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Niko McCarty 🧫 Profile picture
@NikoMcCarty
Aug 7, 2023 • 12 tweets • 7 min read • Read on X
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🧬📚 10 Books to Learn Synthetic Biology

The field is so broad and moves so fast — DNA synthesis, gene circuits, protein design! — that it can be hard to know where to get started.

Here are the books that I recommend, in order. 🧵 twitter.com/i/web/status/1…
1. The Machinery of Life
By David Goodsell

To engineer biology, you first need to understand its basic contours: How DNA, RNA & proteins work together to coordinate the behaviors of a cell.

This book is a gentle, visual introduction.
amazon.com/Machinery-Life…
2. Cell Biology by the Numbers (free)
By Ron Milo & Rob Phillips.

A basic grasp of biophysics will help you build mental models to engineer cells. This book covers the basics: How big is a protein? How fast is transcription? How do cells power it all?

https://t.co/KaiJSFVXgBbook.bionumbers.org
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3. Molecular Biology of the Cell (you can read old versions online)
By Bruce Alberts et al.

This remains the standard molecular biology textbook. Pay special attention to Chapters 1-7. There is also some text that describes standard methods, like PCR.

https://t.co/ntteJWpnponcbi.nlm.nih.gov/books/NBK21054/
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4. Synthetic Biology - A Primer & BioBuilder
By several authors.

Two books that cover the basics of synthetic biology, from DNA engineering to simple gene circuits.



https://t.co/NedTZLkjDJ https://t.co/5tEh2EODhJamazon.com/Synthetic-Biol…
amazon.com/BioBuilder-Syn…

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5. Underground Garden Club (free)

Not a book, but a great resource for online lectures and in-person events (mostly at Genspace in New York City) to learn bioengineering.

One track is "Microbe-Brewery Crew," where you learn to make chemicals + food.

https://t.co/ZWD28In0clundergroundgarden.club
Image
6. CRISPRpedia (free)

CRISPR gene-editing is becoming an invaluable tool for synthetic biologists. It's used to delete, add, or modify DNA and RNA in living cells.

This free, online book from UC Berkeley covers the basics.

innovativegenomics.org/crisprpedia/
7. A Computer Scientist's Guide to Cell Biology (optional)

Software engineers often email me to ask how they can get started in synthetic biology. The switch is not gentle, but this book incorporates useful mental models to help you make the transition.

https://t.co/VAQNHXl6oIamazon.com/Computer-Scien…
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8. An Introduction to Systems Biology
By Uri Alon

An outstanding introduction to biological circuits, and how to build them, from one of the field's foremost practitioners.

Some of the math gets a bit intense, so you should learn some calculus first.

https://t.co/g04DaVEst6amazon.com/Introduction-S…
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9. Physical Biology of the Cell
By Rob Phillips

An incredibly deep dive into biophysics. Mastering this book will make you a more quantitative and thoughtful genetic designer.

Accompanying course:

https://t.co/39hzMAtagZrpgroup.caltech.edu/aph161/index.h…
amazon.com/Physical-Biolo…
10. Deep Learning
By Goodfellow, Bengio & Courville

Machine learning will play an increasingly important role in engineered biology. This free book teaches the basics.

Accompanying MIT course (with biology focus!):

https://t.co/XEzKQmsY4l https://t.co/I7HNrBOQeDmit6874.github.io
deeplearningbook.org
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Thanks for reading.

There is a need for deeper, more comprehensive books on synthetic biology. And I think we won't have to wait too long for that. 👀

Subscribe to my newsletter to learn more: readcodon.com

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More from @NikoMcCarty

Niko McCarty 🧫 Profile picture
Oct 30, 2024
Last Sunday, @AsimovPress published an article explaining why it's so hard to diagnose tuberculosis.

Here are 10 interesting things we learned about TB while editing it:

1. TB (not malaria) is the deadliest infectious disease. It kills >1.2M people each year. Image
2. At its "peak" in the 19th century, TB killed 1-in-4 people in Europe and America.

It killed Chopin, Thoreau, Kafka, and Eleanor Roosevelt. The disease was dubbed "the white plague," as it made victims pale.

(Edvard Munch painted his sister, who died of TB at the age of 15.) Image
3. TB was also, oddly, romanticized by poets at the time.

