Coming to a TechCrunch update near you!

Credit: BigStock Image via GeekWire

disclaimer: many of these have drawbacks, some glaringly obvious, but I hope these imagined futures spark your imagination and creativity

Pagerank for “Expert Opinion” — Brian Chesky said in this interview with Reid Hoffman, that the key to being an infinite learner is finding the source of truth on any question asap. Doing self-study of biology, I can attest that the importance of a focused question and finding the right source is extremely important.

Not only that, but with all the misinformation, feeds optimized for advertising and virality, and COVID breeding distrust of…


This is a first pass of my opinion on Synthetic Biology’s prospects based on my learning so far. At the end, I briefly mention some companies in the space I think are interesting as well. If you have a sec, I’d really appreciate any of your feedback here or in the comments (anything from points of disagreement to recommendations for further research are greatly appreciated).

Summary

Fossil fuels and mechanization gave every individual access to the work capacity equivalent of hundreds of people. With fossil fuels declining, the climate warming, and our population expanding, we will have to find ways to…


Loved this image from the Whole Cell Sim paper. Shows the simulation of DNA/RNA polymerase acting on a section of the genome through time.

This update covers Monday 05/31 and 06/01

My Notes

SynBioBeta Biobattery (made of DNA) story

Whole cell mycoplasma simulation paper

Protein Dreaming paper

ICLR Paper that examines how to interpret BERT attention when applied to DNA sequence modeling


This update covers about 5 of the last 7 days. I spent a bulk of my time looking at the timeline of the field’s development and what people’s hopes are for the future roadmap for biotechnology. I also spent a few days writing up some plans on how a company could be designed to do iPOP on a really large scale while staying open-source or at least transparent (more on this to come). …


My goal before the end of the quarter is to work on some mini-project where I can use some of my new knowledge. Given my cs/ai background, I through modeling biological systems would be a fun thing to work on. My laptop totally died though, so I am still figuring out how I can get some coding done, perhaps on my family’s decade-old iPad, or on my brother’s school-provided chromebook after school ends. I’m going to link the papers I’ve been spending the last couple days reading, as well as a drive link to a pdf of my notes going…


Sorry for the brief hiatus, I had a bunch for family stuff since Friday and was pretty busy yesterday (not much textbook progress). I did do some other interesting reading in the time I had though.

Chart displaying all the omic data from iPOP

First, I finally got to checking out the Synder lab! It was really interesting to learn about how they are instrumenting the human body through the iPOP project. The original 2012 paper is very interesting (all of these are linked on the iPOP page) and you can get a quick, 15-ish minute, overview by checking out the TED talks on the lab homepage.

For…


Intro to the Series

Hey all, in the spirit of working in public, I also wanted to share the directed research I’ve been doing with Prof. Jim Campbell, from Stanford’s history department. He famously teaches History of South Africa, which I took in the Winter, just before COVID hit the US. That class made me realize that history has a very interesting power to “denaturalize” things we take for granted.

A great example Prof. Campbell gave me of this power is the “Chicago house”. Most of us in America will recognize the standard construction of homes here, with 2-by-4s neatly spaced a few inches…


Artificial Chromosomes

Resources

Artificial Chromosomes: Ideal Vectors?

One of the referred papers, about mini chromosomes created by using telomeres to direct breakage of a Y chromosome

Another (MUCH MORE RECENT) article on Human Artificial Chromosomes (HAC)

wikipedia page for HAC

Vocab: selectable marker gene (like the one in the paper is for anti-biotic resistance), cis-/trans-acting, spheroplast transformation, alphoid DNA, transfection, cytogenic characterization, acrocentric DNA, episome, inverted meiosis, recombinase, heterochromatin, kinetochore, centromeric chromatin

Questions

Have we created artificial sites in DNA that make adding/turning off modules of our own genome easier to do?

Why does the circular DNA turn into a linear molecule…


These weeks, I finished parts 1 and 2 in Voet and Voet, the first three segments of the Khan Academy series, and the first 5 chapters in the Klein book. The OChem basics covered there are making sense to me now, but some of the details of isomerism and a lot of the details regarding functional groups in Voet and Voet I am struggling with.

As you can see I wasn’t great about note-taking on my laptop these first weeks, most of it is on print-outs and paper, which I don’t want to transcribe so I can push forward with…


I’m loving learning about enzymes, it’s really so much fun. Just having read the England article and some of those origins of life articles from week 1 is giving me so many ideas to play with. This is the first time biology has felt conceptually rich for me, like math or physics.

Please note that the italicized text are my own thoughts and speculation, the rest of the notes section has accepted facts from textbooks, credible sources, etc. The questions listed are also just questions and their implications should not be taken as any form of realized understanding.

Links

Mol. Bio…

Ishan Gaur

Science, Society, and Startups | Stanford ‘22

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