Tag: evolution

Multicellular Emergence

Environments favoring clumpy growth are all that’s needed to quickly transform single-celled yeast into complex multicellular organisms.

During the first 100 days, the clusters in all 15 of the tubes 2x in size. Then they mostly plateaued until the 250th day, when the sizes in 2 of the tubes that didn’t use oxygen started to creep upward again. Around day 350, Bozdağ noticed something in 1 of those tubes. There were clusters he could see with the naked eye. “As an evolutionary biologist … you think it’s a chance event. Somehow they got big, but they are going to lose out against the small ones in the long run — that is my thinking. I didn’t really talk about this with Will at the time.” But then clusters showed up in the 2nd tube. And around day 400, the 3 other tubes of mutants that couldn’t use oxygen kicked into gear, and soon all 5 tubes had massive structures in them, topping out at about 20000X their initial size. “I wasn’t honestly sure if this was a system that would saturate at 1000 cells. We have to continue evolving them and see what they can do. We need to see, if we push these guys as far as we can for decades, for 10000s of generations. If we don’t do that, I will always regret not having taken the opportunity. It’s a once-in-a-lifetime opportunity, to try to push a nascent multicellular critter to become more complex and see how far we can take them.”


2022-11-05: Multicellularity has metabolic benefits

the hollow spheres were Vibrio’s solution to the complicated challenge of eating at sea. An individual bacterium can produce only so much enzyme; breaking down alginate goes much more quickly when Vibrio can cluster together. It’s a winning strategy — up to a point. If there are too many Vibrio, the number of bacteria outstrips the available alginate.

The bacteria resolved the conundrum by developing a more complex life cycle. The bacteria live in 3 distinct phases. At first, an individual cell divides repeatedly and the daughter cells huddle in growing clumps. In the second phase, the clumped cells rearrange themselves into a hollow sphere. The outermost cells glue themselves together, forming something rather like a microscopic snow globe. The cells inside become more mobile, swimming about as they consume the trapped alginate. In the third phase, the brittle outer layer ruptures, releasing the well-fed inner cells to start the cycle anew.
By altering their life cycle to include a multicellular stage, the bacteria can digest the alginate efficiently: Their numbers increase, and the hollow shell helps to concentrate the enzymes. Meanwhile, the structure of the community prevents too many cells from being born. The cells in the shell lose the opportunity to reproduce, but their DNA lives on in the next generation anyway, since all the cells in the orb are clones.

Cockatoo Culture

Even when residents in these areas weigh down the tops of their bins with bricks or stones, cockatoos have figured out how to knock these heavy objects to the ground. Once that barrier is removed, the hungry birds can crack the lid open with their beak, prop it on their heads and walk it back until it fully flips on its hinges, as the videos show below. This unique skill has now become so widespread in Sydney, researchers think the parrots are imitating and learning from one another – a sign of cultural evolution.

To throw is Human

300 ka ago, H. sapiens might have been very proficient at using thrown weapons. Humans are so good at throwing because our body stores energy in our shoulders. But based on the results of experiments with athletes, as well as studies of fossil and modern skeletal measures, the capacity for high-speed throwing was already present in H. erectus—placing humanity’s particular talent for pitching all the way back to 2 ma ago.

The Human Family Tree

Our planet was very different 100 ka ago, and if we could survey that time, we would be astounded by the human diversity across its surface. To enumerate what little we know with certainty, there were at a minimum: modern humans, Neanderthals, at least 3-4 varieties of Denisovans, and 2 pygmy Homo populations in Southeast Asia. Likely there were still remnant Homo erectus in Southeast Asia as well, and other diverged lineages within Africa, and a new Homo in Nesher Ramla, Israel, in the Middle East with affinities to Neanderthals.


2023-02-04: More evidence of a much more distributed situation

“Cognitive revolutions”—such as the widespread shift some 300 ka BP from clunky, handheld stone tools to more refined blades and projectile points—were probably instances of different populations with distinctive cultural and biological features coming together and recombining their genes and ideas.

