Tag: science

Constructor Theory

Counterfactuals do appear in existing laws, but these laws are regarded as second class. They are not incorporated wholeheartedly. Constructor theory puts counterfactuals at the very foundation of physics, so that the most fundamental laws can be formulated in these terms. Concepts like work and heat can’t be captured fully with trajectories and laws of motion, because in the standard conception they are considered emergent and approximate. In constructor theory we can talk about them using exact statements about possible and impossible transformations.

2023-05-04: Assembly theory is an intellectual cousin

Assembly theory started when Cronin asked why, given the astronomical number of ways to combine different atoms, nature makes some molecules and not others. It’s one thing to say that an object is possible according to the laws of physics; it’s another to say there’s an actual pathway for making it from its component parts. “Assembly theory was developed to capture my intuition that complex molecules can’t just emerge into existence because the combinatorial space is too vast”.
Assembly theory makes the seemingly uncontroversial assumption that complex objects arise from combining many simpler objects. The theory says it’s possible to objectively measure an object’s complexity by considering how it got made. That’s done by calculating the minimum number of steps needed to make the object from its ingredients, which is quantified as the assembly index (AI).
Complex mixtures of molecules made by living systems — a culture of E. coli bacteria, natural products like taxol (a metabolite of the Pacific yew tree with anti-cancer properties), beer, and yeast cells — typically had significantly higher average AIs than minerals or simple organics.

The analysis is susceptible to false negatives — some products of living systems, such as Ardbeg single malt scotch, have AIs suggesting a nonliving origin. But perhaps more importantly, the experiment produced no false positives: Abiotic systems can’t muster sufficiently high AIs to mimic biology. If a sample with a high molecular AI is measured on another world, it is likely to have been made by an entity we could call living.
Cronin and Walker hope that assembly theory will ultimately address very broad questions in physics, such as the nature of time and the origin of the second law of thermodynamics. But those goals are still distant.

Humans are 0.01% of Biomass

Anyone who has walked through a jungle or wandered a grassland may already have guessed that humans are a pretty small part of Earth’s organic matter. The carbonaceous winners are plants, which make up 80% of all biomass on Earth. Bacteria comes in second at 13% and fungus is third at just 2%. Of the 550 gigatons of biomass carbon on Earth, animals make up ~2 gigatons, with insects comprising 50% of that and fish taking up 0.7 gigatons. Everything else, including mammals, birds, nematodes and mollusks are ~0.3 gigatons, with humans weighing in at 0.06 gigatons. “The fact that the biomass of fungi exceeds that of all animals’ sort of puts us in our place”

Expert COVID-19 long-haulers

Most of the other treatments haven’t had the funds for extensive trials, and without proper research, some drugs run the risk of getting overhyped based on limited information. “The early bets financially were made on investing in vaccine trials and investing in monoclonal antibodies. What received relatively less funding and attention were drugs that were already FDA-approved that could be repurposed for COVID.” his goal with COVIDSalon is to provide a dedicated hub of treatment information so people don’t have to sift through a barrage of old articles. A large segment of COVIDSalon aims to help COVID long-haulers. At the moment, only a small number of trials are focusing on long-haulers. James also highlights drugs like fluvoxamine that have alleviated long-term symptoms in a test of COVID-19 patients, plus others such as the nutritional supplement GlyNAC, which is worth watching but is still in very early-stage trials. The way that long-haulers have organized throughout the pandemic—discussing their symptoms in Facebook and Slack groups, and pushing medical professionals to pay attention to their ailments—echoes the patient advocacy that James helped popularize during the AIDS epidemic. Through publications such as ATN, many people with AIDS knew as much about the latest niche medical findings as licensed doctors did. “I think that’s the same with the long-haulers. Everyone is learning about the long-term consequences of this in real time.”

