jfarlow

16 ms·

91.
by jfarlow 8y ago
Those would be Kymographs: https://en.wikipedia.org/wiki/Kymograph https://www.google.com/search?q=fluorescence+Kymograph&tbm=i...
92.
by jfarlow 9y ago
(please help me where I'm wrong other scientists... But here's my basic knowledge.) Leather as you know it are combinations a few different (known) structural proteins secreted from mammals between skin cells, after the skin cells
93.
by jfarlow 9y ago
There is such a trope - I wouldn't call it accurate. We're learning a lot very fast. But DNA (like most biology) is multi-modal and has roles at many different scales - from the scale of milliseconds to cellular lifetimes, to or
94.
by jfarlow 9y ago
The fun part here is that, technically, once they get a 'good enough' product and workflow up and running, adding/changing/incorporating biological properties is (mostly) just a DNA-based bit-flip away. We at Serotiny ar
95.
by jfarlow 9y ago
Here's the sequence of the viral-like sequence they're calling Steamer : https://www.ncbi.nlm.nih.gov/nuccore/KF319019 We've got a bunch of similar viral-like DNA within our own genomes. And it appears
96.
by jfarlow 9y ago
Congratulations to both Ginkgo & Transcriptic! The newly-forming intimate relationship between bio and advanced digital and automation processes is very fun to watch.
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by jfarlow 9y ago
The EFF plays the role of simplifying, amplifying, codifying, and messaging to the rest of the country exactly what is 'obvious' to the (relatively small) tech community. They are exactly and precisely our spokes-people for what
98.
by jfarlow 9y ago
This is the end-goal. The delivery of synthetic genetic payloads in a live organism is still a bit tricky. Certain therapies do do this by injecting a synthetic 'virus' directly into your bloodstream. However, since it's so
99.
by jfarlow 9y ago
Cancer = you, but misregulated. Code for various tissues are turned on at 'incorrect' times, including code for profliferateNow(), ignoreAutoDestruct(), and can start running contradictory code like beNeuronLike() and beMuscleLik
100.
by jfarlow 9y ago
Looks like there's a known effect where quinine alters the binding capabilities of antibodies, giving the antibodies affinities to substrates that they would not otherwise bind to [1]. https://www.ncbi.nlm.nih.gov/core&
101.
by jfarlow 9y ago
It turns out that if you want to correct sickle cell disease, you (just) have to revert the single the bit of genetic instruction that permits hemoglobin proteins to atomically interlock like legos. The aggregation only occurs when the pro
102.
by jfarlow 9y ago
A bit of a late reply, sorry, but it's a great question. We found many design decisions we had to confront - more than we expected. The largest two include 1) the decision to use an amino acid sequence as ground truth (and not DNA),
103.
by jfarlow 9y ago
Pinecone is our public protein design software. Feel free to play around. Feedback is welcomed. We're trying to build an abstraction layer above DNA sequences so you can build genetic tools to fulfill particular capabilities without
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by jfarlow 9y ago
And electrons. Amplify an energy difference/transfer to a shift in protein conformation, to the cellular-scale presence/absence of noticable molecules, to actions of cells that are collectively organized to respond, to tissues, to
105.
by jfarlow 9y ago
Those are all run by great people and they do great work, pointed in particulary interesting and different directions.
106.
by jfarlow 9y ago
Companies using similar(-ish) technologies as applied to CRISPR directly: Synthego: https://tools.synthego.com/ Desktop Genetics: https://www.deskgen.com/landing/ Open Source Community using deep learn
107.
by jfarlow 9y ago
> How do you get information out of a living cell without destroying it? Using the existing systems of sensing/data-exfiltration already used by life. Fireflies produce light, jellyfish glow, plants curl up in darkness, fungi bud,
108.
by jfarlow 9y ago
What you're seeing here (and in other places), is us advancing to the tool-making stage of biological nanotechnologies. And this is one aspect of it. We've been gorging on grounded knowledge in the past 2 decades with the abilit
109.
by jfarlow 9y ago
We've collected a number of the various Cas variants into Pinecone if anyone wants to play around with the proteins [1]. In this article they speak of cheap detection, but in some sense those are the natural technological requirements
110.
by jfarlow 9y ago
There is room for multiple approaches - as biology itself proves. Asimov has a pretty interesting approach and a really good team. Tooling in the regulatory space of biology allows one to subtlety alter the mass transfer within existing net
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by jfarlow 9y ago
And there's still more! Live Webcam from Spaceman: https://www.youtube.com/watch?v=aBr2kKAHN6M
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by jfarlow 9y ago
I've not smiled so hard in quite a while :)
113.
by jfarlow 9y ago
Only in that RNA, as an intermediate between the relatively immutable DNA-based source code, and the running protein programs acts as a nice intermediate with which to compress, alter, and otherwise regulate how the code actually runs. RNA
114.
by jfarlow 9y ago
(Previous HN discussion here: https://news.ycombinator.com/item?id=16139798 ) So this 'Arc' protein has been in our genomes for quite some time. One of the two papers published simultaneously last month demonstra
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by jfarlow 9y ago
To be clear, I'm not the writer of the original post about DNA as code. I created Serotiny and our protien design software, and was providing my thoughts on the post given my background.
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by jfarlow 9y ago
> lacking the pressure that would lead to focused/cooperative effort and lots of resources pouring in Until literally a few months ago, hacking at the level of the protein abstraction was relegated to academics. Then Chimeric Antig
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by jfarlow 9y ago
It's what we do! https://serotiny.bio/notes/pinecone/ :: http://biologylabs.utah.edu/jorgensen/wayned/ape/ as C :: assembly We'd even hope it's a bit like 'basic
118.
by jfarlow 9y ago
Proteins are 1-dimensional chains of 'lego-like' molecules that fold into atomically-precise 3D tools. There are ~20 types of legos that have properties that differ along a number of axis like hydrophobicity, charge, reactivity, s
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by jfarlow 9y ago
We did, brother & I. We're trying to make useful the abstraction layer above DNA. We think there's much benefit to thinking and placing complexity at the protein level, and back-calculating the DNA, completely offloading the
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by jfarlow 9y ago
Adding to that conceptual challenge is separating in time the various components of the regulation and manipulation in the above analogies. Low-level programmers have an intuition of the 'time-cost' value of various hardware call

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