LUCA (Last Universal Common Ancestor)

Write4U

Valued Senior Member
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.

 
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?
 
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.
 
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.
 
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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.
 
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.
 
Here seems as good as place as any to post this.

The biggest questions in Biology involve abiogenesis - life from non life and how did we get the first cell.

One stepping stone was the acquisition of cell organelles via prokaryotes and how they evolve with the cell including reproductive independence.

Cell organelles rely on the cell, endosymbionts have independence this paper features Angomonas deanei

"A. deanei represents an intermediate stage between an endosymbiotic bacterium—which is still genetically autonomous—and an organelle, which is almost entirely controlled by the host cell. The endosymbiont has lost genes, which are essential for its autonomous survival. Genes in the nucleus of the host cell have now replaced their functions."

The article


The full paper

 
Then this may fit nicely.

Quantum mechanical biology

Moscow State University of M.V.Lomonosov, VMK Faculty
,
Chair of supercomputers and quantum informatics January 21, 2015

Abstract
This article focuses on the approach to biology in terms of quantum mechanics. Quantum biology is a hypothesis that allows experimental verification, and pretends to be a further refinement of the known gene-centric model. The state of the species is represented as the state vector in the Hilbert space, so that the evolution of this vector is described by means of quantum mechanics.
Experimental verification of this hypothesis is based on the accuracy of quantum theory and the ability to quickly gather statistics when working with populations of bacteria. The positive result of such experiment would allow to apply to the living computational methods of quantum theory, which has not yet go beyond the particular ”quantum effects”.
1 Introduction
The main difficulty of biology is that we ourselves are its object. It seems that this loop will not allow biology to become a branch of physics even in perspective. Accumulated and continue to accumulate huge size data on ”what happens in a living being”, but there is no coherent theory to explain ”why this is happening”(see, for example, computer models in [6]). The real explanation must give us the opportunity to build a plausible model of life as we build a model of the processes in inanimate nature, described by differential equations.
Plausibility here we understand according to Turing: if we can not by external signs distinguish the model from a live prototype. Of course, it is not a simulation like android robots, but a model of life with reproduction and evolution, moreover, such a model, which would naturally fit into conventional physical models of nonliving environment of biological objects. Attempts to build such a model are reduced, ultimately, to a good systematization of knowledge about ”how things work”, but their predictive power is small
more.... https://www.academia.edu/61589196/Quantum_Mechanical_Biology?email_work_card=view-paper
 
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The biggest questions in Biology involve abiogenesis - life from non life and how did we get the first cell.
Isn't it a simple question of dynamics? What's the difference between dynamic chemistry and dynamic bio-chemistry? We call it life but not because it displays dynamic properties. Some self-repeating chemistry is plenty dynamic enough to represent as a life form.
Crystal growth is but one example.

The mystery appears when we observe the apparent emergence of "voluntary response" (and habituation) in bio-chemical systems such as the Mimosa Pudica, rather than "brute reaction" that appears in purely chemical systems, such as the continuous cycle of ozone depletion by CFC.
 
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Here seems as good as place as any to post this.

The biggest questions in Biology involve abiogenesis - life from non life and how did we get the first cell.

One stepping stone was the acquisition of cell organelles via prokaryotes and how they evolve with the cell including reproductive independence.

Cell organelles rely on the cell, endosymbionts have independence this paper features Angomonas deanei

"A. deanei represents an intermediate stage between an endosymbiotic bacterium—which is still genetically autonomous—and an organelle, which is almost entirely controlled by the host cell. The endosymbiont has lost genes, which are essential for its autonomous survival. Genes in the nucleus of the host cell have now replaced their functions."

The article


The full paper

That's very interesting. I was aware that the mitochondrion was thought to be the result of an endosymbiont. Are there other organelles now thought also to be due to an ancestral endosymbiont? Which ones would these be?

Interesting too that it is the genes controlling cell division that have atrophied. Makes sense of course, but one wonders what would cause that to happen, esp. if it is thought to have occurred repeatedly, with a whole series of different one-time endosymbionts to form different organelles.
 