We made oxygen on Mars

An experiment on board the Mars Perseverance rover designed to produce breathable oxygen from carbon dioxide has been switched on and is working! On April 20 it produced 5 grams of oxygen — not a huge amount, but it’s designed to make as much as 10 grams per hour, and this is the very first time oxygen has been converted from native air on another planet. MOXIE by itself can’t produce that much, but again it’s not designed to actually do that, it’s just to make sure the tech works. Still, just 4 MOXIEs could keep a human breathing on Mars. That first amount it made, 5 grams, is enough for ~10 minutes worth of breathing for a single person.

Real vs deal friends

These are what some social scientists call “expedient friendships”—with people we might call “deal friends”—and they are probably the most common type most of us have. The average adult has 16 people they would classify as friends. Of these, 3 are “friends for life,” and 5 are people they really like. The other 8 are not people they would hang out with 1-on-1. We can logically infer that these friendships are not an end in themselves but are instrumental to some other goal, such as furthering one’s career or easing a social dynamic. Expedient friendships might be a pleasant—and certainly useful—part of life, but they don’t usually bring lasting joy and comfort. If you find that your social life is leaving you feeling a little empty and unfulfilled, it might just be that you have too many deal friends, and not enough real friends.

Engram

Almost all neuroscientists base their search—for the physical basis of memory (the engram)—on the assumption that temporal-pairing causes learning. They are dedicated to this assumption—even though, as Rescorla pointed out 50 years ago, experimental attempts to define temporal-pairing have always failed. This failure is as striking now as it was 50 years ago. Anything that gets neuroscientists to abandon the idea that temporal-pairing is a useful scientific concept is a step toward discovering the physical basis of memory. Each neuron contains billions of (almost) incomprehensibly-tiny molecular machines. Molecular biologists have developed an astonishing array of techniques for visualizing/manipulating the actions of these little machines. These techniques will allow molecular biologists to follow the machines inside this huge neuron to the engram—to the tiny machine that encodes the experience-gleaned facts so that these learned/remembered facts can inform later behavior.

2021-11-19: This feels like a really big deal:

Biology feels different right now. New broadly enabling technologies and tools are driving forward progress in nearly every specific field at a rapid pace. The large scale adoption and application of a powerful set of common tools has created a virtuous cycle of further technology refinement and engineering. The rate of iteration is increasing, and previously intractable problems are now within reach. While RNA-seq and MPRAs are both valuable approaches, they come with some limitations. Fundamentally, each measurement represents a single static slice of a dynamic process which is only inferred by attempting to piece together the slices. The quality of the reconstruction is limited by sampling density. What if we could measure these systems continually as they occurred in a way that didn’t require destructive sampling? Here, the fundamental idea is that “DNA is the natural medium for biological information storage, and is easily ‘read’ through sequencing.” This forms the basis for this new technology: ENGRAM (ENhancer-driven Genomic Recording of transcriptional Activity in Multiplex). The workflow of this technique is very similar to that of the MPRA introduced above, but with an important twist. Instead of destroying the cell and sequencing a ratio of barcodes, the transcription event is recorded by the insertion of a barcode into a locus of DNA in the cell via prime editing. They went further and showed that they could effectively multiplex this technique by reading out all 3 signals in response to stimulants in a single population of cells. Even more, they showed a proof-of-concept for reading out the order in which events occurred.

Human Challenge Trials

we need far more human challenge trials, and far less garbage people like ethicists.

In interviews, former challenge trial participants described motives for their participation that ranged from the light-hearted — several imagined it would be a fun story to tell at scientific conferences and parties — to the serious. Some spoke of altruistic motives, often shaped by personal experiences. “I spent a couple years in Africa; I was in the Peace Corps. I think for me, seeing that firsthand, and knowing that there might be some way that maybe I can be a part of figuring out whether or not we can make a vaccine for malaria definitely played a big part in it for me.”

Microwave boilers

Arrays of these devices beam microwaves into water in a boiler, heating it up. The pipes that carry the water are also made of microwave-sensitive materials, as is the insulation that lags them. And a heat exchanger recycles residual waste warmth. The upshot is a boiler that is 96% efficient. The best existing gas boilers rarely exceed 90%.