“How pale I look!” wrote the poet, Lord Byron. “I should like, I think, to die of consumption … because then the women would all say, ‘see that poor Byron — how interesting he looks in dying!’” Image
Read 11 tweets
Niko McCarty 🧫 Profile picture
Aug 6, 2024
This is an ongoing thread for my series, "30 Essays to Make You Love Biology." ❤️🧬

I'll pin it on my profile.
Day 1. "I should have loved biology," by James Somers.

Day 2. "Cells are very fast and crowded places" by
@kenshirriff

Read 14 tweets
Niko McCarty 🧫 Profile picture
Jun 27, 2024
There were an insane number of "big" biotechnology papers published this week.

The Bridge RNA gene-editing papers are important. But here are 7 more advances.

Many new CRISPR tools, epigenetic editing for prion disease, gene drives for plants & more...🧵
1. Bridge RNAs are a programmable DNA editing system that can insert, delete, and flip DNA sequences.

A compact, flexible genome engineering tool.

2. A tool called TATSI enables precise DNA insertion in plants.

It works by fusing transposase proteins with CRISPR nucleases to deliver custom DNA to specific sites in the genome. So far, it's been tested in Arabidopsis and soybean plants. https://www.nature.com/articles/s41586-024-07613-8
Read 10 tweets
Niko McCarty 🧫 Profile picture
Apr 16, 2024
My last tweet about China:

In Shanghai, I visited BluePHA, a synthetic biology startup that uses engineered microbes to manufacture biodegradable plastics.

They make ~5,000 metric tons/year, have products available on the market, and are scaling to 50,0000 tons/year. 🧵
Image
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BluePHA makes PHAs, a type of polyester made by many organisms in nature. The company can mold these PHAs into lots of different plastic products, such as cups (right) or spools of thread (left) to make bags and clothes.
Image
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Many plastics sold on the market are touted as "biodegradable," but aren't actually biodegradable.

PLAs, a common culprit, only break down at high temperatures. They will not disappear if placed in the soil in your backyard.

PHAs are fully biodegradable at normal temperatures.
Read 9 tweets
Niko McCarty 🧫 Profile picture
Feb 21, 2024
Cells are fast and crowded places. Numbers help us make sense of them.

Here are five of my favorite "bionumbers."

1. ATP synthase spins 134 times/second. That is much faster than the propeller on most piston airplanes, and about half the r.p.m. of a Boeing 737 jet engine.
2. An mRNA is (much) larger than the protein it codes for.

A single nucleotide of RNA is 3x heavier than an amino acid. Three nucleotides are required to encode each amino acid; not to mention the untranslated regions, polyA tail, and so on.

(Sources are in image descriptions.) https://book.bionumbers.org/which-is-bigger-mrna-or-the-protein-it-codes-for/
3. A cell is 70% water by mass.

Of the remaining 30%, proteins account for more than half (55%). DNA accounts for very little; about 3% of dry mass. https://book.bionumbers.org/what-is-the-macromolecular-composition-of-the-cell/
Read 6 tweets
Niko McCarty 🧫 Profile picture
Feb 14, 2024
Water accounts for about 70% of a cell's mass.

But, interestingly, there are many water-dwelling, photosynthetic microbes that express GAS VESICLES. These are protein compartments, filled with gas, that help the cells float up or down in water to capture sunlight.

A visual ode: https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.nih.gov%2Fnews-events%2Fnih-research-matters%2Fmonitoring-bacteria-body-ultrasound&psig=AOvVaw37EO_HukAMKXu8w3pLK7kd&ust=1707951858141000&source=images&cd=vfe&opi=89978449&ved=0CBUQjhxqFwoTCNj9h9C2qYQDFQAAAAAdAAAAABAF
Heinrich Klebahn, a German microbiologist, was first to discover gas vesicles amongst some cyanobacteria that he collected from a lake. Image
Gas vesicles come in many shapes and sizes.

Sometimes they are short, and other times they are long.

Gas vesicles are made from between 8-14 genes. These genes can be engineered to change the properties of gas vesicles. https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fnrmicro2834&psig=AOvVaw16G0OhDLUHDmCIsWzb7mmv&ust=1707951699024000&source=images&cd=vfe&opi=89978449&ved=0CBUQjhxqFwoTCIDblIS2qYQDFQAAAAAdAAAAABAJ
Read 6 tweets

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