Author Topic: Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)  (Read 5516 times)

Recusant

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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #15 on: September 14, 2018, 08:50:05 PM »
The sword ("it's just a theory!") and shield ("were you there?") of Creationism will stand those who wield them in good stead when it comes to dealing with this. It's merely a computer model, and all that's being claimed is that a particular peptide may have been part of the formation of life on Earth. No matter--knowledge continues to advance.

"Scientists identify protein that may have existed when life began" | ScienceDaily

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How did life arise on Earth? Rutgers researchers have found among the first and perhaps only hard evidence that simple protein catalysts -- essential for cells, the building blocks of life, to function -- may have existed when life began.

Their study of a primordial peptide, or short protein, is published in the Journal of the American Chemical Society.

In the late 1980s and early 1990s, the chemist Günter Wächtershäuser postulated that life began on iron- and sulfur-containing rocks in the ocean. Wächtershäuser and others predicted that short peptides would have bound metals and served as catalysts of life-producing chemistry, according to study co-author Vikas Nanda, an associate professor at Rutgers' Robert Wood Johnson Medical School.

Human DNA consists of genes that code for proteins that are a few hundred to a few thousand amino acids long. These complex proteins -- needed to make all living-things function properly -- are the result of billions of years of evolution. When life began, proteins were likely much simpler, perhaps just 10 to 20 amino acids long. With computer modeling, Rutgers scientists have been exploring what early peptides may have looked like and their possible chemical functions, according to Nanda.

[Continues . . .]
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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #16 on: October 21, 2018, 05:50:54 PM »
"But you weren't there!"

"Chemists find a recipe that may have jump-started life on Earth" | Science

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In the molecular dance that gave birth to life on Earth, RNA appears to be a central player. But the origins of the molecule, which can store genetic information as DNA does and speed chemical reactions as proteins do, remain a mystery. Now, a team of researchers has shown for the first time that a set of simple starting materials, which were likely present on early Earth, can produce all four of RNA’s chemical building blocks.

Those building blocks—cytosine, uracil, adenine, and guanine—have previously been re-created in the lab from other starting materials. In 2009, chemists led by John Sutherland at the University of Cambridge in the United Kingdom devised a set of five compounds likely present on early Earth that could give rise to cytosine and uracil, collectively known as pyrimidines. Then, 2 years ago, researchers led by Thomas Carell, a chemist at Ludwig Maximilian University in Munich, Germany, reported that his team had an equally easy way to form adenine and guanine, the building blocks known as purines. But the two sets of chemical reactions were different. No one knew how the conditions for making both pairs of building blocks could have occurred in the same place at the same time.

Now, Carell says he may have the answer. On Tuesday, at the Origins of Life Workshop here, he reported that he and his colleagues have come up with a simple set of reactions that could have given rise to all four RNA bases.

[Continues . . .]
"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
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Tank

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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #17 on: October 21, 2018, 06:37:20 PM »
Interesting as usual.
If religions were TV channels atheism is turning the TV off.
“Religion is a culture of faith; science is a culture of doubt.” ― Richard P. Feynman
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Recusant

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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #18 on: February 12, 2019, 09:12:14 PM »
Further research on the possible routes by which life first formed.

"Membraneless protocells could provide clues to formation of early life" | ScienceDaily

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Membraneless assemblies of positively- and negatively-charged molecules can bring together RNA molecules in dense liquid droplets, allowing the RNAs to participate in fundamental chemical reactions. These assemblies, called "complex coacervates," also enhance the ability of some RNA molecules themselves to act as enzymes -- molecules that drive chemical reactions. They do this by concentrating the RNA enzymes, their substrates, and other molecules required for the reaction. The results of testing and observation of these coacervates provide clues to reconstructing some of the early steps required for the origin of life on Earth in what is referred to as the prebiotic "RNA world." A paper describing the research, by scientists at Penn State, appears January 30, 2019 in the journal Nature Communications.

"We're interested in how you go from a world with no life to one with life," said Philip C. Bevilacqua, Distinguished Professor of Chemistry and of Biochemistry and Molecular Biology at Penn State and one of the senior authors of the paper. "One can imagine a lot of steps in this process, but we are not looking at the most elemental steps. We are interested in a slightly later step, to see how RNA molecules could form from their basic building blocks and if those RNA molecules could drive the reactions needed for life in the absence of proteins."

[. . .]

"It was previously known that RNA molecules can assemble and elongate in solutions with high concentrations of magnesium," said Poudyal. "Our work shows that coacervates made from certain materials allow this non-enzymatic template-mediated RNA assembly to occur even in the absence of magnesium."

