Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)

[zorkan]

Yes but, how do expect those who believe in another version will find joy at that?
How does it explain zombies in the bible?
Remember that the dead rose from their graves.
That's what I call abiogenesis.

[Asmodean]

How does it explain zombies in the bible?

[mock-pseudointellectualism, for some reason with ze French accént]Ah, but you see that is a metaphor for the constituent elements of a human body being recycled back into the ecosystem upon death, thus giving rise to the new life, oui? Some call it reincarnation, some call it zombiefication, some call it the circle of life. [/French, etc]

[zorkan]

So which came first; zombies, xenomorphs, or xenozombies?

It's all in the bible, you know.
Ezekiel 37, 7-10:
7 So I prophesied as I was commanded. And as I was prophesying, there was a noise, a rattling sound, and the bones came together, bone to bone.
8 I looked, and tendons and flesh appeared on them and skin covered them, but there was no breath in them.
9 Then he said to me, "Prophesy to the breath; prophesy, son of man, and say to it, 'This is what the Sovereign LORD says: Come, breath, from the four winds and breathe into these slain, that they may live.' "
10 So I prophesied as he commanded me, and breath entered them; they came to life and stood up on their feet—a vast army.

[Asmodean]

Well, xenozombies are just foreign zombies, so no particular chicken-and-eggs there. Xenomorphs... Being parasitic, they had to arise after other life forms, so if those life forms were subject to zombiefication, then xenomorphs arose after zombies.

Hmm... Yes. Yes, first, there were vast zombie hordes, and then there was a chainsaw massacre.

...Then xenomorphs and them pesky foreign zombies, stealing graves from the natives and mooching off the richness of their soil.

[Recusant]

Good stuff. 

I freely admit that rainwater possibly enabling the formation of the first protocells via interacting with coacervate droplets is less colorful. 

"Rain may have helped form the first cells, kick-starting life as we know it" | The Conversation

Billions of years of evolution have made modern cells incredibly complex. Inside cells are small compartments called organelles that perform specific functions essential for the cell's survival and operation. For instance, the nucleus stores genetic material, and mitochondria produce energy.

Another essential part of a cell is the membrane that encloses it. Proteins embedded on the surface of the membrane control the movement of substances in and out of the cell. This sophisticated membrane structure allowed for the complexity of life as we know it. But how did the earliest, simplest cells hold it all together before elaborate membrane structures evolved?

In our recently published research in the journal Science Advances, my colleagues from the University of Chicago and the University of Houston and I explored a fascinating possibility that rainwater played a crucial role in stabilizing early cells, paving the way for life's complexity.

[Continues--essentially, rainwater is deionized which promotes the formation of a possible precursor of the cell membrane.]

The paper is open access:

"Did the exposure of coacervate droplets to rain make them the first stable protocells?" | Science Advances

Abstract:

Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs.

In this study, we show that distilled water, mimicking rain/freshwater, leads to the formation of electrostatic crosslinks on the interface of coacervate droplets that not only suppress droplet fusion indefinitely but also allow the spatiotemporal compartmentalization of RNA on a timescale of days depending on the length and structure of RNA.

We suggest that these nonfusing membraneless droplets could potentially act as protocells with the capacity to evolve compartmentalized ribozymes in prebiotic environments.

[zorkan]

Being parasitic, they had to arise after other life forms, so if those life forms were subject to zombiefication, then xenomorphs arose after zombies.

Really, how do you know that?

My source is the Book Of Zorka.
"Life arose by Zombiefication". (Chapter 1, In the Beginning).
This is not unlike the first verses of Chapter 1 of The Book of Jasher, which didn't make it into the bible.

https://sacred-texts.com/chr/apo/jasher/1.htm

Note also: "Only the dead will inherit the earth." (Chapter 4, End of Days).

[Asmodean]

Ah, but your blasphemously-unholy Not-The-Gray-Tome of a book is wrong.

You can't zombiefy a undead or a alive. Zombiefication only works properly on the recently-deceased. thus, you need something to die, in the sense of no longer live, for the T-virus to then at the moment of death take over its soon-to-be-rotting corpse, grow a bunch of appendages with eyes on it and have Leon S. Kennedy shoot it with a gun. That's how it is, because that's how the Gray Tome sayeth it is.

[zorkan]

I think you'll find the Gray Tome is wrong and the Book of Zorka is right.

[Recusant]

This isn't panspermia per se, and we already knew there are some amino acids in space, but peptides forming in space is something new I think. 

