Month: January 2007

Horizontal gene transfer

A mechanism for evolution where big chunks of DNA migrate between different species via bacteria. This results in faster and more sudden evolutionary branching than what you get with the more familiar mechanisms of sexual selection or random single-point

a massive network of recent gene exchange connecting bacteria from around the world: 10K unique genes flowing via HGT among 2235 bacterial genomes.

2008-10-05: The transfer can lead to recursive genomes

Scientists have discovered a copy of the entire genome of a bacterial parasite residing inside the genome of its host species. Lateral gene transfer may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, with dramatic implications for evolution. This may allow species to acquire new genes and functions extremely quickly.

2013-11-12: The transfer can also be time-shifted

You can compare it to a bunch of bacteria which poke around a trash pile looking for fragments they can use. Occasionally they hit some ‘second-hand gold,’ which they can use right away. At other times they run the risk of cutting themselves up. There is potential risk when multi-resistant bacteria exchange small fragments of ‘dangerous’ DNA, e.g., at hospitals, in biological waste and in wastewater.

2021-06-09: It might even happen in animals, perhaps via sperm.

The barriers to horizontal transfer in eukaryotes looked insurmountable until the herring genome was published. The herring genome holds many copies of transposons, mobile chunks of DNA that can copy and paste themselves in a genome, but they are absent from other fish with 1 exception. 3 of them flank the rainbow smelt’s AFP gene, in the same order seen around the herring AFP gene. These sequences are “definitive proof” that a small chunk of a herring chromosome made its way into a smelt’s. 94% of the transfers involved ray-finned fishes; less than 3% involved birds or mammals. The explanation could hinge on herring’s famously exuberant spawning efforts. The vast majority of sperm fail to find eggs, degrade, and release their DNA. The DNA could stick to the gametes from other species spawning in the same area, and then get dragged into an egg cell during fertilization.


2021-10-21: It also happens in the human microbiome, which is less surprising since that’s just bacteria.

when humans started to colonize the island of japan 40 ka ago, they did not have the genes for digesting seaweed. Bacteria in the japanese gut borrowed the necessary genes from marine bacteria via horizontal gene transfer, and since the adaption proved evolutionarily beneficial, it was preserved. of course, anti-GMO nuts fear this horizontal gene transfer the most (if they are scientifically literate enough to understand the concept, and not just spout confused concepts like “natural” vs “artificial”). it should be quite obvious from this awesome example that mammals have had to cope with horizontal gene transfer throughout their history. GMO offers nothing new we haven’t encountered before.

2022-10-28: Transfer via viruses or parasites could explain how HGT happens between Eukaryotes.

The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

Is there something about the environment of Madagascar that makes it a hot spot for gene transfers? The abundance of parasites on the island might also be a contributing factor. Leeches may bring blood containing the snake’s jumping gene into the frogs, or perhaps the jumping gene is already in the leech’s own genome from previous contacts with snakes. Then maybe an unidentified virus does the rest.

2023-01-19: Tycheposons

The findings describe a new class of genetic agents involved in horizontal gene transfer, in which genetic information is passed directly between organisms — whether of the same or different species — through means other than lineal descent. The researchers have dubbed the agents that carry out this transfer “tycheposons,” which are sequences of DNA that can include several entire genes as well as surrounding sequences, and can spontaneously separate out from the surrounding DNA. Then, they can be transported to other organisms by one or another possible carrier system including tiny bubbles known as vesicles that cells can produce from their own membranes.

2023-08-04: Mavericks, or Polintons, are large DNA transposons that contain genes with homology to viral proteins. They are the largest and most complex DNA transposons known. Mavericks are one of the long-sought vectors of horizontal gene transfer. They are related to giant viruses and virophages.

Mavericks are an ancient and fragmented class of jumping genes prevalent in the genomes of protists, fungi and animals, including humans. These massive mobile elements were initially assumed to be inactive, mutated relics of obsolete genes. But later research revealed that Mavericks can be reactivated, and that they can mediate horizontal gene transfer between some species of protists. Complete, intact Mavericks had never been characterized in a multicellular organism.

Fugue

Man as robot

Joe Bieger wandered the city for nearly a month lost in a fugue state, a strange form of amnesia thought to be triggered by stress or other conflict. One morning, Joe stepped out of his house to walk his dogs and, within moments, had all his memories erased.