The coacervates are composed of positively charged molecules called polyamines and negatively charged polymers which cluster together to form membraneless compartments in a solution. Negatively charged RNA molecules are also attracted to the polyamines in the coacervates. Within the coacervates the RNA molecules are as much as 4000 times more concentrated than in the surrounding solution. By concentrating the RNA molecules in the coacervates, RNA enzymes are more likely to find their targets to drive chemical reactions.

[Continues. . .]

The full paper is available for free: "Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates" | Nature Communications
"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #19 on: February 13, 2019, 07:31:32 PM »
That must have been an amazingly exciting moment.
Hell is empty and all the devils are here. Wm Shakespeare


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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #20 on: April 03, 2019, 02:48:26 AM »
Maybe it was not just an RNA world.

"Building blocks of DNA and RNA could have appeared together before life began on Earth" | ScienceDaily


Quote
Scientists for the first time have found strong evidence that RNA and DNA could have arisen from the same set of precursor molecules even before life evolved on Earth about four billion years ago.

The discovery, published April 1 in Nature Chemistry, suggests that the first living things on Earth may have used both RNA and DNA, as all cell-based life forms do now. In contrast, the prevailing scientific view -- the "RNA World" hypothesis -- is that early life forms were based purely on RNA, and only later evolved to make and use DNA.

"These new findings suggest that it may not be reasonable for chemists to be so heavily guided by the RNA World hypothesis in investigating the origins of life on Earth," says co-principal investigator Ramanarayanan Krishnamurthy, PhD, associate professor of chemistry at Scripps Research.

[. . .]

RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) are chemically very similar, but chemists have never been able to show how the one could have been converted to the other on the early Earth, except with the help of enzymes produced by early organisms. Due in part to this lack of a demonstrated pre-life or "pre-biotic" chemical path connecting RNA to DNA, researchers in this field have been inclined to think that the simpler, more versatile one, RNA, was the basis for the first life forms -- or at least for an early stage of life prior to the emergence of DNA. RNA is able to store genetic information as DNA can, is able to catalyze biochemical reactions as protein enzymes can, and otherwise probably could have performed the basic biological tasks that would have been necessary in the first life forms.

Although origin-of-life researchers in recent decades have largely come to embrace the RNA World hypothesis, Sutherland, Krishnamurthy, Harvard's Jack Szostak and others have accumulated evidence that RNA and DNA may have arisen more or less all at once in the first life forms.

[Continues . . .]
"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
— H. L. Mencken


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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #21 on: April 03, 2019, 09:31:03 PM »
It seems (to a layman like myself) like the cosmos has a self-organizing aspect as part of its fabric, so it's really not all that surprising that this level of organization should appear spontaneously. 

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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #22 on: April 15, 2019, 05:08:39 AM »
Why ponds might have been a more likely environment than oceans for the first appearance of life.

"Earliest life may have arisen in ponds, not oceans" | EurekAlert

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Primitive ponds may have provided a suitable environment for brewing up Earth's first life forms, more so than oceans, a new MIT study finds.

Researchers report that shallow bodies of water, on the order of 10 centimeters deep, could have held high concentrations of what many scientists believe to be a key ingredient for jump-starting life on Earth: nitrogen.

In shallow ponds, nitrogen, in the form of nitrogenous oxides, would have had a good chance of accumulating enough to react with other compounds and give rise to the first living organisms. In much deeper oceans, nitrogen would have had a harder time establishing a significant, life-catalyzing presence, the researchers say.

"Our overall message is, if you think the origin of life required fixed nitrogen, as many people do, then it's tough to have the origin of life happen in the ocean," says lead author Sukrit Ranjan, a postdoc in MIT's Department of Earth, Atmospheric and Planetary Sciences (EAPS). "It's much easier to have that happen in a pond."

[. . .]

[I]n this new study, he identifies two significant "sinks," or effects that could have destroyed a significant portion of nitrogenous oxides, particularly in the oceans. He and his colleagues looked through the scientific literature and found that nitrogenous oxides in water can be broken down via interactions with the sun's ultraviolet light, and also with dissolved iron sloughed off from primitive oceanic rocks.

Ranjan says both ultraviolet light and dissolved iron could have destroyed a significant portion of nitrogenous oxides in the ocean, sending the compounds back into the atmosphere as gaseous nitrogen.

