Last month the EU officially approved mealworms as safe for human consumption, sparking a bunch of articles on how bugs are the food of the future. In order to produce a kilogram of bug-based food, you need ~10k bugs. On the one hand, bugs probably don’t matter much morally. On the other hand, 10k is a lot. Do bugs have moral value? What about the other limit? Plausibly the most morally correct action, short of becoming vegetarian, would be to eat the largest animal there is. And according to the Talmud the righteous in Heaven dine on the flesh of Leviathan, which suffices to feed all of them forever. Hypothesis confirmed!
Tag: science
City Microbiomes
Researchers took 4700 samples from mass transit systems in 60 cities across the world, swabbing common touch points like turnstiles and railings in bustling subways and bus stations across the world. Using metagenomic sequencing, they created a global atlas of the urban microbial ecosystem, the first systematic catalog of its kind. The results suggest that no 2 cities are alike, with each major metropolis studied so far revealing a unique molecular echo of the microbial species that inhabit it, distinct from populations found in other urban environments.
2023-10-12: Dark matter
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 27k metagenomes and identify 1.17b protein sequences longer than 35 amino acids with no similarity to any sequences from reference genomes. Using massively parallel graph-based clustering, we group these proteins into 106k novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
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.
See also these Chernobyl fungi
a robot sent into the still-highly-radioactive Chernobyl reactor had returned with samples of black, melanin-rich fungi that were growing on the ruined reactor’s walls. “Just as the pigment chlorophyll converts sunlight into chemical energy that allows green plants to live and grow, our research suggests that melanin can use a different portion of the electromagnetic spectrum – ionizing radiation – to benefit the fungi containing it” Since ionizing radiation is prevalent in outer space, astronauts might be able to rely on fungi as an inexhaustible food source on long missions or for colonizing other planets
Parasitical Life Extension
Infected Temnothorax ants live at least 3x longer than their siblings, and perhaps in excess of 10 years, approaching that of ant queens, who can survive up to 20 years. When Foitzik cracks open infected Temnothorax colonies, the parasitized workers do little more than stare expectantly skyward. Down to the molecular level, the parasite is pulling the strings. She has split open Temnothorax abdomens and counted up to 70 tapeworms inside. From there, the worms can unleash a slurry of proteins and chemicals that futz with the ant’s core physiology, likely impacting their host’s hormones, immune system, and genes. What they achieve appears to be a rough pantomime of how ant queens attain their mind-boggling life span, a feat humans still don’t understand. The tapeworms’ grasp of ant aging is far more advanced than ours.
20 ka Civilization?
Recent digs in the forest steppes of Russia have found a large circular structure built over 25 ka ago, using material from up to 60 mammoths. The labor invested here is much less than needed for the construction of Göbekli Tepe and, as a result, isn’t in and of itself sufficient evidence of a complex society—but this is no temporary structure.
The old paradigm of agriculture and civilization beginning after the last ice age, and proceeding on a materially overdetermined set course of progress, seems to rest on increasingly shaky theoretical grounds. As a consequence, the hypotheses of what we expect to find and what kind of digs we want to fund have to be revised as well. Not just because our timelines of monumental architecture and complex society have been thrown into question by Göbekli Tepe, but because of evidence of early cultivation, such as small-scale farming 23 ka ago at the Ohalo II site near the Sea of Galilee. Over 10 ka prior to when we had first thought agriculture began, at least some of our ancient ancestors had gathered over 140 plant species in 1 place, evidently sowing and harvesting early edible cereals and using rudimentary tools to turn them into flour.
With both agriculture and monumental construction much older than what was thought before, we should likely rethink the origins of urban life as well. How old might settlements of 100s or 1000s of people be? How frequently did such civilizations arise, only to fall and be forgotten? I strongly suspect they might be 8 ka older than we believed previously. I’m happy to take a Long Bet with a qualified challenger skeptical of such a claim, that in 20 years, we will know of at least 1 such permanent settlement older than 20 ka. Perhaps such a bet can, in its small way, help stimulate some interest in hunting for such sites.
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.
Histones
Work on the structure and function of histones in ancient, simple cells has made the central importance of these proteins to gene regulation even clearer. Billions of years ago, archaea were already using histones, but with looser rules and much more variety. By curving the DNA around the nucleosome, the histones prevent it from clumping together and keep it functional. With more DNA, cells could wrap more nucleosomes and enable the histones to reduce more copper, which would support more mitochondrial activity. It wasn’t just that histones allowed for more DNA, but more DNA allowed for more histones.
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.
Human Glycome Project
The glycoletters in the data set could have formed nearly 1.2 trillion different glycowords. Yet, surprisingly, the researchers’ results indicated that only 19866 distinct glycowords were present across all the available sequences. The evidence suggested that all organisms follow very similar rules in assembling them and use essentially the same biomolecular language to define their structure.
Gregor J. Rothfuss 