Tag: biology

Hemimastigotes

Researchers have discovered a new kind of organism that doesn’t fit into the plant, animal, or any other kingdom of known organisms. 2 species of the microscopic organisms, called hemimastigotes, were found in dirt. Hemimastigotes were first seen and described in the 19th century, and ~10 species have been described over the past 100 years. But up to now, no one could figure out how they fit into the evolutionary tree of life. Based on the new genetic analysis, it looks like you’d have to go back 1 ga before you could find a common ancestor of hemimastigotes and any other known living thing.

Biology is in charge

If you were around pre-1900s, and wanted to contribute to biology, you should have been a physicist (Robert Hooke, a physicist discovers the first cell, making a better microscope is a major driver of progress). In which field should you work to maximize progress in biology today? …But something interesting happened around the 1950s. If you look at the most important techniques in biology, in the second half of the 1900s, they’re all driven by tools discovered in biology itself. Biologists aren’t just finding new things – they’re making their new tools from biological reagents. PCR (everything that drives PCR, apart from the heater/cooler which is 1600s thermodynamics, is either itself DNA or something made by DNA), DNA sequencing (sequencing by synthesis – we use cameras/electrical detection/CMOS chips as the output, but the hijacking the way the cell makes DNA proteins remains at the heart of the technique), cloning (we cut up DNA with proteins made from DNA, stick the DNA into bacteria so living organisms can make more copies of it for us), gene editing (CRISPR is obviously made from DNA and with RNA attached), ELISA (need the ability to detect fluorescence – optics – and process the signal, but antibodies lie at the heart of this principle), affinity chromatography (liquid chromatography arguably uses physical principles like steric hindrance, or charge, but those can be traced back to the 1800s – antibodies and cloning have revolutionized this technique), FACS uses the same charge principles that western blots do, but with the addition of antibodies…

Recursive parasites

Scientists studying wasps that target oak leaves found that a second parasite, a vine, can get its tendrils into the homes set up by the wasps, called galls, subverting their diversion of the host’s resources. After that, things don’t go so well for the wasp. When the researchers dissected 51 love-vine-infested galls from 1 wasp species, they found that 45% contained a mummified adult wasp, compared with only 2% of uninfested galls. That suggests that the love vine interferes with the wasp’s nutrition such that it develops fully but is not able to leave. And the host tissue within dissected galls was twisted toward the vine’s entry points, hinting that it was co-opting the gall’s nutrients.

Sabercat extinction

Sabercat extinction has been understood in terms of top-down ecological stress, a victim of ‘trophic cascade’, just as the top predators of the ocean today are dying off because populations of prey fishes are collapsing beneath them. The plight of today’s big cats also seems to echo the downfall of Smilodon: we know that leopards, tigers, jaguars and other big cats require large swathes of habitat that are connected through ecological corridors, providing them with plenty of ground to stalk, and enough prey to survive. Decrease the habitat and food supply, and the cats suffer. But what if we could trace the clues back the other way? What if the extinction of Smilodon could help us understand what wiped out so many of the species it relied upon for food? New research on this question could help us untangle the frighteningly mysterious nature of extinction — in the past and future — itself. For now, the exact reason why Smilodon disappeared remains unknown. Loss of food is a likely cause, but that answer only moves the question a step back to why Smilodon’s prey died out. The sabercat was a casualty in a wider extinction at the end of the Pleistocene that marked the end of the Ice Age and the beginning of a world over which our species has disproportionate influence. Some researchers like to call this the Anthropocene, but whether or not such a designation truly fits depends on how long our species lasts. What might the fossil record look like 100m years from now? The Pleistocene extinction could come to shade into the modern biodiversity crisis with little or no break in between. The close of the Ice Age might have been the beginning of a new age, or it could have been one dramatic blip in an ongoing mass extinction, tracking the rise of human dominance. Some of the garbage that ends up preserved in La Brea’s asphalt might help future archaeologists untangle this mystery.

42 ka earthworm revival

1 worm came from an ancient squirrel burrow in a permafrost wall of the Duvanny Yar outcrop in the lower reaches of the Kolyma River – close to the site of Pleistocene Park which is seeking to recreate the Arctic habitat of the extinct woolly mammoth. This is around 32 ka old. Another was found in permafrost near Alazeya River in 2015, and is around 42 ka old.

Vertebrate-microbe symbiosis

Yet amazingly, there is an animal-that-screams-animal in which an alga also dwells. That would be the spotted salamander Ambystoma maculatum. When it is an embryo, cells of the alga Oophila amblystomatis somehow end up inside it. Technically, the salamander’s now a photosynthetic animal. This salamander is the sole known example of a vertebrate playing host to a symbiotic microorganism of any kind, photosynthetic or no. And needless to say, something very interesting — no one is yet sure exactly what — is going on between the 2. Past experiments have clearly shown that the salamander benefits from its unconventional living arrangements. How the algae feel about the situation has been rather less clear. Intracellular algae showed clear signs of stress and oxygen and sulfur deprivation, producing lots more heat shock and autophagy-related proteins in response to finding themselves inexplicably inside a salamander. So why does the Oophila, the salamander alga, put up with its apparently dreary living conditions inside its host? It’s an intriguing question that lacks a clear answer, but there are clues. The alga is found nowhere else in nature besides salamander egg capsules. Algal cells remain visible inside young salamanders for a long time. Even when they are no longer obvious, algal DNA remains detectable in adult salamanders in the oviducts and the male reproductive tract. Freshly laid eggs contain encysted algal cells. And those algal cells in the capsule don’t seem nearly as put-upon as those inside embryos. Where might they come from? Is it possible that the alga is passed from generation to generation of salamander, a perpetual part of the animal? If so, the salamander has given the algae the ultimate gifts: a free ride, a home, and immortality, at least for the life of the host species. If that is the case, it was probably a bargain worth making.

