Tag: biology

K/T extinction event

66 ma ago, maybe on a Tuesday afternoon, life was the same as it had been the day before or 1 ka before or pretty much 1 ma before. Things were good for our feathered dinosaur buddies. Until a tiny, tiny detail in the sky changed.

2021-04-06: Chicxulub created rainforest

the dinosaur extinction was also a massive reset event for neotropical ecosystems, putting their evolution on an entirely new path leading directly to the extraordinary, diverse, spectacular and gravely threatened rainforests in the region today.

2022-10-05: The Chicxulub Impact Produced a Powerful Global Tsunami

The Chicxulub asteroid impact produced a global tsunami 30k times more energetic than any modern-day tsunami produced by earthquakes. Here we model the first 10 min of the event with a crater impact model, and the subsequent propagation throughout the world oceans using 2 different global tsunami models. The Chicxulub tsunami approached most coastlines of the North Atlantic and South Pacific with waves of 10m high and flow velocities of 1 m/s offshore. The tsunami was strong enough to scour the seafloor in these regions, thus removing the sedimentary records of conditions before and during this cataclysmic event in Earth history and leaving either a gap in these records or a jumble of highly disturbed older sediments.

Radiolyctic Life

Radioactive decay can sustain life deep below the surface. Radiation from unstable atoms in rocks can split water molecules into hydrogen and chemically reactive peroxides and radicals; some cells can use the hydrogen as fuel directly, while the remaining products turn minerals and other surrounding compounds into additional energy sources. Radiolysis is instrumental not just in the hydrogen and sulfur cycles on Earth, but in the cycle most closely associated with life: that of carbon. Analyses of water samples from the same Canadian mine showed very high concentrations of acetate and formate, organic compounds that can support bacterial life. Moreover, measurements of isotopic signatures indicated that the compounds were being generated abiotically. The researchers hypothesized that radiolytic products were reacting with dissolved carbonate minerals from the rock to produce the large quantities of carbon-based molecules they were observing.


See also these Chernobyl fungi

a robot sent into the still-highly-radioactive Chernobyl reactor had returned with samples of black, melanin-rich fungi that were growing on the ruined reactor’s walls. “Just as the pigment chlorophyll converts sunlight into chemical energy that allows green plants to live and grow, our research suggests that melanin can use a different portion of the electromagnetic spectrum – ionizing radiation – to benefit the fungi containing it” Since ionizing radiation is prevalent in outer space, astronauts might be able to rely on fungi as an inexhaustible food source on long missions or for colonizing other planets

Parasitical Life Extension

Infected Temnothorax ants live at least 3x longer than their siblings, and perhaps in excess of 10 years, approaching that of ant queens, who can survive up to 20 years. When Foitzik cracks open infected Temnothorax colonies, the parasitized workers do little more than stare expectantly skyward. Down to the molecular level, the parasite is pulling the strings. She has split open Temnothorax abdomens and counted up to 70 tapeworms inside. From there, the worms can unleash a slurry of proteins and chemicals that futz with the ant’s core physiology, likely impacting their host’s hormones, immune system, and genes. What they achieve appears to be a rough pantomime of how ant queens attain their mind-boggling life span, a feat humans still don’t understand. The tapeworms’ grasp of ant aging is far more advanced than ours.

Transposons

Scientists have long known that transposons can fuse with established genes because they have seen the unique genetic signatures of transposons in a handful of them, but the precise mechanism behind these unlikely fusion events has largely been unknown. By analyzing genes with transposon signatures from nearly 600 tetrapods, the researchers found 106 distinct genes that may have fused with a transposon. The human genome carries 44 genes likely to have been born this way.

The structure of genes in eukaryotes is complicated, because their blueprints for making proteins are broken up by introns. These noncoding sequences are transcribed, but they get snipped out of the messenger RNA transcripts before translation into protein occurs. A transposon can occasionally hop into an intron and change what gets translated. In some of these cases, the protein made by the fusion gene is a mashup of the original product and the transposon’s splicing enzyme (transposase).

Once the fusion protein is created, “it has a ready-made set of potential binding sites scattered all over the genome”, because its transposase part is still drawn to transposons. The more potential binding sites for the fusion protein, the higher the likelihood that it changes gene expression in the cell, potentially giving rise to new functions. “These aren’t just new genes, but entire new architectures for proteins”.

2023-03-30: Introns might be parasitic

If introners find their way into hosts primarily through horizontal gene transfers in aquatic environments, that could explain the irregular patterns of big intron gains in eukaryotes. Terrestrial organisms aren’t likely to have the same bursts of introns, since horizontal transfer occurs far less often among them. The transferred introns could persist in genomes for many millions of years as permanent souvenirs from an ancestral life in the sea and a fateful brush with a deft genomic parasite.

Introners acting as foreign, invasive elements in genomes could also be the explanation for why they would insert introns so suddenly and explosively. Defense mechanisms that a genome might use to suppress its inherited burden of transposons might not work on an unfamiliar genetic element arriving by horizontal transfer.

Histones

Work on the structure and function of histones in ancient, simple cells has made the central importance of these proteins to gene regulation even clearer. Billions of years ago, archaea were already using histones, but with looser rules and much more variety. By curving the DNA around the nucleosome, the histones prevent it from clumping together and keep it functional. With more DNA, cells could wrap more nucleosomes and enable the histones to reduce more copper, which would support more mitochondrial activity. It wasn’t just that histones allowed for more DNA, but more DNA allowed for more histones.

Basketball-sized Cells

Possibly the largest Eukaryote cells:

These single-celled organisms, called xenophyophores, can grow as large as basketballs. Xenophyophores growing on the sediment can resemble carnations, roses, or lattices, and like corals in shallow water, their bodies create a unique habitat in the deep sea. Though surveys are difficult to conduct at the depths where they live and much of the abyssal plains have not been explored, we do know that xenophyophore meadows may cover large areas and that they inhabit the Atlantic and Pacific oceans. Xenophyophores “represent a little known element of marine biodiversity”. They are also, she added, “very fragile—so vulnerable to human disturbance.

2022-02-24: And the largest Prokaryote:

Thiomargarita magnifica, a bacterium living in Caribbean mangroves is visible to the naked eye, growing up to 2 centimeters—as long as a peanut—and 5000x bigger than many other microbes. What’s more, this giant has a huge genome that’s not free floating inside the cell as in other bacteria, but is instead encased in a membrane, an innovation characteristic of much more complex cells, like those in the human body. It implies the 2 branches of life are not as different as previously thought. The genome was huge, with 11m bases harboring 11k genes. Typically, bacterial genomes average 4m bases and 4k genes. The genome was so big because there are 500k copies of the same stretches of DNA.

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”

Non-neural bioelectricity

a group of cells stores memory in their electrical impulses, which affects cell division.

We found a pretty amazing phenomenon, which is that if you make so-called “Picasso frogs” — these are tadpoles where the jaws might be off to the side, the eyes are up here, the nostrils are moved, so everything is shifted — these tadpoles make largely normal frog faces. Now, this is amazing, because all of the organs start off in abnormal positions, and yet they still end up making a pretty good frog face. And so what it turns out is that this system, like many living systems, is not a hardwired set of movements, but actually works to reduce the error between what’s going on now and what it knows is a correct frog face configuration. This kind of decision-making that involves flexible responses to new circumstances, in other contexts, we would call this intelligence. And so what we need to understand now is not only the mechanisms by which these cells execute their movements and gene expression and so on, but we really have to understand the information flow: How do these cells cooperate with each other to build something large and to stop building when that specific structure is created?