"Life's chemistry may begin in the cold darkness of space" | Science Daily

Scientists at Aarhus University have overturned a long-standing assumption about how life's essential ingredients emerge. New experiments show that the basic components needed to build proteins can form naturally in space, a finding that increases the likelihood that life could exist elsewhere in the universe.

Peptides are short chains made when individual amino acids link together. When many peptides bond, they form proteins, which are essential for life as we know it. Identifying where and how these protein precursors originate is a key step in understanding how life might begin.

To test this process, the researchers placed glycine inside the chamber and exposed it to simulated cosmic rays using an ion accelerator at HUN-REN Atomki. They then analyzed the chemical reactions that followed.

"We saw that the glycine molecules started reacting with each other to form peptides and water. This indicates that the same process occurs in interstellar space," Alfred Thomas Hopkinson says. "This is a step toward proteins being created on dust particles, the same materials that later form rocky planets."

The research was carried out at advanced laboratories at Aarhus University and at a European research facility in Hungary (HUN-REN Atomki). The experiments were led by researchers Sergio Ioppolo and Alfred Thomas Hopkinson.

Inside a specially designed chamber, the researchers recreated the harsh environment found in vast clouds of cosmic dust located thousands of light-years from Earth. These regions are among the coldest and emptiest places in the universe.

Temperatures in such dust clouds reach about -260°C, and pressure is so low that researchers must constantly remove stray gas particles to maintain an ultra-high vacuum. Under these carefully controlled conditions, the team studied how particles behave when exposed to radiation, closely matching what happens in real interstellar space.

"We already know from earlier experiments that simple amino acids, like glycine, form in interstellar space. But we were interested in discovering if more complex molecules, like peptides, form naturally on the surface of dust grains before those take part in the formation of stars and planets," Sergio Ioppolo says.

[Continues . . .]

The paper is behind a paywall.

Abstract:

The origin of the molecular building blocks of life is a central question in science. A few α-amino acids, such as glycine, the simplest proteinogenic amino acid, have been detected in meteorites and comets, indicating an extraterrestrial origin for some prebiotic molecules. However, the formation of peptides, short chains of α-amino acids linked by peptide bonds, has remained unresolved under astrophysical conditions.

Here we show that the building blocks of proteins can form in interstellar ice analogues exposed to ionizing radiation without the presence of liquid water. Using isotopically labelled glycine irradiated with protons at cryogenic temperatures, we detect the formation of glycylglycine, the simplest dipeptide, along with deuterated and undeuterated water as by-products. The formation of peptide bonds is confirmed by infrared spectroscopy and high-resolution mass spectrometry, which also reveal the production of other complex organic species.

These findings demonstrate a non-aqueous route to peptide formation under space-like conditions and suggest that such molecules could form in the cold interstellar medium and be incorporated into forming planetary systems. Our results challenge aqueous-centric models of early biochemical evolution and broaden potential settings for the origins of life.

[Recusant]

Enter SpudCell, not a true living cell yet, but something that demonstrates several of the characteristics of living cells. They better cut it out or YHVH is going to be upset. On the other hand, maybe all they need to do is pray over it a bit and YHVH will deign to endow their experiment with that divine spark. 

"For The First Time, Scientists Say They've Built a Synthetic Cell From Scratch" | ScienceAlert

Scientists from the University of Minnesota say they have created the first-ever synthetic cell built entirely from scratch, and seen it go through an entire 'life' cycle – including reproduction.

"This is the most fascinating and important thing I've ever done in my work, and the realization that it's actually happening was rather slow to sink in," synthetic biologist Kate Adamala, a co-lead on the project told ScienceAlert.

"We've replicated in chemistry what only used to be possible in biology: the complete set of behaviors of a cell. It proves that the most fundamental functions of life, like growth and replication, do not need a mysterious magical spark," she says.

The project is called SpudCell, and it has a genome of just 90 kilobase pairs (kbp). For comparison, the human genome is about 3 million kpb, and biologists previously assumed that a living cell would require at least 113 kpb of genetic data to function properly.

According to Adamala and her colleagues, SpudCell appears to stretch these limits, though their research is yet to be formally published and has not been peer-reviewed.

[Continues . . .]

A preprint (not yet peer reviewed) version of the paper is available:

"A Chemically Defined Synthetic Cell Capable Of Growth And Replication" | bioR_xiv

Abstract:

Cells are the fundamental unit of life. Yet there is no natural cell for which all its life-essential functions are understood.