Octopus panspermia?

Evidence of the octopus evolution show it would have happened too quickly to have begun here on Earth. “Thus the possibility that cryopreserved Squid and/or Octopus eggs, arrived in icy bolides several 100M years ago should not be discounted as that would be a parsimonious cosmic explanation for the Octopus’ sudden emergence on Earth 270 ma BP.”

2022-01-29:

3 hearts, pumping blue-green blood because their oxygen carrying metal is copper (versus iron in the heme of our blood). They can spend 30 minutes out of the water, to scoot between tidepools.

Alien intelligence: from a distant branch in the tree of life, the octopus is the only invertebrate to have developed a complex, clever brain. Our common evolutionary ancestor is a tubule so ancient, neither brains nor eyes yet existed. They evolved independently, on land and by sea. From the Cambrian explosion of sensing, body plans, and predation, minds evolved in response to other minds. It was an information revolution. It’s where experience begins.

The octopus brain rings around its throat. 500M neurons, similar to dog (vs. human: 86B, fly: 100K).

The octopus has over 50 different functional brain lobes (versus 4 in human)

And furthermore, 60% of its neurons are out in the arms, with a high degree of autonomy. A severed arm can carry on as if nothing has changed for several hours.

It is a distributed mesh of ganglia (knots of nerves) in a ladder-like nervous system. Recurrent neural loops serve as a local short-term memory latch.

“The octopus is suffused with nervousness; the body is not a separate thing that is controlled by the brain or nervous system.” Unconstrained by bone or shell, “the body itself is protean, all possibility. The octopus lives outside the usual body/brain divide.” (PGS)

Structurally, our eyes ended up strikingly similar to the octopus (camera-like with a focusing lens, through a transparent cornea and iris aperture to a retina backing the optic nerves). But octopus eyes have a wide-angle panoramic view, and they move independently like a chameleon.

Their horizontal slit pupil stays horizontal as the body moves, like a steady cam. This is made possible by special balance receptors called statocysts (a sac with internal sensory hairs and loose mineralized balls that roll around with movement and gravity).

They can see polarized light, but not color (making their color-matching camouflage skills all the more intriguing; they also see with their skin).

Their playful interactions with humans exhibit mischief and craft, a sign of mental surplus

Humans internalized language as a tool for complex thought (we can hear what we say and use language to arrange and manipulate ideas). Octopuses are on a different path.

Their entire skin is a layered screen, with about a megapixel directly controlled by the brain.

Skin color, pattern and fleshy texture can change in 0.7 seconds.

3 layers of skin cells control elastic sacks of pigments, internal iridescent reflections, even polarization (which the octopus can see), over a white underbody. They are regulated by acetylcholine, one of the earliest neurotransmitters in evolution.

The octopus can create a voluntary light show on its skin, e.g., a dark cloud passing over the local landscape, or a dramatic display to confuse a predator while fleeing.

30 ritualized displays for mating and other signaling.

Some octopuses have regions of constant kaleidoscopic restlessness, like animated eye shadow.

1600 suckers. 16 kg of lift capacity per sucker. 10k tasting chemoreceptors per sucker. Each is controlled individually.

Octopus muscles have radial + longitudinal fibers (agile like our tongues, not our biceps).

Opposing waves of activation can create temporary elbows at the region of constructive overlap, or pass food sucker-to-sucker like a conveyor belt.

The octopus’ arm muscles can pull 100x its own weight.

It can squeeze through a hole about the size of its eyeball.

Their ink squirts contain oxytocin (perhaps to soothe prey) and dopamine, the “reward hormone” (perhaps to trick predators that they had caught the octopus in the billowy cloud).

2022-02-17:

Soft-bodied cephalopods such as the octopus are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled mRNAs and small RNAs in 18 tissues of the common octopus. We show that the major RNA innovation of soft-bodied cephalopods is a massive expansion of the miRNA gene repertoire. These novel miRNAs were primarily expressed in neuronal tissues, during development, and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, strikingly, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.

Soil Microbiome

Bruns is using high-throughput sequencing, among other tools, to tease apart this “DNA soup” that is contained within soil. Her research on nitrogen-cycling microbes at the field scale fits into the bigger picture of reducing nutrient transport to coastal dead zones. “Overall, 50% of the nitrogen in fertilizer that’s applied to crops is not taken up by the crops. Instead it leaches to the groundwater or runs off in sediment. Much of that nitrogen eventually makes its way into the Gulf of Mexico and the Chesapeake Bay, where it upsets ecosystems. I’m interested in how we can stop this process at the source, how we can make our nitrogen application and management methods less wasteful.”

In silico labeling

The new deep-learning network can identify whether a cell is alive or dead, and get the answer right 98% of the time (humans can typically only identify a dead cell with 80% accuracy) — without requiring invasive fluorescent chemicals, which make it difficult to track tissues over time. The deep-learning network can also predict detailed features such as nuclei and cell type (such as neural or breast cancer tissue).