jfarlow

7 ms·

1.
by jfarlow 4mo ago
Network effects + energetic fficiencies. On an energy landscape that includes integration over very short and very long lifetimes, the thalweg of utility/energy rests right about where the current codon optimizations are. And any sch
2.
by jfarlow 9mo ago
This is a challenge, even for someone who has professionally used the breadth of proteins. I really like the test. I'm actually kind of surprised at my own pulling on knowledge to make a guess - it's an orthogonal way to think a
3.
by jfarlow 9mo ago
And the atoms in the proteins and DNA that are exactly replicated to the atom each have a feature sizes resolved at fractions of a nanometer in 3 dimensions (and likely in time/dynamics too).
4.
by jfarlow 1y ago
Here's the full sequence of the protein, found in the supplement [1] KSSEPASVSAAERRAETEQHKLEQENPGIVWLDQHGRVTAENDVALQILGPAGEQSLGVAQDSLEGIDVVQLHPEKSRDKLRFLLQSKDVGGSPVKSPPPVAMMINIPDRILMIKVSSMIAAGGASGTSMIFYDVTDLTTEPSGLPAGGSAPSHHHHHH It is
5.
by jfarlow 1y ago
This is an AI-generated response, and is inaccurate. That was one of the first cases of _germline_ gene editing using CRISPR - NOT "the first instance of gene editing." There have been quite a few other genetic editing tools that
6.
by jfarlow 1y ago
"Custom" in that this therapy was designed AFTER a specific patient showed a need, and then given to _that_ patient. In most every other context a particular class of disease is known, a drug designed, and then patients sought th
7.
by jfarlow 1y ago
It also can actually allow you to identify positions within the image at a greater resolution than the pixels, or even light itself, would otherwise allow. In microscopy, this is called 'super-resolution'. You can take many image
8.
by jfarlow 1y ago
Serotiny: https://en.wikipedia.org/wiki/Serotiny
9.
by jfarlow 1y ago
>to build something but to not know how it actually works and yet it works. Welcome to Biology!
10.
by jfarlow 2y ago
Clearly RAM-stingy Apple has found a use for RAM - almost certainly in loading local LLMs. Llama 8G loads and runs pretty well on the new M-series Macs with a reasonable amount of RAM.
11.
by jfarlow 3y ago
There are a number of companies working on 'in vivo' deliveries for CARs. Oftentimes using the same tools as proven out by the Moderna vaccine.
12.
by jfarlow 3y ago
There are two kinds of personalization in a [CAR] [T] therapy: 1) using the patient's own cells [personalization of T Cells] 2) customized therapeutic genetic payload, per patient [personalization of the CAR] There are current competin
13.
by jfarlow 3y ago
I've designed a device that utilizes mechanical force to transmit information that was around 5nm in diameter. It was based on the human Notch receptor. It's a few hundred amino acids in length, folded to produce a protein that
14.
by jfarlow 4y ago
Using the above chemistry, you can attach DNA oligos to lipids, DNA oligos to proteins, fluorophores to DNA, fluorophores to proteins at particular locations or other complex drugs to DNA, protein or lipids. Once you get DNA oligos in there
15.
by jfarlow 4y ago
Serotiny | Remote (US), Bay Area, CA | Full-Time | https://serotiny.com Serotiny invents synthetic proteins to treat cancer and genetic diseases. We have a novel approach to designing proteins that couples synthetic biology, hig
16.
by jfarlow 4y ago
Serotiny | Bioinformatics Scientist - Next Generation Sequencing + Protein Design | Remote (US), Bay Area, CA | https://serotiny.com/ Serotiny invents synthetic proteins to treat cancer and genetic diseases. We have a novel
17.
by jfarlow 4y ago
Serotiny | Bioinformatics Scientist - Next Generation Sequencing + Protein Design | Remote (US), Bay Area, CA | https://serotiny.com/ Serotiny invents synthetic proteins to treat cancer and genetic diseases. We have a novel
18.
by jfarlow 4y ago
Serotiny | Bioinformatics Scientist - Next Generation Sequencing + Protein Design | Remote (US), Bay Area, CA | https://serotiny.com/ Serotiny invents synthetic proteins to treat cancer and genetic diseases. We have a novel
19.
by jfarlow 5y ago
The Base Editor (and Prime Editor, etc.) _is_ CRISPR (Cas9) but with additional components fused to it that provide it additional features allowing it to edit in a more elegant way over the naked Cas9. https://serotiny.bio/n
20.
by jfarlow 6y ago
The number of [nucleic-acid-delivered] gene therapies in Phase II & Phase III trials right now is huge - because of this progress in delivery [of nucleic acids]. Gene therapies for the eye, for hemophilia, for sickle cell, many many ca
21.
by jfarlow 6y ago
Delivery of the RNA is hard. To the right cell type, not immediately degraded, not accidentally integrated into a critical part of the genome, with a payload that is actually effective, etc. The original gene therapies (early 2000s) were e
22.
by jfarlow 6y ago
>Even the cells infected with the mRNA will need to be removed by the immune system using cytotoxic T-cells I don't think that this is accurate.
23.
by jfarlow 6y ago
In short - certain ones, yes. This should be one step (that was a bottleneck) in helping a company with a fixed budget do an order or magnitude more 'experiments' with the same amount of resources. Lab resources are expensive an
24.
by jfarlow 6y ago
Very cool! I've actually built similar models for myself to build that intuition. They're so helpful and generally hard to find. I agree that scale is generally poorly taught. I personally think having even a modest intuition fo
25.
by jfarlow 6y ago
Goodsell's book, "Machinery of Life" is fantastic at giving a first-pass representation of the basic interactions in a cell that are otherwise invisible. https://ccsb.scripps.edu/goodsell/machinery-of-lif
26.
by jfarlow 6y ago
Search space for the first billion or so years was likely around atoms/chemistry. Search space for the next billion or so years was likely around mutations in well-defined genetic space (4 nucleic acids as building blocks, 20 amino ac
27.
by jfarlow 6y ago
Brownian motion dominates at the scale of a protein. In other words, the energy imparted by the ambient temperature is orders of magnitude greater than that that could be established through momentum of objects with that little mass. So e
28.
by jfarlow 6y ago
One issue is that the scales don't well-match. And there are actually many time-scales beneath us, not just a few (and that biology/life is working at them all - including those on the order of millions of years. An event lik
29.
by jfarlow 6y ago
Most vaccines come with an 'adjuvant' [1] that activates the immune system in order to encourage the development of antibodies. Sometimes these are chunks of toxins that your body recognizes a toxic, but without the actual part of
30.
by jfarlow 6y ago
^ That is a _fantastic_ talk for someone who know's some physics get a quick grasp of the state of the field, the different approaches being taken from a set of first principles, and how to evaluate them.

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