Then this may fit nicely.

Quantum mechanical biology

Moscow State University of M.V.Lomonosov, VMK Faculty
,
Chair of supercomputers and quantum informatics January 21, 2015

Abstract


1 Introduction

The main difficulty of biology is that we ourselves are its object. It seems that this loop will not allow biology to become a branch of physics even in perspective. Accumulated and continue to accumulate huge size data on ”what happens in a living being”, but there is no coherent theory to explain ”why this is happening”(see, for example, computer models in [6]). The real explanation must give us the opportunity to build a plausible model of life as we build a model of the processes in inanimate nature, described by differential equations.

more.... https://www.academia.edu/61589196/Quantum_Mechanical_Biology?email_work_card=view-paper
This paper is from the crank publisher Academia.edu, where Reiku posts his nonsense and has nothing to do with the topic. It seems to be an attempt to use quantum mechanical methods to model the evolution of a population of organisms. However the translation is so bad it hard to tell. The author, "Yuri Oshigov" appears to have no internet presence, though there is an eminent Russian mathematics don called Yury Osipov. I wonder if this is a crank trying to pass himself off as that guy.

Anyway irrelevant, so we can forget it.
 
Anyway irrelevant, so we can forget it.

Moscow State University of M.V.Lomonosov, VMK Faculty,
Chair of supercomputers and quantum informatics,
January 21, 2015

Happens to be my birthday.

Aside from credentials, what does the paper propose that cannot be true, is irrelevant, and must be forgotten?

p.s. is the table of elements part of our Universal Common Ancestry? Where does common ancestry begin? We are talking about abiogenesis, no?

Ancestor: a plant, animal, or object that is related to one existing at a later point in time:
 
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Makes sense of course, but one wonders what would cause that to happen, esp. if it is thought to have occurred repeatedly
The biggest questions.
For instance, what did the cell do for energy before the mitochondria came along? It is thought to belong to the family Rickettsiaceae that cause some pretty nasty diseases today.

Besides cell organelles there is DNA that has a life of its own, plasmids. I encountered these at University early on and this illustrates just how messy Biology is, they break the rules.
Gene transfer between cells with no cellular reproduction, lateral gene transfer. How on earth did that evolve?
I did not get answers on that in the 1980s so things would have changed.
This is what gets my goat with Creationist posters when they cite the cell as the perfect, intricate creation.
Which cell? When? If it was perfect why did it add genes? Add a mitochondria?
 
No this about cellular evolution.
And how did the first prokaryote cell evolve without an ancestral connection to mineral interactons?

7.3: Evolutionary History of Prokaryotes​

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Table of contents
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

more....https://bio.libretexts.org/Courses/Lumen_Learning/Biology_for_Majors_II_(Lumen)/07%3A_Module_4-_Prokaryotes/7.03%3A_Evolutionary_History_of_Prokaryotes

We know how an Eukaryote cell evolved via surface tension caused by affinity.

3.4: Eukaryotic Origins​

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  • OpenStax
  • OpenStax
The fossil record and genetic evidence suggest that prokaryotic cells were the first organisms on Earth. These cells originated approximately 3.5 billion years ago, which was about 1 billion years after Earth’s formation, and were the only life forms on the planet until eukaryotic cells emerged approximately 2.1 billion years ago. During the prokaryotic reign, photosynthetic prokaryotes evolved that were capable of applying the energy from sunlight to synthesize organic materials (like carbohydrates) from carbon dioxide and an electron source (such as hydrogen, hydrogen sulfide, or water).
Photosynthesis using water as an electron donor consumes carbon dioxide and releases molecular oxygen (O2) as a byproduct. The functioning of photosynthetic bacteria over millions of years progressively saturated Earth’s water with oxygen and then oxygenated the atmosphere, which previously contained much greater concentrations of carbon dioxide and much lower concentrations of oxygen. Older anaerobic prokaryotes of the era could not function in their new, aerobic environment. Some species perished, while others survived in the remaining anaerobic environments left on Earth. Still other early prokaryotes evolved mechanisms, such as aerobic respiration, to exploit the oxygenated atmosphere by using oxygen to store energy contained within organic molecules. Aerobic respiration is a more efficient way of obtaining energy from organic molecules, which contributed to the success of these species (as evidenced by the number and diversity of aerobic organisms living on Earth today). The evolution of aerobic prokaryotes was an important step toward the evolution of the first eukaryote, but several other distinguishing features had to evolve as well.

