Tag: science

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.

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.

Haber-Bosch

50% of the nitrogen in our bodies came from the Haber–Bosch process. It’s in every protein and every strand of DNA. Ponder that — “50% of the nitrogen in your blood, your skin and hair, your proteins and DNA, is synthetic.” The Haber-Bosch process catalyzes the production of ammonia (NH3) from N2 and H2 gas. We need “fixed nitrogen”, available to our organic chemistries as atomic nitrogen. It is the limiting factor for the growth of all food. While nitrogen gas is about 80% of our atmosphere, not one atom of it is available for our use when tightly bound by the triple bond of N2 gas, the strongest chemical bond in nature. It is sequestered all around us. In nature, N2 is liberated to atomic nitrogen in small amounts by lightning strikes (it needs 1000°C) and slowly by nitrogen-fixing bacteria in the soil. Hager argues that if we reverted to relying on just those natural sources, 3b people would die of starvation in short order — our soils simply could not produce enough food for the mouths now on Earth. The Haber process consumes 4% of the world’s natural-gas production and 1.5% of the world’s energy supply.

2021-11-30: There’s a potential replacement:

The process is as clean as the electricity used to power it, and produces around 53 nanomoles of ammonia per second, at Faradaic efficiencies around 69%. The highest reported previous efficiencies for ammonia electrolysis sat around 60%, with the exception of 1 other lithium cycling approach that managed 88%, but required high temperatures of 450 °C. The team says it’s massively scalable, capable of operating either at industrial scale, or in extremely small on-site operations. “They can be as small as a thick iPad, and that could make a small amount of ammonia continuously to run a commercial greenhouse or hydroponics setup, for example.” This kind of distributed production model, as we explored looking at FuelPositive’s modular, container-sized ammonia production units, would have additional benefits in that it would eliminate the distribution and transport that contribute significantly to the financial and emissions costs of the current ammonia model.

2022-05-04: What happens when you think you can do without Haber-Bosch.
2022-07-22: The same team was able to improve ammonia electrolysis further, with 3x yield and nearly 100% energy efficiency.

We investigate the role of the electrolyte in this reaction and present a high-efficiency, robust process enabled by compact ionic layering in the electrode-electrolyte interfacial region. The interface is generated by a high-concentration imide-based lithium salt electrolyte, enabling stabilized ammonia yield rates of 150±20 nmol s-1 cm-2 and current-to-ammonia efficiency closely approaching 100%.

Universal Tick Vaccine

Over 10 diseases can be transmitted by tick bites. The most well-known is Lyme disease, caused by a bacterium called Borrelia burgdorferi. In the past, vaccines have successfully been developed to specifically target this Lyme disease bacterium. However, this new vaccine candidate takes a different approach, using mRNA technology to target the tick itself. This particular vaccine directs cells to produce a number of proteins found in the saliva of the black-legged tick Ixodes scapularis. This vaccine is unique in the way it targets a carrier of a pathogen rather than the pathogen itself. This means it should offer a broad-based protection from all kinds of tick-induced disease and not just a single pathogen. “When you feel a mosquito bite, you swat it. With the vaccine, there is redness and likely an itch so you can recognize that you have been bitten and can pull the tick off quickly, before it has the ability to transmit B. burgdorferi.”

2022-02-24: A gene drive might be an alternative:

This approach is already being applied to malaria-transmitting mosquitoes, but scientists have run into a wall trying to use CRISPR to prevent tick-borne diseases — or, more accurately, a hard shell. The problem is that scientists need to be able to insert their CRISPR system into ticks when they’re at the embryo stage. But ticks grow in eggs coated in a hard wax, which can literally shatter the glass needles used for injections. “Previously, no lab has demonstrated genome modification is possible in ticks. Some considered this too technically difficult to accomplish.” They have now demonstrated 2 different techniques that make gene editing a viable option for fighting tick-borne diseases. So far, all we know is that it’s possible to get a CRISPR system into ticks — we still don’t know what edits, if any, can prevent the spread of tick-borne diseases.

RNAi pesticides

If you could introduce dsRNA into a pesky pathogen—a particularly irritating fungus, for example—you could instruct that pathogen’s cells to destroy its own mRNA and stop it from making crucial proteins. In essence, they could switch off genes within pathogens at will. RNA crop sprays could have some major advantages over the current toolbox of chemical-based pesticides. Microbes break down RNA in the soil within a couple of days, which lessens the problem of environmental buildup. And because RNA sprays would target genes specific to individual species, there is—at least theoretically—a much lower chance that other organisms would get caught in the crossfire. Even 2 very similar species have enough genetic differences that it’s possible to make RNA sprays that target one bug while leaving the other one alone. Resistance is always a concern. “It’s unavoidable. But we will do everything we can to make sure that growers use the products the way we believe minimizes that risk.” Growers might be directed to use dsRNA only at certain times of the year, and that since RNA breaks down so quickly in the environment it’s less likely that pests will be exposed enough to develop resistance. RNA sprays will likely be mixed with existing pesticides—attacking pests from several angles rather than taking a single one-spray-to-kill-them-all approach. “It’s [reducing] the number of ag chemicals that are used, but not full replacement of them”.

1021

New research pinpoints an exact date Vikings from Europe were in North America: 1021 (1000 years ago this year), 430 years before Christopher Columbus was even born. How was this determination possible? Because the Sun erupted in an immense series of storms that altered Earth’s atmosphere, leaving measurable changes in tree rings at the time. A team of scientists looked at wood found at the L’Anse aux Meadows Viking site. In 3 cases the trees had been physically cut down, and moreover, they were clearly cut with metal tools — Vikings had metal implements at the time, but indigenous people did not. The wood was all from different trees (one was fir, and another juniper, for example). The key parts here are that the wood was all from trees that had been alive for many decades, and all had their waney edge intact as well.

Wavelets

Built upon the ubiquitous Fourier transform, the mathematical tools known as wavelets allow unprecedented analysis and understanding of continuous signals.

Fourier transforms have a major limitation: They only supply information about the frequencies present in a signal, saying nothing about their timing or quantity. It’s as if you had a process for determining what kinds of bills are in a pile of cash, but not how many of each there actually were. “Wavelets definitely solved this problem, and this is why they are so interesting” A signal could thus be cut up into smaller areas, each centered around a specific wavelength and analyzed by being paired with the matching wavelet. Now faced with a pile of cash, to return to the earlier example, we’d know how many of each kind of bill it contained. Part of what makes wavelets so useful is their versatility, which allow them to decode almost any kind of data. “There are many kinds of wavelets, and you can squish them, stretch them, you can adapt them to the actual image you are looking at”. The wave patterns in digitized images can differ in many aspects, but wavelets can always be stretched or compressed to match sections of the signal with lower or higher frequencies. The shapes of wave patterns can also change drastically, but mathematicians have developed different types, or “families,” of wavelets with different wavelength scales and shapes to match this variability.