Tag: images

Retron Library Recombineering

RLR generates up to millions of mutations simultaneously, and “barcodes” mutant cells so that the entire pool can be screened at once, enabling massive amounts of data to be easily generated and analyzed. “RLR enabled us to do something that’s impossible to do with CRISPR: we randomly chopped up a bacterial genome, turned those genetic fragments into single-stranded DNA in situ, and used them to screen millions of sequences simultaneously. RLR is a simpler, more flexible gene editing tool that can be used for highly multiplexed experiments, which eliminates the toxicity often observed with CRISPR and improves researchers’ ability to explore mutations at the genome level.”

K/T extinction event

66 ma ago, maybe on a Tuesday afternoon, life was the same as it had been the day before or 1 ka before or pretty much 1 ma before. Things were good for our feathered dinosaur buddies. Until a tiny, tiny detail in the sky changed.

2021-04-06: Chicxulub created rainforest

the dinosaur extinction was also a massive reset event for neotropical ecosystems, putting their evolution on an entirely new path leading directly to the extraordinary, diverse, spectacular and gravely threatened rainforests in the region today.

2022-10-05: The Chicxulub Impact Produced a Powerful Global Tsunami

The Chicxulub asteroid impact produced a global tsunami 30k times more energetic than any modern-day tsunami produced by earthquakes. Here we model the first 10 min of the event with a crater impact model, and the subsequent propagation throughout the world oceans using 2 different global tsunami models. The Chicxulub tsunami approached most coastlines of the North Atlantic and South Pacific with waves of 10m high and flow velocities of 1 m/s offshore. The tsunami was strong enough to scour the seafloor in these regions, thus removing the sedimentary records of conditions before and during this cataclysmic event in Earth history and leaving either a gap in these records or a jumble of highly disturbed older sediments.

The Circles of Friendship

The innermost layer of 1.5 is the most intimate; clearly that has to do with your romantic relationships. The next layer of 5 is your shoulders-to-cry-on friendships. They are the ones who will drop everything to support us when our world falls apart. The 15 layer includes the previous 5, and your core social partners. They are our main social companions, so they provide the context for having fun times. The next layer up, at 50, is your big-weekend-barbecue people. And the 150 layer is your weddings and funerals group who would come to your once-in-a-lifetime event. The layers come about primarily because the time we have for social interaction is not infinite. You have to decide how to invest that time, bearing in mind that the strength of relationships is directly correlated with how much time and effort we give them.

While I quibble with the names and sizes of these circles, it still seems directionally correct.

Game in a Font

World’s first video game in a font! You read that right! It’s a video game in a font! A font as in “Time New Roman”. The entire game is enclosed in fontemon.otf, no javascript, no html, all font. You can play it anywhere! Your word processor! Your image editor! Your code editor! Even works with syntax highlighting. All the places you should never play games, but now you can because no one will stop you!

How big of a game can you make in a font? Fontemon has

4696 individual frames
2782 frames in its longest path
131 branches from 43 distinct choices
314 sprites
1085 words of text
But, just how much content can you fit, if you push it to the limit?

Max: 2^16 frames (65536)
Max: Longest path ~3277 frames
Max: Branches are a bit more complicated.
Max: 2^16 (65536) sprites
Max: No specific limit on words, but other limits (frames, and sprites) apply
Of all of those, I really want to talk about #2 Max: Longest path ~3277 frames.
Every design decision I've made for this game:

How to draw the sprites
Which type of substitution to use (Ligature substitution)
How to handle branches (again, Ligature substitution)
was directly influenced by this limitation. In fact, of all of the limitations,
this is the rate-limiting step. Almost all optimizations I've done, have been to
push this number upwards.

Mapping Angkor

Most people don’t realize that Angkor Wat is just 1 of more than 1000 temples in the greater Angkor region. This settlement may have been home to 900k people at its height in the 13th century. Angkor was comparable to the 1m people who lived in ancient Rome at its height. Researchers were able to map 10Ks of archaeological features at Angkor. Because Angkorian people built their houses out of organic materials and on wooden posts, these structures are long gone and not visible on the landscape. But lidar revealed a complex urban landscape complete with city blocks consisting of the mounds where people built their houses and small ponds located next to them. This work has created one of the most comprehensive maps of a sprawling medieval city in the world, leading us to ask: How did the city develop over time, and how many people lived here?