Here we demonstrate a complete cell cycle for a synthetic cell undergoing selection, with genome replication, growth, resource acquisition via feeding, and genetically encoded division. The cell is encoded via a 90kb genome that includes functions needed for resource uptake, transcription, translation, growth, genome replication, and division.

The resulting synthetic cell is sufficiently encouraging to support routinization of synthetic cell engineering workflows, and will ultimately underlie diverse applications across all of biotechnology.

[Recusant]

Twice for good luck.

"'Only One Conclusion': Radical Study Suggests Life on Earth Arose Twice" | Science Alert

The fact that you, or I, or any living creature, is here at all is a series of astonishing strokes of luck stretching back more than 4 billion years.

One of the biggest hurdles was the very first one: How did life emerge from a primordial soup of stuff that very much wasn't alive?

A radical new study, published in Science Advances, suggests that this unlikely threshold may actually have been crossed not once, but twice.

Two of the main lineages of life – bacteria and archaea – may have independently figured out the secrets of metabolism that upgraded them from non-living to living, according to the new study, which focused on the most rudimentary set of chemical reactions thought to enable this transformation.

"The surprise is that the enzymes that catalyze those reactions are not conserved across the evolutionary divide that separates bacteria and archaea," says William Martin, a biologist at Heinrich Heine University Düsseldorf in Germany.

Generally speaking, life is considered matter that responds to its environment, takes in energy, grows, and reproduces itself.

That sounds like it should cover the basics, but even that broad a statement is imperfect. After all, viruses can do most of those, but aren't traditionally considered 'alive'.

One aspect of life that is universal – and which viruses lack – is metabolism, the collection of chemical reactions that organisms use to make molecules that are vital for their everyday functioning.

Enzymes are the workhorse proteins that act as catalysts for these reactions in organisms, but that raises a weird chicken-and-egg question.

Enzymes themselves are products of chemical reactions – so how did the first lifeforms begin metabolizing things, including making enzymes, without the help of other enzymes?

The answer, it seems, lies in their surroundings.

[. . .]

The researchers investigated the protein structures of core metabolic enzymes in the genomes of bacteria and archaea, and developed a method and algorithm to order them in complexity. From there, they could determine which ones evolved in which order, and put together a rough timeline.

"We found that the last universal ancestor of all cells, LUCA, possessed enzymes for only about half of the reactions of metabolism," says Martin.

"The other half was catalyzed by metals in the environment where LUCA arose."

The team found that there were likely four different phases in the development of catalysis (enzyme-driven reactions). The first relied solely on metals in the environment.

Once enough of the useful molecules built up, the not-quite-living-yet proto-cells (which included LUCA) could start developing their own enzymes that performed some of the functions of those metal catalysts.

Over time, later proto-cells developed more and more enzymes, reducing their dependency on external metals, until they no longer needed them at all. Only at that point would they be considered 'free-living cells'.

Importantly, the researchers say, this didn't occur until after bacteria and archaea had separated. These two branches figured out their own ways to tackle the same problems.

"We can see cases where the ancestors of bacteria and archaea independently evolved structurally distinct enzymes to catalyze the same essential metabolic reaction," says Natalia Mrnjavac, a biologist at Heinrich Heine University Düsseldorf.

"Such parallel inventions could have paved the way to the independent emergence of free-living bacteria and archaea."

[Continues . . .]

The paper is open access:

"Intermediate stages in the origin of metabolism at a phosphorylating hydrothermal vent" | Science Advances

Abstract:

The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides, and cofactors. At the origin of metabolism, there were no enzymes—how did it start? Empirical studies addressing early metabolic evolution are lacking.

Harnessing protein structures for metabolic enzymes, we identify intermediate states in primordial metabolic assembly. We show that enzymatic metabolism in the universal common ancestor was incomplete, undergoing final assembly independently in the lineages leading to bacteria and archaea.

Native transition metals—iron, cobalt, nickel, and palladium—served as the catalytic forerunners of both enzymes and cofactors at metabolic origin, while phosphite supplied energy, as it phosphorylates adenosine 5′-monophosphate to adenosine 5′-diphosphate and serine to phosphoserine using native metal catalysts in water.

Phosphite and native metals occur in serpentinizing hydrothermal systems, identifying an energy-supplying, catalytic site of metabolic origin. Cofactors liberated nascent metabolism from native metal catalysts, engendering its autocatalytic state.