tag > Biology
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Machine Learning for the Genetic Engineering of Fungal Secondary Metabolite Clusters: A Novel Framework for Alien Communication
The Search for Extraterrestrial Intelligence (SETI) has long scanned the skies for radio signals. But what if an advanced civilization's signature isn't a broadcast, but a biological program?
Hypothesis
Mastery over a planet's biology is the ultimate technology. Instead of fleeting electromagnetic waves, a persistent, self-replicating message could be encoded into the very blueprint of life - an engineered gene cluster in a hardy organism like a fungus, designed to survive deep space and seed itself on new worlds.
Fungal Gene Clusters: Nature's Data Cassette
Fungal secondary metabolite (SM) clusters are modular genetic programs. Enzymes like Polyketide Synthases (PKSs) are built from domains (A-T-C-KR-ER-ACP...) in a precise order. This sequence is a code. In theory, it could be repurposed. A non-functional, hyper-complex cluster discovered in a space-borne spore might not be for making a toxin - it could be a biochemical QR code, a message etched in DNA that can last for eons and travel between stars.
Machine Learning is the Decoder
Decoding such a message, however, would be impossible by eye. It would require advanced machine learning—trained on every known natural and engineered biological pattern—to first recognize the cluster as artificially designed, then reverse-engineer its domain sequence into a payload: an image, a mathematical constant, a map.
This isn't just speculation - it's a new lens for our own research. As we use AI to genetically engineer fungal SM clusters for new drugs and materials, we are learning to write and read this deep language of biology. We are developing the very tools needed to one day ask: Is this fungus from Earth, or is it a message in a bottle, waiting for a reader smart enough to understand it?
We're not just engineering fungi. We're building the translator for a conversation that may have already begun.
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How 20 Smuggled Chinese Hamsters Built a Pharmaceutical Empire
Chinese Hamster Ovary, or CHO, cells are widely used in the pharmaceutical industry. And, incredibly, these cells can be traced back to just twenty hamsters that were packed into a crate and smuggled out of China in the 1940s.
Chinese scientists had been using these hamsters — native to northern China and Mongolia — to study pathogens since at least 1919. The hamsters were unusually well-suited to scientific research because they have short gestation periods (18-21 days), a natural resistance to human viruses and radiation, and it was thought, early on, that they possessed just 14 chromosomes, making them easy to work with for mutation studies. (They actually have 22 chromosomes.)
During the Chinese civil war, a rodent breeder in New York named Victor Schwentker worried that, if the Communists won the war, he’d never be able to get his hands on these special rodents. So in 1948, Schwentker sent a letter to Robert Briggs Watson, a Rockefeller Foundation field staff member, and asked him to “acquire” some hamsters so he could begin breeding them.
Watson collected ten males and ten females and packed them into a wooden crate with help from a Chinese physician (who was later imprisoned for this act). Watson slipped the crate out of the country on a Pan-Am flight from Shanghai, just before the Communists took control.
In New York, Schwentker received the hamsters and then began breeding and selling them to other researchers.
In 1957, a geneticist named Theodore Puck, intent on creating a new mammalian “model system” for in vitro experiments, learned about the Chinese hamster and contacted George Yerganian, a researcher at the Dana-Farber Cancer Institute, to obtain a specimen. Yerganian shipped Puck one female hamster.
Puck took a small piece from this hamster’s ovary, plated the cells onto a dish, and passaged them repeatedly. He eventually isolated a clone that could divide again and again; an “immortalized” CHO cell with a genetic mutation that rendered it immune to normal senescence.
Today, descendants of these immortalized CHO cells make about 70 percent of all therapeutic proteins sold on the market, including Humira (USD 21 billion in sales in 2021) and Keytruda ($17 billion). Many of these drugs are monoclonal antibodies, or Y-shaped proteins that lock onto, and neutralize, foreign objects inside the body.
CHO cells are well suited to biotherapeutics because they can perform a biochemical reaction called glycosylation. Many human proteins, including antibodies, are decorated with chains of sugars that control how they fold or interact with other molecules in the body. Only a few organisms, mostly mammalian cells and certain yeasts, can do this chemical reaction.
I first learned about this history from a really spectacular article in LSF Magazine, called "Vital Tools: A Brief History of CHO Cells." I recommend it. (You can find it with a quick search.)
Video
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Non-Human Alters
Non-human alters are parts of individuals with dissociative identity disorder (DID) that see themselves as animals, fantasy creatures, or hybrids. Like all other alters, non-human alters are the result of trauma and an already severely dissociative mind.
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There's a bacteriophage that turns bacteria into “liquid crystals.”
Specifically, Pseudomonas aeruginosa bacteria make Pf phages, which are rod-shaped, negatively-charged, and measure about 2 micrometers in length (roughly the length of an E. coli cell). These phages leave the cells and enter their surroundings. There, they mix with polymers, also secreted by the cells, to form a crystalline matrix.
Surprisingly, this is good for the cells. Although the phages kill some of them, it also makes their biofilms stickier and able to withstand certain antibiotics. These bacteria + phages are prevalent in cystic fibrosis patients; they've formed a sort of symbiotic relationship.
The Pf phages are made from thousands of repeating copies of a coat protein, called CoaB, which wraps around a single-stranded, circular DNA genome. These genes are integrated directly on the bacterial chromosome.
The bacteria “turn on” these phage genes when placed in a viscous environment with low oxygen levels. This is like a trigger to start forming a biofilm. And the cells make a lot of phages; about 100 billion per milliliter.
These liquid crystals form because of a physics principle called “depletion attraction.” If you just mix a bunch of loose or flexible polymers together (such as long carbon chains) they will not form a liquid crystal. But if you mix stiff rods (the phages) with loose polymers at a high enough concentration, the polymers will force the phages close together to create a material that flows like a liquid despite being ordered like a crystal. See the video below.
