Author: Gregor J. Rothfuss

Multi Density Water

Water, the most commonplace of liquids, is also the strangest. It has at least 66 properties that differ from most liquids – high surface tension, high heat capacity, high melting and boiling points and low compressibility. 1 school of thought is that water is not a complicated liquid but ‘2 simple liquids with a complicated relationship’. For some, this statement contradicts the basic principles of physical chemistry; for others it explains just why water behaves in such an anomalous way. Researchers have been searching for this putative liquid–liquid phase transition ever since, and evidence has slowly accumulated that it really exists. New experiments now supply what seems to be a direct observation of such a transformation between liquid states of different density – not in pure water but in solutions of the sugar trehalose. Understanding how such supercold solutions behave could have implications for biology and cryopreservation – where damage to biological tissues by ice crystals must be avoided – as well as for the water-rich states that might exist in the atmospheres of gas giants. Liquids are structurally disordered, so it’s not immediately obvious how they can support 2 distinct structures with different densities. But that does seem to be possible for liquids in which some degree of directional bonding, such as hydrogen bonds between adjacent water molecules, makes distinct local structures possible.

Vai Script

The Vai script of Liberia was created from scratch in about 1834 by 8 completely illiterate men who wrote in ink made from crushed berries. Because of its isolation, and the way it has continued to develop up until the present day, we thought it might tell us something important about how writing evolves over short spaces of time. The 8 Vai creators set out to design symbols for each of their language’s syllables, inspired by a dream. Their chosen symbols represented physical things like a pregnant woman, water, and bullets, as well as more abstract traditional emblems. Over the first 171 years of its history, the Vai script did become increasingly compressed. The simplification occurred over generations of users; symbols with the highest complexity were simplified the most. These changes are far from random. Languages pass a kind of natural selection process via memory and learning, where the hardest to recall features do not survive. As the letters became less complex, they also became more uniform. This is despite the language never having been adopted for mass production or for bureaucratic needs. These uses are what seemed to help standardize other languages – for example, Mesopotamia’s writing standardization coincided with the implementation of state-wide systems.

Competitive AI

OpenAI:

We built a neural theorem prover for Lean that learned to solve a variety of challenging high-school olympiad problems. These problems are not standard math exercises, they are used to let the best high-school students compete against each other. The prover uses a language model to find proofs of formal statements. Each time we find a new proof, we use it as new training data, which improves the neural network and enables it to iteratively find solutions to harder and harder statements. We achieved a new state-of-the-art (41.2%) on the miniF2F benchmark, a challenging collection of high-school olympiad problems.

DeepMind:

we created a system called AlphaCode that writes computer programs at a competitive level. AlphaCode achieved an estimated rank within the top 54% of participants in programming competitions by solving new problems that require a combination of critical thinking, logic, algorithms, coding, and natural language understanding.

Genome Tectonics

Researchers tracked changes in chromosomes that occurred as much as 800 ma BP. They identified 29 big blocks of genes that remained recognizable as they passed into 3 of the earliest subdivisions of multicellular animal life. Using those blocks as markers, the scientists deduced how the chromosomes fused and recombined as those early groups of animals became distinct. The researchers call this approach “genome tectonics.” Researchers can trace the evolution of entire chromosomes back to their origin. They can then use that information to make statistical predictions and rigorously test hypotheses about how groups of organisms are related. But what would cause blocks of genes to stay linked together? 1 explanation for this phenomenon, which is called synteny, relates to gene function. It may be more efficient for genes that work together to also be physically located together; that way, when a cell needs to transcribe genes, it doesn’t have to coordinate transcription from multiple locations on different chromosomes. Unless a chromosome rearrangement conveys a big functional advantage, it’s inherently hard for the rearrangement to spread. And rearrangements are typically not advantageous: During meiosis and the formation of gametes, all chromosomes need to pair up with a matching partner. Without a partner, an odd-sized chromosome won’t become part of a viable gamete, so it is unlikely to make it into the next generation. Small mutations that reshuffle the gene order within chromosomes can still occur.

PURLs

PURLs are only as good as the maintenance work that has gone into updating the underlying URLs when they inevitably change. And in the lucky cases where the underlying URL haven’t changed, all the work that has gone into managing the infrastructure behind that URL namespace in order for that URL to stay the same. how many of the PURLs still work? This is complex enough for an actual research project and not just a quick blog. Over in the notebook I started by sampling all the target URLs (N=405637 n=662). In the process I noticed that it was oversampling some domains quite a bit like my.yoolib.net. So I tried again, but instead of sampling all the URLs I sampled the PURL namespaces (N=21894, n=644) and picked a random URL from each PURL namespace. This seemed to work better but still seemed to oversample, with hostnames list http://www.olemiss.edu showing up quite a bit. It looks like they might create a new PURL namespace for every finding aid they put up.

Of course, testing whether a URL still works is surprisingly tricky business: the response could be 200 OK but say Not Found, or it could be a totally different page (content drift)

Birth certificates

75% of the births in the US in the late 19th and early 20th centuries went unregistered. Though the US pioneered the institutionalization of a decennial census, it lagged behind European countries in recording births, deaths, and marriages. Such records were not considered a federal matter, and the various states were all over the map with what they collected, if anything.

Progressive Era reformers got state and federal governments to adopt official records of birth during the first 40 years of the 20th century. These replaced affidavits, which were sworn and notarized statements by a child’s parent(s). Affidavits proved untrustworthy when it came to child labor laws: parents cheated, and notaries lied.