This mosaic evolution would explain certain seemingly unexplainable findings. For example, researchers found human fossils in the Democratic Republic of Congo that dated to 22 ka BP but physically resembled people living 300 ka BP. In Senegal, scientists uncovered 12 ka BP stone toolkits that could easily be transplanted to a situation 100 ka BP.

These finds probably resulted from periods of isolation where different populations in different parts of the continent each developed distinctive cultural and physical adaptations to their local environments. At the same time, instances of connectivity allowed different populations to acquire beneficial traits, behaviors, and technologies from one another, becoming better adapted and more flexible.

New variants

Many virologists thought this very unlikely, you could never know that a new variety had higher transmission from mere incidence data: you must understand the biological mechanism. Are they correct? Obviously not.

Why did they think that a new, more transmissible variant of COVID-19 was unlikely? There are several reasons. One, they typically deal with viruses that have been around for a long time, like measles ( > 1000 years). An old virus is going to be pretty well-adapted to to humans. Probably it’s at a local optimum, where small changes would reduce infectivity. But you don’t expect that high degree of optimization in a virus that’s brand new in humans: while spreading to very many people, more than 100M, greatly increases the chance of transmission-increasing mutations. Fisherian acceleration.

Like most biologists and MDs, most virologists don’t know any theory, and in fact don’t _believe_ in theory. For this they occasionally pay a price.

Immune System Arms Race

The challenge for the immune system is that mammals do not evolve as fast as viruses. How then, in the face of this disadvantage, can the immune system hope to keep pace with viral evolution? If a protein is fragile, even small changes can render it completely unable to do its job. TRIM5α is not fragile; most random mutations increased, rather than decreased, the protein’s ability to prevent viral infection. TRIM5α can readily gain antiviral activity and, once gained, does not lose it easily during subsequent mutation.

2022-12-02: And new infections can be filmed

The early stages of the virus–cell interaction have long evaded observation by existing microscopy methods due to the rapid diffusion of virions in the extracellular space and the large 3D cellular structures involved. We present an active-feedback single-particle tracking method with simultaneous volumetric imaging of the live cell environment called 3D-TrIm to address this knowledge gap. 3D-TrIm captures the extracellular phase of the infectious cycle in what we believe is unprecedented detail. We report previously unobserved phenomena in the early stages of the virus–cell interaction, including skimming contact events at the millisecond timescale, orders of magnitude change in diffusion coefficient upon binding and cylindrical and linear diffusion modes along cellular protrusions. We demonstrate how this method can move single-particle tracking from simple monolayer culture toward more tissue-like conditions by tracking single virions in tightly packed epithelial cells. This multiresolution method presents opportunities for capturing fast, 3D processes in biological systems.

Essential gene evolution

Essential genes are often thought to be frozen in evolutionary time — evolving only very slowly if at all, because changing or dying would lead to the death of the organism. 100s of millions of years of evolution separate insects and mammals, but experiments show that the Hox genes guiding the development of the body plans in Drosophila fruit flies and mice can be swapped without a hitch because they are so similar. This remarkable evolutionary conservation is a foundational concept in genome research.

But a new study turns this rationale for genetic conservation on its head. Researchers at the Fred Hutchinson Cancer Research Center in Seattle reported last week in eLife that a large class of genes in fruit flies are both essential for survival and evolving extremely rapidly. In fact, the scientists’ analysis suggests that the genes’ ability to keep changing is the key to their essential nature. “Not only is this questioning the dogma, it is blowing the dogma out of the water

TCA cycle origins

Instead of trying to find the precursor to the TCA cycle by swapping in simpler versions of its components, they started by asking what versatile reactants might have been present in the prebiotic world and then looked at how much they could do under various circumstances. Astonishingly, they found that the glyoxylate and pyruvate reacted to make a range of compounds that included chemical analogues to all the intermediary products in the TCA cycle except for citric acid. Comparatively, the chemistry we discovered here was a dream to run: All you really needed to do to get the pathway started was to drop 2 stable reactants into buffered water and stick it on a warm hotplate. The chemistry was extremely robust.

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.