Cyanobacteria are now being used in China to shore up the verges of roads and railways in northern China as well as the margins of oases and farmland. A team plans to seed 133 square kilometer of desert over the next 5 years. The bacteria creates 0.5 to 1.0 centimeter thick biocrust over the desert which helps topsoil to reform and prevents top soil erosion. In its next step, China plans to have 200k square km of desertified land, or 50% of the country’s desert area that can be reversed, harnessed by 2020 and improve living standards for people living in the desert
Month: January 2014
Android / Windows
this is just spectacularly bad. par for the course for intel who really really suck at software: moblin, meego, tizen, smart tv, the list of stillborn projects out of intel is pretty long.
Intel plans a CES coup: Android and Windows in the same computer. Dual OS could dilute Windows dominance, if Microsoft doesn’t kill it first
Germany infrastructure decaying
it’s not just the us that has massive infrastructure problems, it’s everyone except perhaps the chinese, who have invested massively and have the benefit of learning from others by being last. the great rebuilding of the world’s infrastructure will be a major theme for the next 30 years, but will be underreported.
Source Code in TV
most shows use javascript, but the extra-dumb ones like csi use html.
In the TV series CSI:NY some simple HTML is shown

A resilient internet
as you’ll (incorrectly) recall, the internet was designed to survive nuclear attacks. i’m curious what could be done now, 30 years later, to build a truly distributed architecture? we’ve seen various approaches, usually met with LOL or derision (tor, etc), but what could you accomplish today with Mesh networking and a true end to end principle?
Bluetooth Man Google Glass Edition
can we take the glass we gave to that gross man in the shower, and hand it over to ed bassmaster? okthx.
Bacon Bowl
this looks amazing, even to this vegetarian.
Anteater New Year’s Resolutions
That’s right, you guessed it, I’m gonna eat a shit ton more ants. And the thing is, I love it! If you were put on Earth to eat ants, you would love it, too.
You’d look at a menu and be like, “This is all fine and good, but I don’t see any ants on here.” If you were playing chess, you’d be like, “This is all fine and good, but I don’t see any ants on this chessboard.” You’d be on the phone with your mom and you’d be like, “Yeah, yeah, yeah, sure, sure, sure, I’m fine. I’m fine. What about ants?”
CRISPR
CRISPR allows for much better genetic engineering than previous approaches and is a huge deal. It even works in human cells. Probably Nobel prize material.
2015-06-11: 1000x CRISPR
It is now possible to record a human genome (differences relative to a reference is only 2 megabytes. This is instead of 9 terabytes for a human genome with image data. CRISPR improvements are getting to 1 off target in 1 in 100 trillion (10^14) to 1 in 10 million trillion (10^19)
2015-11-11: CRISPR is the real deal
Editas plans to deliver the CRISPR technology as a gene therapy. The treatment will involve injecting into the retina a soup of viruses loaded with the DNA instructions needed to manufacture the components of CRISPR, including a protein that can cut a gene at a precise location. To treat LCA, the company intends to delete 1000 DNA letters from CEP290 in a patient’s photoreceptor cells.
2015-11-12: CRISPR Monsanto Problem
CRISPR is far too important to become entangled in the same web of confusion that has made G.M.O.s such a toxic issue. We ought to have learned something from those troubling and extended shouting matches; scientists, politicians, and everyone else needs to join in on this debate now. Society has no choice but to come to terms with both the potential benefits and the possible risks. That will require a big change: today, there isn’t even really a regulatory mechanism capable of governing products like CRISPR.
2016-03-09: Improvements to CRISPR subtypes like Cpf1 and now Cas9 are happening very quickly. This should reduce errors and increase the power of these gene editing technologies.
2016-10-14: CRISPR corrects sickle cells
Sickle cell disease is a genetic disorder caused by a mutation in one of the hemoglobin genes, which causes deformation of red blood cells and results in occlusion of blood vessels, severe pain crises, and progressive organ injury. To correct the mutation that causes this disease, DeWitt et al. modified hematopoietic stem cells from sickle cell disease patients using a CRISPR/Cas9 gene editing approach. The authors showed that the corrected cells successfully engrafted in a mouse model and produced enough normal hemoglobin to have a potential clinical benefit in the setting of sickle cell disease.
2018-04-26: Improving CRISPR accuracy 10000x
The use of bridged nucleic acids to guide Cas9 can improve its specificity by over 10000x in certain instances — a dramatic improvement.
2019-02-27: Doudna on CRISPR
Do you think that the medical applications of CRISPR in themselves can inform basic science?
For sure. CRISPR technology has been widely adopted by all kinds of scientists, including people like me. I was never doing anything with genome editing before CRISPR came along.
In my lab we’ve had a project over the last few years working on Huntington’s chorea, a degenerative neurological disease. The mutation that causes the disease is a single codon — 3 base pairs in the DNA — that gets repeated many times. If the codon gets repeated too many times, it leads to a defective protein that causes this disease. That’s been known for a long time, but the challenge was, how do you fix it?
We’ve been working on a way to deliver the CRISPR into mouse neuronal cells to make the necessary edits. But one of the curious things that’s come out of that line of work is that we found that only neuronal cells in the mouse brain were getting edited, not [the supportive glial] cells called astrocytes.
These cells are a lot smaller, so it could be that they don’t have enough surface area to take up the CRISPR protein efficiently. Or maybe they don’t respond to DNA cutting and editing in the same way as other cells.
2019-03-01: CRISPR error rates. Gene Editing Is Trickier Than Expected
how many errors are too many? Cells are prone to making their own mistakes—on the order of 1 every 1M-100M base pairs, with more for skin cells, and fewer for sperm and eggs. Does it matter if an overactive gene editor makes that number closer to 1 in 500K?
2019-05-07: CRISPR Inhibitor
The number of stories and journal articles about how CRISPR DNA-editing technology works, has worked, and is planned to work are beyond counting. How about an article about how to stop it in its tracks? That’s this one, just published in Cell from a multicenter team in Cambridge and New York. It describes a screening program for small-molecule inhibitors of S. pyogenes Cas9 (spCas9), because one would want some ways (not all of which currently exist) to turn its effects off in given places and at given times.
2019-10-04: CRISPR documentary
The teaser zooms in on the stomach-stabbing self-experimentations of biohackers like Josiah Zayner and Aaron Traywick. DIY Crispr is just one subplot in the larger narrative about what happens when nature can be minutely controlled, when humans might even preside over their own evolution. Their cameras also follow scientists like Jennifer Doudna and Kevin Esvelt and the first patients in an experimental gene therapy trial to treat hereditary blindness. “Our main hope is to create a discussion around these technologies. People might come away excited. Or they might be scared. But at least that means they’re talking and learning and understanding what’s coming.”
2019-12-18: CRISPR in Humans?
One of the most compelling arguments against CRISPR gene editing, namely the potential for misuse, can also be considered the most compelling argument for CRISPR gene editing. Banning progress on gene editing technology may create a black market, but the continuation of research on gene editing will allow the scientific community to control its use and ensure patient safety
2022-03-07: Another similar claim of a 4000x improvement. The new paper doesn’t mention BNANC, so who knows if these improvements stack. Probably not.
Researchers discovered how some of these errors can happen. Usually, the Cas9 protein is hunting for a specific sequence of 20 letters in the DNA code, but if it finds one where 18 out of 20 match its target, it might make its edit anyway. To find out why this occurs, the team used cryo-electron microscopy to observe what Cas9 is doing when it interacts with a mismatched sequence. To their surprise, they discovered a strange finger-like structure that had never been observed before. This finger reached out and stabilized the DNA sequence so the protein could still make its edit. Having uncovered this mechanism, the team tweaked this finger so that it no longer stabilized the DNA, instead pushing away from it. That prevents Cas9 from editing that sequence, making the tool 4000x less likely to produce off-target mutations. The team calls the new protein SuperFi-Cas9.