2016-11-21:Fugue memories are never recovered

It seems astonishing, at first glance, that a man can live 20 years of life without leaving a mark. And yet, in this regard, Powell was not unique at all. Many people are just as disconnected from the world as Benjaman Kyle. 1000s of people die alone and unidentified each year, and are buried in nameless graves. They represent the most isolated members of society: the elderly, the homeless, the undocumented immigrants far from home—people who have been pushed to society’s margins. Like Powell, they are found stripped—in Powell’s case, literally—of any link to their legal identity. It was only an apparent accident of his brain that caused him to lose his identity in life, not death. Had he died in front of the dumpster in Richmond Hill, his body would not have become an object of national fascination and intense speculation; it would have spent eternity interred in a potter’s field. Instead, he was reborn twice: first as Benjaman Kyle, and then, again, as William Powell.

Social Animal

Adam Brokken’s also working to make Social a fully-realized artificial intelligence, a creature that can better pass the Turing test. “I am also working on a method to have the bot remember conversations, adding more animations based on responses, etc. Whether he will ever live up to his last name, time will tell.” (That is to say, this.)

Adam recognizes the controversies that have swirled around reverse engineered avatars. “I know there has been much drama concerning ‘bots’ in Second Life, and they still do give some ill effects such as texture spamming. I myself have been hit a few times.

NPC are coming to SL. luis called my attention to this: basically eliza in a new package. based on AIML, pretty much the standard these days for AI chatterbots

Lithium scarcity

A world dependent on lithium for its vehicles could soon face even tighter resource constraints than we face today with oil. Lithium-rich South America would become the new Middle East. Concentration of supply would create new geopolitical tensions

2021-06-28: Lithium 3x cheaper

“Over an 18-month period, only 30% of the available lithium is captured because the lithium co-precipitates out of the brine with other salts. By using membranes, we can now control this mechanical separation process, avoid the co-precipitation that causes 60% of that loss, and achieve a 90% recovery rate”

Battery capacity has to scale at least 1000x in the next decade, and Lithium prices are one bottleneck.

2022-05-20: Demand is growing 2x faster than supply.

  • Demand for lithium from the EV industry is growing at 2x the rate of lithium production. As a result, lithium prices have skyrocketed over the past 6 months — 4x last year’s prices in tight markets. By 2025, the US could need up to 75k tonnes per year of lithium to supply new gigafactories.
  • The US currently produces only 1% of global lithium production — 1k tonnes of lithium content. This currently comes from a single brine operation: Albemarle’s Silver Peak site in Nevada.
  • The US theoretically has enough lithium in the ground to meet the growing demand. The USGS reported that the US has 750k tonnes of economically recoverable lithium in 2021. This estimate will continue to grow as new reserves are proven; as recently as 2018, the US had only 30k tonnes of established domestic reserves.
  • The Thacker Pass project in Nevada has received all required permits to begin construction and is the closest to bringing new US lithium production online (5k tonnes of lithium content in Phase 1). Because the lithium at Thacker Pass is found in clay rather than in a brine, it can be extracted quickly with relatively standard technology once facilities are constructed.
  • The heated brines pumped out of the ground for geothermal power in California’s Salton Sea region also contain significant amounts of lithium — 24k tonnes of lithium content passes through these plants a year by NREL’s estimate. Extracting this lithium is hard because of the wide range of other minerals present, combined with relatively low lithium concentrations and elevated temperatures. However, building out more geothermal capacity is an amazing BOGO opportunity: clean energy + lithium, and lots of it!
  • 3 challenges prevent the USA from achieving lithium independence. The first is the long development times needed to bring a new resource to production (4–10+ years). The second is the low average lithium concentration of US deposits, which make them more complicated and expensive to process than Chilean brines, for instance. The third is creating a streamlined (and appropriately staffed) permitting process that ensures that environmental impacts are kept to a minimum, while enabling a predictable outcome for responsible parties.

2023-09-13: The market solved it.

When I first read about the discovery of a vast new deposit of lithium in a volcanic crater along the Nevada-Oregon border, I can’t say that I was surprised. Not because I know anything about geology — but because, as an economist, I am a strong believer in the concept of elasticity of supply.
It’s worth dwelling on the significance of this find, which could help limit climate change and ease geopolitical tensions. The find, 20-40m tons, would be larger than the current largest, 21m tons beneath the salt flats of Bolivia. (The discovery awaits final confirmation, but at least 1 company says it expects to start mining this supply in 2026.) And lithium is of course a crucial ingredient in batteries for electric vehicles, demand for which is surging and which are an important part of any plan to fight climate change.

libsecondlife

This thread over at the libsecondlife forums describes a Second Life server built by a user, a single sim that can be accessed using the standard client software. As near as I can figure, the server was built by examining the client code (and/or reverse-engineering it) along with the information that is passed between client and server in order to get an idea of what the server code would need to look like. What’s more, an early version of the server code has already been made available as an open-source project.

a tiny tiny step towards a distributed metaverse