Radiolyctic Life

Radioactive decay can sustain life deep below the surface. Radiation from unstable atoms in rocks can split water molecules into hydrogen and chemically reactive peroxides and radicals; some cells can use the hydrogen as fuel directly, while the remaining products turn minerals and other surrounding compounds into additional energy sources. Radiolysis is instrumental not just in the hydrogen and sulfur cycles on Earth, but in the cycle most closely associated with life: that of carbon. Analyses of water samples from the same Canadian mine showed very high concentrations of acetate and formate, organic compounds that can support bacterial life. Moreover, measurements of isotopic signatures indicated that the compounds were being generated abiotically. The researchers hypothesized that radiolytic products were reacting with dissolved carbonate minerals from the rock to produce the large quantities of carbon-based molecules they were observing.

Outdoor Dining arms race

What started as a haphazard collection of tables and chairs set up in blocked-off parking spaces has evolved into a seemingly non-negotiable extension of running a restaurant in NYC. There are local construction companies dedicated to building outdoor dining shelters. New restaurants are baking outdoor dining setups into their startup costs. For those who can afford it, the constant upgrading of outdoor dining — still only a temporary allowance in the city — hasn’t showed any signs of slowing down as indoor capacity restrictions have loosened. “It’s like the face of the restaurant now”

Transposons

Scientists have long known that transposons can fuse with established genes because they have seen the unique genetic signatures of transposons in a handful of them, but the precise mechanism behind these unlikely fusion events has largely been unknown. By analyzing genes with transposon signatures from nearly 600 tetrapods, the researchers found 106 distinct genes that may have fused with a transposon. The human genome carries 44 genes likely to have been born this way.

The structure of genes in eukaryotes is complicated, because their blueprints for making proteins are broken up by introns. These noncoding sequences are transcribed, but they get snipped out of the messenger RNA transcripts before translation into protein occurs. A transposon can occasionally hop into an intron and change what gets translated. In some of these cases, the protein made by the fusion gene is a mashup of the original product and the transposon’s splicing enzyme (transposase).

Once the fusion protein is created, “it has a ready-made set of potential binding sites scattered all over the genome”, because its transposase part is still drawn to transposons. The more potential binding sites for the fusion protein, the higher the likelihood that it changes gene expression in the cell, potentially giving rise to new functions. “These aren’t just new genes, but entire new architectures for proteins”.

2023-03-30: Introns might be parasitic

If introners find their way into hosts primarily through horizontal gene transfers in aquatic environments, that could explain the irregular patterns of big intron gains in eukaryotes. Terrestrial organisms aren’t likely to have the same bursts of introns, since horizontal transfer occurs far less often among them. The transferred introns could persist in genomes for many millions of years as permanent souvenirs from an ancestral life in the sea and a fateful brush with a deft genomic parasite.

Introners acting as foreign, invasive elements in genomes could also be the explanation for why they would insert introns so suddenly and explosively. Defense mechanisms that a genome might use to suppress its inherited burden of transposons might not work on an unfamiliar genetic element arriving by horizontal transfer.

Surprise Pasta

3D shapes can now be pre-printed onto flat sheets of uncooked pasta and only revealed during the boiling process. The 2D pasta morphs into 3D shapes when boiled because each piece is lined with tiny grooves, less than 1 mm wide, in particular patterns. The grooves increase the surface area of some parts of a piece of pasta. Areas with a higher surface area absorb water and swell faster

Basketball-sized Cells

Possibly the largest Eukaryote cells:

These single-celled organisms, called xenophyophores, can grow as large as basketballs. Xenophyophores growing on the sediment can resemble carnations, roses, or lattices, and like corals in shallow water, their bodies create a unique habitat in the deep sea. Though surveys are difficult to conduct at the depths where they live and much of the abyssal plains have not been explored, we do know that xenophyophore meadows may cover large areas and that they inhabit the Atlantic and Pacific oceans. Xenophyophores “represent a little known element of marine biodiversity”. They are also, she added, “very fragile—so vulnerable to human disturbance.

2022-02-24: And the largest Prokaryote:

Thiomargarita magnifica, a bacterium living in Caribbean mangroves is visible to the naked eye, growing up to 2 centimeters—as long as a peanut—and 5000x bigger than many other microbes. What’s more, this giant has a huge genome that’s not free floating inside the cell as in other bacteria, but is instead encased in a membrane, an innovation characteristic of much more complex cells, like those in the human body. It implies the 2 branches of life are not as different as previously thought. The genome was huge, with 11m bases harboring 11k genes. Typically, bacterial genomes average 4m bases and 4k genes. The genome was so big because there are 500k copies of the same stretches of DNA.