2023-01-19: CRISPR Cas12a2
“With this new system we’re seeing a structure and function unlike anything that’s been observed in CRISPR systems to date”.
While other CRISPR systems bind to their target sequence, make their cut, and then stop, when Cas12a2 binds to its target, it seems to “activate,” transforming in shape.
“It’s a change in structure that’s extraordinary to observe — a phenomenon that elicits audible gasps from fellow scientists”. Once activated, the protein can bind to any genetic material that comes near it, whether its single-stranded RNA, single-stranded DNA, or double-stranded DNA. Cas12a2 then starts shredding the material, making multiple cuts in indiscriminate locations.
Because the genetic material can belong to the bacteria itself, the result can be cellular death. CRISPR causes the infected cell to self-destruct — rather than let it become a virus factory.
2023-04-01: A much better drug delivery
Microbiologists were learning more about an unusual group of bacteria that use molecular spikes to pierce a hole in the membranes of host cells. The bacteria then transport proteins through the perforation and into the cell, exploiting the host’s physiology in their favor. Using the artificial-intelligence program AlphaFold, which predicts protein structures, the team designed ways to modify the tail fibre so that it would recognize mouse and human cells instead. They then loaded the syringes with various proteins, including Cas9 and toxins that could be used to kill cancer cells, and delivered them into human cells grown in the lab, and into the brains of mice. Similar to the early days of CRISPR–Cas9 research, the bacterial syringes are studied by only a handful of labs, and their roles in microbial ecology are only beginning to be understood.
2023-12-15: There are far better technologies like base and prime editing, than CRISPR.
That’s really what inspired us to develop base editing in 2016 and then prime editing in 2019. These are methods that allow you to change a DNA sequence of your choosing into a different sequence of your choosing, where you get to specify the sequence that comes out of the editing process. And that means you can, for the first time in a general way, programmable change a DNA sequence, a mutation that causes a genetic disease, for example, into a healthy sequence back into the normal, the so-called wild type sequence, for example. So base editors work by actually performing chemistry on an individual DNA base, rearranging the atoms of that base to become a different base.

The most boring calendar
Calendar of Welsh telephone boxes fails to sell a single copy
a true collectible, and will be worth a lot one day (kinda like the famous budweiser steins)