These liquid crystal biofilms are hard to get rid of. The negatively-charged phages block many antibiotics (like aminoglycosides, which are positively-charged) from entering cells. Liquid crystals also retain water, so these biofilms can survive on drier surfaces.
Paper: Filamentous Bacteriophage Promote Biofilm Assembly and Function
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7 amazing frog facts 🐸
- Some frogs are basically transparent. Glass frogs have see-through skin on their bellies. You can literally see their beating heart and organs.
- Frogs can freeze solid and come back to life. Wood frogs survive winter by freezing almost completely. Their heart stops, they don’t breathe, then they thaw in spring and hop away like nothing happened.
- They drink water through their skin. Frogs don’t need to drink with their mouths. They absorb water directly through a special patch of skin on their belly called the “drink patch”.
- Some frogs are extremely poisonous without making poison themselves. Poison dart frogs get their toxins from the insects they eat. In captivity, without those insects, they become harmless.
- The world’s largest frog is huge. The Goliath frog can grow up to 32 cm long and weigh over 3 kg. That’s heavier than many cats.
- Frogs can be louder than chainsaws (relative to size). Certain frogs amplify their calls using inflatable vocal sacs. For their body size, they are among the loudest animals on Earth.
- Some frogs can glide through the air. “Flying frogs” don’t actually fly, but they spread their webbed feet and glide from tree to tree like tiny parachutists.
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The brain doesn’t “store data”; it maintains resonant attractors that compress meaning into dynamics. Each oscillatory pattern is a lossy, context-dependent summary of prior experience that can be expanded (decoded) when needed. In other words: The brain’s oscillations are not just rhythms, they are compressive, generative codecs of reality.
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No man is an island
"No man is an island,
Entire of itself;
Every man is a piece of the continent,
A part of the main.If a clod be washed away by the sea,
Europe is the less,
As well as if a promontory were:
As well as if a manor of thy friend's
Or of thine own were.Any man's death diminishes me,
Because I am involved in mankind.
And therefore never send to know for whom the bell tolls;
It tolls for thee."- John Donne, Meditation XVII, 1624
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The tetrahelix model of DNA
Buckminster Fuller proposed the tetrahelix model as a physical and conceptual analogue to the DNA double helix, suggesting it could explain fundamental biological patterning and the complexity of DNA. The tetrahelix is a structure of interconnected tetrahedra that forms a helical column, with ten tetrahedra completing one full 360° turn. Fuller believed this structure's characteristics, such as its rigidity and nested helical patterns, mirrored aspects of DNA's structure and function.
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Magnetosomes
Magnetosomes are unique intracellular structures found in magnetotactic bacteria, which are a diverse group of bacteria that orient themselves along magnetic field lines. These structures have a permanent magnetic moment due to the magnetic minerals they contain.
The term magnetosome derives from the Greek words "magneto," meaning magnet, and "soma," meaning body. Each magnetosome consists of a small, membrane-bound crystal of a magnetic mineral, most commonly magnetite (Fe3O4) or greigite (Fe3S4). These crystals are biological in origin and are synthesized by the bacteria themselves. The magnetosomes within a cell align to form a chain, effectively creating a tiny biological compass needle.
The fact that these magnetosomes influence the direction of motion of magnetotactic bacteria is a remarkable example of nature's ingenuity. This process, known as magnetotaxis, enables the bacteria to navigate effectively in their environment. The bacteria use the Earth's magnetic field to orient themselves and swim in a preferred direction, which is typically downward, into the sediment where the environment is oxygen-poor and more conducive to their survival.
The magnetosome chain acts like a compass needle, aligning the bacteria with the Earth's magnetic field. This alignment is not perfect, and the bacteria tend to swim in a helical path rather than a straight line. However, this behavior ensures that, on average, they will move in the direction of their preferred habitat.
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"Although Max Delbrück held some anti-reductionist views; he conjectured that ultimately a paradox—akin perhaps to the waveparticle duality of physics—would be revealed about life."
Max Debrück and some members of the Phage group at Caltech in 1949.
Interview with Delbrück, 1980
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Downsampling in the human visual system:
Retina: ~130 million photoreceptors
↓ (huge compression)
Optic nerve: ~1 million ganglion cells
↓ (further processing)
V1 cortex: ~280 million neurons (but organized hierarchically)
Plus: Your fovea (central vision) has high resolution, but peripheral vision is heavily downsampled. Your brain reconstructs a "full resolution" world from mostly low-res input.
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Constructivist biosemiotics foundations.
Source: a, bPunch’s cartoon that show succinctly the cognitivist third-person hypothesis and the alternative one. a In the cognitivist third-person hypothesis, to catch his prey, for the observer, the kingfisher must represent in its brain the Snell’s refraction law by information processing. b The constructivist lecture show how the significance levels can be seen arising from the underlying structural network of the kingfisher and the model of the observer. c René Magritte’s painting (1928–29) pointing out the levels of realms in cognitive relations. A painted pipe is just an approximate map of a real pipe. d M.C. Escher’s Print Gallery lithograph showing how a young man is standing inside the same print as the one he is looking at. A constructivist interpretation in first-person indicates that what is observed is an active and enactive relation of the observer, depicting the complex closed loop of embodiment relations. e Rosen’s Modeling Relation shows that the observation of natural systems, governed by causal relations, is a cognitive act reflected in the relations of measurement and prediction subject to mathematical systems of inferential rules. If the mathematical system corresponds to the causal relations, then it can be assumed as a ‘Natural Law’. f Maturana draws how nervous system, though organizationally closed, use language to loop-through the other. g Minimization of free energy by active inference and prediction error indicates one possible formal representation of cognition and autopoiesis
