic protocols, that is also probably a great opportunity to get a better feel for the hands-on work of Biology. - [Sequencing by Synthesis](https://www.youtube.com/watch?v=fCd6B5HRaZ8) by Illumina. - [Nanopore Sequencing](https://nanoporetech.com/how-it-works) by Oxford Nanopore - [DNA Synthesis Overview](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5204324/) - [DNA Plasmid Design](https://amymli0.medium.com/how-to-design-plasmids-from-scratch-4008a2c40df3) - Using [DNA Digestion](https://www.addgene.org/protocols/restriction-digest/) and [DNA Ligation](https://www.addgene.org/protocols/dna-ligation/) to cut and splice together DNA to make larger plasmids. - [PCR](https://www.genome.gov/genetics-glossary/Polymerase-Chain-Reaction) to amplify genomes.