Month: July 2020

Car-free NYC

The huge subsidy of free parking in NYC needs to stop. article is nicely visual to make the point how the city could look like instead.

2021-11-12: Curbed as a very nice breakdown of various topics like garbage, delivery, safety etc.

we tried to imagine what a comprehensive transformation would produce on a generic Manhattan block, to the extent that one exists. We chose Third Avenue between East 33rd and 34th Streets because of its concentration of terriblenesses and virtues. It is congested, dense, torn up, noisy, and lively. Lined by towers and tenements, plied by trucks and fed by tunnels, it’s a short walk from offices, hospitals, and trains. Yet we also embraced its frenzy. Our goal was not to impose the serenity of a provincial Dutch city or to streamline the block into anodyne efficiency. New York without friction wouldn’t be New York.

Ghost Kitchens

how ghost kitchens might evolve

For restaurants that have already established themselves in the physical world, ghost kitchens can be a way to adapt to shifting trends. Frjtz, a San Francisco restaurant beloved for its Belgian-style fries, closed its brick-and-mortar location in the Mission in 2019, after 20 years in business, and now operates—delivery only—via CloudKitchens. Delivery-only kitchens can also work as a sort of triage effort for restaurants that are doing well. Recently, the owners of DOSA, a 15-year-old upscale Indian restaurant with locations in Oakland and San Francisco, told Eater they planned to move to a virtual model: a central commissary kitchen will supply food to a network of 20 delivery-only kitchens, where it can be reheated and delivered. In recent years, Souvla, a rabidly popular chain of fast-casual Greek restaurants in San Francisco, saw 30% of its business come from delivery. The restaurant group recently converted its commissary kitchen in SoMa into a “delivery-only restaurant,” intended to accommodate large orders and catering.

2022-04-30:

Consolidating kitchens has yet another side benefit: aside from increasing the sample size of restaurants and thus lowering the variance, it has higher employee utilization and less food waste. Food and labor costs are both 33% of restaurant operating costs, and the average profit margin from restaurants is 3-5%; a 3-point improvement in either food waste or labor waste adds 1 point of net margin, and getting both of those makes a restaurant 40% more profitable. Low-margin businesses are tough, but if there’s a way to improve them it creates a lot of operating leverage.

Prison TikTok

Behind bars, but still posting on TikTok

The reason that people find that so shocking but interesting to watch is because we have been sold this false bill of goods that the people behind bars are animals. This shows that they are somebody’s mother, somebody’s father, somebody’s kid. And they do in fact sometimes laugh, despite the brutality all around them.

Chirality

Cosmic rays may explain life’s bias for right-handed DNA

Ultimately, the fact that researchers struggle to find a theory that balances the rise of chirality against the destruction of biological materials suggests that our ancestors may have been lucky to find that fine line. There is something special about planets like the Earth that protect this kind of chemistry.

2021-08-02: More details on this astounding achievement. They were able to sequence a 1.5 kilobase chiral DNA plus the Pasteur encoding stunt.

The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day.

2022-10-28: The same group doing the next step, a chiral RNA polymerase. This one is about 10% larger than previous work on the DNA polymerase as measured in kDA.

Zhu chemically synthesized a 100-kDA mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of high-quality l-RNAs as long as 2.9 kilobases. A massive, 883 amino acid protein, it lay well beyond the limits of traditional chemical synthesis. But an analysis of T7s x-ray crystal structure showed the enzyme could likely be split into 3 sections, each stitched from short segments. In solution, the fragments naturally folded into their proper 3D shapes and assembled themselves into a working T7.

The mirror-image RNAs fashioned by the polymerase were far more stable than the normal versions produced by a regular T7, because they were untouched by the naturally occurring RNA chewing enzymes that almost unavoidably contaminate such experiments and quickly destroy normal RNAs.

Now, Zhu needs to make the remaining components of a mirror-image ribosome. The 3 RNA fragments they synthesized make up 66% of the total mass of a ribosome. What remains are the 54 ribosomal proteins and several proteins that work in concert with the ribosome, all of which are smaller and thus likely easier to synthesize. Then the question is whether the full parts kit will assemble into a ribosome.

Even if they do, the resulting molecular machines might still not be functional. In order to churn out proteins, ribosomes must work in conjunction with a suite of additional helper proteins. To make this work inside a living cell, Church thinks it will be necessary to rewrite an organism’s genetic code so the engineered ribosome can recognize all those proteins, particularly the 20 that ferry amino acids for building new proteins.


2023-08-28: nonlinear optics to detect chirality

They have realized a technique that can completely distinguish enantiomers in solution in an all-optical manner: no chemical tags, no particular UV/VIS absorbance needed from the compound structures, etc. And it is extremely fast and extremely sensitive, as opposed to traditional methods like optical rotation, circular dichroism, etc.

2023-09-08: What about magnetism?

Magnetic surfaces on minerals in bodies of water on the primordial Earth, charged by the planet’s magnetic field, could have served as “chiral agents” that attracted some forms of molecules more than others, kicking off a process that amplified the chirality of biological molecules, from RNA precursors all the way to proteins and beyond. Their proposed mechanism would explain how a bias in the makeup of certain molecules could have cascaded outward to create a vast network of chiral chemistry supporting life.

It’s not the only plausible hypothesis, but “it’s one of the coolest because it ties geophysics to geochemistry, to prebiotic chemistry, and ultimately to biochemistry”

COVID-19 & Architecture

The pedestrian streets were overdue, a counter to the dominance of cars. “It’s a ridiculous situation that so much of urban space is given up to the stupid boxes standing around most of the time.” The upheaval makes it easier to imagine dramatic changes. “When you have a momentary lapsing of the status quo, it allows everyone to see that something’s possible.”

Primordial Magnetism

One possibility is that cosmic magnetism is primordial, tracing all the way back to the birth of the universe. In that case, weak magnetism should exist everywhere, even in the “voids” of the cosmic web — the very darkest, emptiest regions of the universe. The omnipresent magnetism would have seeded the stronger fields that blossomed in galaxies and clusters.