LUCA (Last Universal Common Ancestor)

[Write4U]

This is exciting news.

Have a peek a this video that ranges from the close estimate of LUCA (Last Universal Common Ancestor), to an AI assisted way of protein folding that seems to great promise. "The protein folding problem may have been solved"!, as reported by a researcher.

 

[Sarkus]

Please don't expect anyone to sit through a 15+ minute video when you're not prepared to at least explain what it is you're talking about, and the relevance it has to anything.

What is LUCA? Why is it important / of interest? Why is protein-folding of importance? What is the 'problem" to which you refer? What does the video suggest/conclude?

 

[exchemist]

Please don't expect anyone to sit through a 15+ minute video when you're not prepared to at least explain what it is you're talking about, and the relevance it has to anything.

What is LUCA? Why is it important / of interest? Why is protein-folding of importance? What is the 'problem" to which you refer? What does the video suggest/conclude?

LUCA is the Last Universal Common Ancestor, a hypothetical organism whose characteristics evolutionary biochemists can infer from modern biochemistry. It is effectively the most complex life form to appear before the various branches of life split from one another.

But I agree, I’m not watching a video that the poster can’t be bothered to at least summarise, to show why we should devote time to it.

 

[Write4U]

Did either of you read the title of the video. "2024's Biggest Breakthrough in Biology" .

It is a news video of several scientific breaktroughs that warranted one a 2024 Nobel prize, and you expect me to give you my analysis of the details? Please, I am not that ambitious.

These were researches conducted by respected research facilities
It caught my attention and I offered it in good faith, in hope of a more knowlegeable discussion by actual scientists. Give me a break.

Here is a copy of a synopsys by the authors of the video.

322,664 views Dec 18, 2024

We investigate three of 2024’s biggest breakthroughs in biology including new understanding of the common ancestor of all modern life, a surprising discovery about the connection between the brain and the immune system, and the ongoing impact of AI on the field of biology which led to the Nobel Prize in Chemistry for researchers working on protein structure prediction and protein design. Read about more breakthroughs from 2024 at Quanta Magazine: https://www.quantamagazine.org/the-ye...

00:05 Modern Life's Ancient AncestorAn interdisciplinary group applied the latest tricks of phylogenetics — using genes and genomes to build evolutionary trees — to trace all of modern life back to our shared ancestor.

This ancient cell, or population of cells, is known as LUCA, which stands for “last universal common ancestor,” the one from which everything alive today emerged. The work suggested that LUCA was a surprisingly complex cell and dated LUCA to some 4.2 billion years ago — earlier than researchers had thought.
https://www.quantamagazine.org/all-li...

04:50 Surprising Brain-Body ConnectionOne of the most mind-blowing discoveries of the year is about the integration of the brain and body.

Most immunologists have long assumed that the immune system is self-regulating. For the first time, researchers have found a neural circuit, located in the brainstem, that adjusts the immune system. This circuit senses inflammatory molecules in the body and then dials their levels up or down to protect healthy tissues
https://www.quantamagazine.org/the-br...

09:18 AI Transforms Protein Science

In 2024, hardly a week could go by without some big new paper related to Google DeepMind’s AlphaFold
2: a neural network that can accurately predict the three-dimensional structure of a folded protein from the one-dimensional string of its amino acid molecules In May, Google DeepMind released AlphaFold3, which predicts the shapes of proteins as they interact with other molecules. Then, in October, the Nobel Prize in Chemistry was awarded to John Jumper and Demis Hassabis from Google DeepMind, the creators of AlphaFold2, and David Baker from the University of Washington, who revolutionized the design of proteins using AI.
https://www.quantamagazine.org/how-ai...

Is that enough? Too much? What you expected? This is not about me. It is about science.

 

[TheVat]

Seems like each one would be a thread. LUCA is about cladistic analysis, if anyone is interested. 2024 was indeed a good year for furthering the reconstruction of the LUCA genome using cladistic analysis, suggesting a complex organism that likely lived around 4.2 billion years ago, with a genome size comparable to modern bacteria. There was a paper in "Nature Ecology and Evolution." The OP could post the abstract, if they want. It would be sorta like this:

Abstract​

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.



The interesting takeaway is that LUCA is now seen as part of an ecosystem - hence the need for an immune system.

 

[exchemist]

Seems like each one would be a thread. LUCA is about cladistic analysis, if anyone is interested. 2024 was indeed a good year for furthering the reconstruction of the LUCA genome using cladistic analysis, suggesting a complex organism that likely lived around 4.2 billion years ago, with a genome size comparable to modern bacteria. There was a paper in "Nature Ecology and Evolution." The OP could post the abstract, if they want. It would be sorta like this:

Abstract​

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.



The interesting takeaway is that LUCA is now seen as part of an ecosystem - hence the need for an immune system.

Ah, that’s better. Here’s a link to the whole paper: https://www.nature.com/articles/s41559-024-02461-1

So LUCA is thought to have been an anaerobic, acetogenic autotroph, possibly thermophilic, using CO2 and H2 to produce acetate and acetyl-CoA. They say there is no evidence of photosynthesis but that’s not surprising. Could be consistent with the thermal vent hypothesis. Also interesting to note its descendants may have incorporated by gene transfer genetic material from now dead, pre-LUCA branches of life.