Tag: biology

Hybrid Fish

Sturddlefish go shockingly far beyond classic crossbreeds like mules and ligers, whose parent species sit close together on the tree of life. Sturddlefish result from the merger of different taxonomic families. It’s like if they had a cow and a giraffe make a baby. Then he quickly corrected himself, because the lineages of those 2 ruminants split only 40 ma ago. The evolutionary paths of paddlefish and sturgeons diverged 184 ma ago. For those fish to breed is more like if a human came out of a platypus egg.

Anglerfish sexual parasitism

The anglerfish deleted its immune system to fuse with its mate

There are few animals more bizarre than the anglerfish, a species that has so much trouble finding a mate that when the male and female do connect underwater, males actually fuse their tissue with the females for life. After the merger, the 2 share a single respiratory and digestive system

Coronaviruses

Eventually I think we will categorize all the recent betacoronavirus outbreaks (Sars-1, Sars-2, MERS) as part of this broader process, and require a vaccination strategy that can be quickly deployed against new recombinations from this original ancestral betacoronavirus as they randomly emerge from the primordial stew across many animal species, including ours. The evidence thus far points to recombinations resulting in the emergence of a distinct dangerous variant with some regularity.

2020-11-23: Horseshoe bat origin?

2 lab freezers in Asia have yielded surprising discoveries. Researchers have found a coronavirus that is closely related to SARS-CoV-2, the virus responsible for the pandemic, in horseshoe bats stored in a freezer in Cambodia. A team reported the discovery of another closely related coronavirus — also found in frozen bat droppings.

The viruses are the first known relatives of SARS-CoV-2 to be found outside China, which supports the World Health Organization’s search across Asia for the pandemic’s animal origin. Strong evidence suggests that SARS-CoV-2 originated in horseshoe bats, but whether it passed directly from bats to people, or through an intermediate host, remains a mystery.

Subantarctic life

John Priscu’s search for life that thrives under ice took him to subglacial lakes at the South Pole. Now he has his eye on Mars and Europa.

And there are sessile animals under the ice:

The researchers think it’s likely that the drift of this marine snow has been flipped on its side, so that the food source is moving horizontally instead of vertically. The researchers determined that there are productive regions 630-1500 km away. It may not be much, but it’s possible that enough organic material is riding these currents to feed these creatures. That’s an extraordinary distance, given that in the deepest part of the ocean, the Challenger Deep near Guam, marine snow produced at the surface has to fall 11 km down to reach the seafloor. To reach the animals on this Antarctic rock, food would have to travel as much as 133x that distance—and it would have to do so by floating sideways.

Individuality information theory

This information theory of individuality offers a very general way to think about biological units. They hope it will inspire algorithms that could allow you to extract figure from ground, organism from environment. Such algorithms could be applied to streams of data collected over time to pinpoint correlations of information that signify the emergence of individuals.

Within this theory, individuals can be cells, tissues, organisms, colonies, companies, political institutions, online groups, artificial intelligence or cities — even ideas or theories. What we’re trying to do is discover a whole zoo of life forms that extend far beyond what we have conventionally called living,

Chirality

Cosmic rays may explain life’s bias for right-handed DNA

Ultimately, the fact that researchers struggle to find a theory that balances the rise of chirality against the destruction of biological materials suggests that our ancestors may have been lucky to find that fine line. There is something special about planets like the Earth that protect this kind of chemistry.

2021-08-02: More details on this astounding achievement. They were able to sequence a 1.5 kilobase chiral DNA plus the Pasteur encoding stunt.

The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day.

2022-10-28: The same group doing the next step, a chiral RNA polymerase. This one is about 10% larger than previous work on the DNA polymerase as measured in kDA.

Zhu chemically synthesized a 100-kDA mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of high-quality l-RNAs as long as 2.9 kilobases. A massive, 883 amino acid protein, it lay well beyond the limits of traditional chemical synthesis. But an analysis of T7s x-ray crystal structure showed the enzyme could likely be split into 3 sections, each stitched from short segments. In solution, the fragments naturally folded into their proper 3D shapes and assembled themselves into a working T7.

The mirror-image RNAs fashioned by the polymerase were far more stable than the normal versions produced by a regular T7, because they were untouched by the naturally occurring RNA chewing enzymes that almost unavoidably contaminate such experiments and quickly destroy normal RNAs.

Now, Zhu needs to make the remaining components of a mirror-image ribosome. The 3 RNA fragments they synthesized make up 66% of the total mass of a ribosome. What remains are the 54 ribosomal proteins and several proteins that work in concert with the ribosome, all of which are smaller and thus likely easier to synthesize. Then the question is whether the full parts kit will assemble into a ribosome.

Even if they do, the resulting molecular machines might still not be functional. In order to churn out proteins, ribosomes must work in conjunction with a suite of additional helper proteins. To make this work inside a living cell, Church thinks it will be necessary to rewrite an organism’s genetic code so the engineered ribosome can recognize all those proteins, particularly the 20 that ferry amino acids for building new proteins.


2023-08-28: nonlinear optics to detect chirality

They have realized a technique that can completely distinguish enantiomers in solution in an all-optical manner: no chemical tags, no particular UV/VIS absorbance needed from the compound structures, etc. And it is extremely fast and extremely sensitive, as opposed to traditional methods like optical rotation, circular dichroism, etc.

2023-09-08: What about magnetism?

Magnetic surfaces on minerals in bodies of water on the primordial Earth, charged by the planet’s magnetic field, could have served as “chiral agents” that attracted some forms of molecules more than others, kicking off a process that amplified the chirality of biological molecules, from RNA precursors all the way to proteins and beyond. Their proposed mechanism would explain how a bias in the makeup of certain molecules could have cascaded outward to create a vast network of chiral chemistry supporting life.

It’s not the only plausible hypothesis, but “it’s one of the coolest because it ties geophysics to geochemistry, to prebiotic chemistry, and ultimately to biochemistry”

Hummingbird vision

The tests showed that the birds could see every nonspectral color that the researchers threw at them. Color pairs that were closer together in hue resulted in more mistaken visits but still beat the 50/50 odds of the control experiments. Even if the neural mechanisms for color vision were clear, and even if color-mixing experiments attest to avian tetrachromacy, we still could not answer the more philosophical question of what nonspectral colors really look like to birds. Does UV+green appear to birds as a mix of those colors (analogous to a double-stop chord played by a violinist) or as a sublime new color (analogous to a completely new tone unlike its components)? We cannot say.