“The solution to the problem of enforcing child labor laws was, ironically, to shift the authority to authenticate a child’s birth away from the people who had actually witnessed it—parents. Professionally produced, birth certificates objectified a child’s age and identity, making a truth that existed apart from the personal relations that created the child.”

This was all part of the “bureaucratization, standardization, and quantification of information that accompanied modernization” and the birth of the “information state.” Documentary written evidence was privileged over the “oral and transient.”

1.5 ma Language?

Everett examines the culture of the first known human species, Homo erectus, focusing especially on their physical and cultural evolution such as tools, travel, and settlements. He then makes the case that these accomplishments are best explained by the invention of language. Language in turn is shown to be the transfer of information by symbols, where other components of language, such as grammar, play roles in support of symbolic communication. Concrete evidence for symbols among erectus populations is found in their tool construction and “dialectal” tool distinctions.

Small Molecule Medicine

Unless you are old or chronically sick, it’s likely that the only drug you’ve ever taken that hasn’t been a small molecule is a vaccine. Indeed, drugs that aren’t small molecules are so strange and rare we usually don’t think of them as “drugs” but as a separate entity: vaccines, monoclonal antibodies, anabolic steroids.

But, like, the vast majority of molecules found in our body, and in all of organic life, are not classified as “small”. And the vast majority of the things doing something interesting are not really molecules, but more so fuzzy complexes of molecules (ribosomes, lysosomes, lipoproteins, membranes).

So why are virtually all drugs small molecules? Prima facie we’d expect most of them to be complexes made up of 10s to 1000s of very large molecules.

The answer lies in several things:

Easy to mass-produce

Simple to administer

Cheap to store

Homogenous in effect

Quick to act

Medicine is slowly undergoing the process of learning how to work with complex molecules. In parallel with normal medicine, I’d like to think that biohackers with the ability to custom order whatever they can dream of, will lead the way with self-experimentation. Figuring out the limits and benefits from individualized design and continuous monitoring. For now, this is mainly click-bait, people injecting a bioluminescence gene with CRISPR kinda stuff, but some of it isn’t. As an example, the guy from ThoughtEmporium self-designed a therapy to get rid of lactose intolerance (though the solution is not permanent, it lasts for a few months). 100s of other such people are engaging in similar experiments, and the more people do it, the more resources become available, the easier it will get, and the better the ROI. As this happens, social acceptance will follow and pharmaceutical companies will get more on the deal.

Agrivoltaics

Using vertically mounted bifacial modules allows for more arable land. And if you don’t know what bifacial solar panels are, they can collect solar energy from both sides of the panel. This type of installation would work particularly well in areas that suffer from wind erosion, since the structures reduce wind speeds which can help protect the land and crops grown there. The bifacial panels also can generate more power per square meter than traditional single faced panels and don’t require any moving parts. Then there’s also the option of mounting panels on stilts, which allows farming machinery to pass underneath. In this design you have to maintain a certain clearance between rows to protect the stilts from the machinery, so there is a modest arable land surface loss, usually 3-10%.

2022-09-14: A similar thought process is to combine solar with dams.

Utilizing even small tracts of water can yield outsized benefits. EDP’s Alqueva array, for instance, takes up just 0.016% of the reservoir total surface area. The relative footprint is even smaller when taking into account the reduced need for transmission infrastructure, as the project can plug into the dam’s pre-existing lines.

Moreover, panels and water can have a symbiotic relationship. Modeling the effects of floating panels on water reservoirs found that floating solar panels could reduce evaporation of the water beneath them by 42%. Conversely, solar panels lose generating capacity as they heat up, and the water helps keep panels cool — and 10% more efficient.

2023-06-26: Luminescent Solar Concentrators strike a good balance of energy / agricultural performance.

The idea of Agri-LSC is to allow visible light that crops use for photosynthesis to pass through the panel, while capturing wavelengths of light that are unusable for plants, like infrared and ultraviolet, and converting them into electricity or even transforming them to aid with crop growth. UbiGro is a transparent film that implements a method of LSCs to increase yield for everything from strawberries to cannabis by 20%. They recently teamed up with the solar module company Heliene to add UbiGro film to solar panels, simultaneously generating electricity from low light while aiming to increase plant yield.

https://www.youtube.com/watch?ww-_U7_oQbY?t=325

Casein Fermentation

Vegan cheese has been quite disgusting to date. But not the mozzarella that I tasted. The missing ingredient has been the casein protein of milk (and until now, it could only be had from milk). Melding innovative microbial fermentation science and traditional cheesemaking, New Culture’s mozzarella is the first animal-free cheese to melt and stretch. When I tasted it, it tasted, smelled, and stretched like milk cheese. The cheese is healthier (cholesterol and lactose-free) and better for the environment: of all food products, cheese requires the most water and is 3rd in greenhouse gas emissions and land use. Producing cheese from casein fermentation rather than animal milk reduces greenhouse gas emissions, and land and water usage by orders of magnitude, making the New Culture approach radically more climate-friendly than animal farming.

2023-03-13: A bit more progress

28 companies have sprouted up to develop milk proteins made by yeasts or fungi. The companies’ products are already on store shelves in the form of yogurt, cheese and ice cream, often labeled “animal-free.” The burgeoning industry, which calls itself “precision fermentation,” has its own trade organization, and big-name food manufacturers such as Nestlé, Starbucks and General Mills have already signed on as customers.
The dairy industry, with its clout and hefty lobbying budget, may not agree there is room for everyone: In 2022, US cow dairy had ceded 16% of all retail milk sales to plant-based milk. Plant-based milk companies also may not welcome the competition, especially if cultivated dairy products are positioned as more sustainable and less resource-intensive. A glass of almond milk takes 90 liters of water to produce.