"We showed that if you include these two new sinks that people hadn't thought about before, that suppresses the concentrations of nitrogenous oxides in the ocean by a factor of 1,000, relative to what people calculated before," Ranjan says.

[. . .]

The debate over whether life originated in ponds versus oceans is not quite resolved, but Ranjan says the new study provides one convincing piece of evidence for the former.

"This discipline is less like knocking over a row of dominos, and more like building a cathedral," Ranjan says. "There's no real 'aha' moment. It's more like building up patiently one observation after another, and the picture that's emerging is that overall, many prebiotic synthesis pathways seem to be chemically easier in ponds than oceans."

[Link to full article]

A cathedral? Oh, the arrogance, the sheer gall of these people!  :lol:
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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #23 on: April 15, 2019, 04:03:25 PM »
A cathedral? Oh, the arrogance, the sheer gall of these people!  :lol:


Good article.

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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #24 on: August 08, 2019, 07:53:50 PM »
I think that this study may tie into some of the work that Jack Szostak's group has done. (A recent article about what Szostak has been up to--"How Life Began" | Harvard Magazine).

The Key to Life's Emergence? Bubbles, New Study Argues" | LiveScience

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Before life on Earth emerged, by about 3.5 billion years ago, the oceans were a soup of randomly jumbled molecules. Then, somehow, some of those molecules arranged themselves into well-organized strings of DNA, protective cell walls, and tiny organ-like structures capable of keeping cells alive and functioning. But just how they accomplished this organization has long baffled scientists. Now, biophysicists at Ludwig–Maximilians University in Munich think they have an answer: bubbles.

[. . .]

Bubbles were everywhere in Earth's early seascape. Warm, deep-sea volcanoes spurted fizzy plumes. Those airy orbs, settled on the porous volcanic rock. These were the conditions that Braun and his colleagues sought to replicate. They created a vessel out of a porous material that mimicked the texture of volcanic rock, then filled it, in turn, with six different solutions, each modeling a different stage in the life-formation process. One solution, representing an early step, contained a sugar called RAO, which would have been necessary in the construction of nucleotides, the building blocks of RNA and DNA. Other solutions, representing the later stages, contained RNA itself, as well as the fats necessary to construct cell walls. [7 Theories on the Origin of Life]

Then, the researchers heated the solution on one end and cooled it on the other. They were creating something called a "thermal gradient," in which the temperature gradually changes from one end to another, similar to the way the water near deep-sea thermal vents gradually changes from hot to cold.

"It's like a micro-ocean," Braun said.

In each solution, the temperature change forces the molecules to clump — and they gravitated toward the bubbles that naturally form under these conditions. Almost immediately, they began reacting.

Sugars formed crystals, a kind of skeleton for RNA and DNA nucleotides. Acids formed longer chains, taking another step toward the formation of complex, RNA-like molecules. Finally, the molecules arranged themselves into structures that resembled simple cells. In a basic sense, Braun said, cells are molecules encased in bags made of fats. That's exactly what happened on the surface of his bubbles: Fats arranged themselves in spheres around the RNA and other molecules.

Most surprising to Braun and his colleagues, he said, was how rapidly these changes happened, in under 30 minutes.

"I was amazed," he said. Though this is the first time he and his colleagues have looked specifically at bubbles, the researchers have previously tried to replicate how these biological molecules undergo the complex reactions needed for life. Normally, he said, these reactions take hours.

Some chemists are skeptical, however, that Braun's bubbles are an accurate representation of the primordial environment. Braun and his colleagues seeded their solution with many of the complex molecules needed for life. Even their simplest solutions still represented later stages of the life-formation process, Ramanarayanan Krishnamurthy, a chemist at the Scripps Institution of Oceanography who was not involved in the study, told Live Science. That's a bit like baking a cake with a box mix, rather than starting from scratch.

In contrast, the ancient oceans may not have had the right conditions to form these initial molecules, Krishnamurthy said.

[Continues . . .]
« Last Edit: August 08, 2019, 08:52:05 PM by Recusant »
"Religion is fundamentally opposed to everything I hold in veneration — courage, clear thinking, honesty, fairness, and above all, love of the truth."
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Re: How Life May Have First Emerged On Earth (Abiogenesis Thread)
« Reply #25 on: August 11, 2019, 10:06:32 PM »
Those primitive ponds may have contained algae useful for food to nourish whatever life forms might have been in place.  Here is another twist on the usefulness of certain algae...................
https://massivesci.com/articles/iwi-algae-protein-nannochloropsis-food-essential-amino-acids/?utm_source=pocket-newtab