Month: May 2021

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.

Clothing started agriculture?

Archaeologists and other scientists are beginning to unravel the story of our most intimate technology: clothing. They’re learning when and why our ancestors first started to wear clothes, and how their adoption was crucial to the evolutionary success of our ancestors when they faced climate change on a massive scale during the Pleistocene ice ages. These investigations have revealed a new twist to the story, assigning a much more prominent role to clothing than previously imagined. After the last ice age, global warming prompted people in many areas to change their clothes, from animal hides to textiles. This change in clothing material, I suspect, could be what triggered one of the greatest changes in the life of humanity. Not food but clothing led to the agricultural revolution.

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

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.

Tron Night Vision

The previous generation of night vision featured a greenish glow, because the images were generated by electrons traveling through a green phosphors tube. The Army’s new tech uses a white phosphors tube. Coupled with whatever secretive image-enhancing technology they’re using, the contrast in the rotoscoping-reminiscent images is startlingly good, and the resolution has been improved as well.

Tiberius, Imperial Detective

This is, I believe, the only time in recorded Roman history that an emperor decided to investigate a murder by examining the scene of the crime. These things just didn’t happen in Rome because they didn’t have the same ideas about evidence and crimes that we have. Their murder trials didn’t involve people looking at daggers or gloves or other bits of physical evidence. They just involved people reciting really good speeches at each other, each using the same rhetorical strategies, mostly about the character of the defendant and/or victim and their general demeanor in life rather than the actual events of the case in question, until the jury or judge picked whichever person they liked best. Examining a crime scene wasn’t a particularly important part of that process. Tiberius going off to have a look at the window from which Apronia fell was therefore very surprising. So surprising, in fact, that Silvanus hadn’t even bothered trying to tidy up after the murder had been committed. The emperor was able to see immediately what Tacitus calls “traces of resistance offered and force employed.” Frustratingly, he does not elaborate on what these signs were. Maybe chairs had been flung across the room, or curtains had been torn down, or there was blood on the soft furnishings. This blows my mind a little bit. Silvanus was a rich man. He had a significant household of enslaved people. And yet he apparently didn’t even bother to ask them to tidy up a bit and make it look rather less like there’d been a fatal incident in the bedroom. No one took it upon themselves to have a wee whizz round with a mop while he was out with the emperor. Presumably, no one expected the august Tiberius to take time out of his busy day being in charge of all of Western Europe and North Africa to nip round for a look. No other emperor would have done this, even for their mum’s best friend’s grandson.

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.