Endosymbiosis​

The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined in the 1960s by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic cell engulfing another, one living within another, and evolving together over time until the separate cells were no longer recognizable as such. This once-revolutionary hypothesis had immediate persuasiveness and is now widely accepted, with work progressing on uncovering the steps involved in this evolutionary process as well as the key players. It has become clear that many nuclear eukaryotic genes and the molecular machinery responsible for replicating and expressing those genes appear closely related to the Archaea. On the other hand, the metabolic organelles and the genes responsible for many energy-harvesting processes had their origins in bacteria. Much remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. Several endosymbiotic events likely contributed to the origin of the eukaryotic cell.

Mitochondria​

Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 micrometers in length and exists in the cell as a moving, fusing, and dividing oblong spheroid (Figure 3.4.13.4.1). However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell engulfed and kept alive a free-living, aerobic prokaryote. This gave the host cell the ability to use oxygen to release energy stored in nutrients. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Mitochondria are shaped like a specific group of bacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed by another membrane-bound organism. The mitochondrial inner membrane involves substantial infoldings or cristae that resemble the textured outer surface of certain bacteria.

more...https://bio.libretexts.org/Courses/Cosumnes_River_College/Contemporary_Biology_(Aptekar)/03%3A_Cell_Structure_and_Function/3.04%3A_Eukaryotic_Origins#:~:text=The%20first%20eukaryotes%20evolved%20from%20ancestral%20prokaryotes%20by,cytoskeleton%2C%20and%20the%20acquisition%20and%20evolution%20of%20organelles.

and

We May Finally Know How The First Cells on Earth Formed​

NATURE04 March 2024
ByDAVID NIELD
Replicating conditions likely to match Earth's early days in the lab, the team combined chemicals such as fatty acids and glycerol to try and create more complex vesicles – bubble-like structures similar to protocells that facilitate cellular processes.
With some tweaking of temperature and acidity, the researchers were able to get the chemical reactions they were looking for, proving that phosphorylation may have been at work as protocells developed in the primordial ooze.

"The vesicles were able to transition from a fatty acid environment to a phospholipid environment during our experiments, suggesting a similar chemical environment could have existed four billion years ago," says chemist Sunil Pulletikurti, from The Scripps Research Institute.

 

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And how did the first prokaryote cell evolve without an ancestral connection to mineral interactons?

7.3: Evolutionary History of Prokaryotes​

  1. picture_as_pdf
    Downloads
    Buy Print CopySubmit Adoption ReportPeer ReviewDonate

Table of contents
Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle nutrients—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

more....https://bio.libretexts.org/Courses/Lumen_Learning/Biology_for_Majors_II_(Lumen)/07%3A_Module_4-_Prokaryotes/7.03%3A_Evolutionary_History_of_Prokaryotes

We know how an Eukaryote cell evolved via surface tension caused by affinity.

3.4: Eukaryotic Origins​

  1. CCBYNCSA
  2. picture_as_pdf
    Downloads
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With some tweaking of temperature and acidity, the researchers were able to get the chemical reactions they were looking for, proving that phosphorylation may have been at work as protocells developed in the primordial ooze.

"The vesicles were able to transition from a fatty acid environment to a phospholipid environment during our experiments, suggesting a similar chemical environment could have existed four billion years ago," says chemist Sunil Pulletikurti, from The Scripps Research Institute.

Reported as off-topic.
 
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