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Biologists Replicate Key Evolutionary Step

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How RNA formed at the origins of life

Date: May 19, 2017
Source: University College London
Summary: A single process for how a group of molecules called nucleotides were made on the early Earth, before life began, has been suggested by a team of researchers.

The crux of the article.

The team demonstrated how purines and pyrimidine nucleotides can both be assembled on the same sugar scaffold to form molecules called ribonucleotides which are used to construct RNA.

Purine and pyrimidine nucleotides are used to create the DNA and RNA. The purine and pyrimidine nucleotides bind to one another through specific molecular interactions that provide a mechanism to copy and transfer information at the molecular level, which is essential for genetics, replication and evolution. Therefore understanding the origins of nucleotides is thought to be key to understanding the origins of life itself.

The team discovered that molecules, called 8-oxo-adenosine and 8-oxo-inosine, which are purine ribonucleotides, can be formed under the same chemical conditions as the natural pyrimidine ribonucleotides. They also found that one chemical precursor can divergently yield both purine and pyrimidine ribonucleotides.

"The mechanism we've reported gives both classes of molecule the same stereochemistry that is universally found in the sugar scaffold of biological nucleic acids, suggesting that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids," said Dr Shaun Stairs (UCL Chemistry), first author of the study.

Edited by dream_weaver

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New study sheds light on origins of life on Earth through molecular function

Date: May 17, 2017
Source: University of Illinois College of Agricultural, Consumer and Environmental Sciences

Debate exists over how life began on Earth, but a new study provides evidence for a 'metabolism-first' model. Scientists have traced the origins and evolution of molecular functions through time. The study shows metabolism and binding arose first, followed by the functional activities of larger macromolecules and cellular machinery.

The hypothesis:

Caetano-Anollés and Ibrahim Koç, a visiting scholar in the department, found evidence for the "metabolism-first" hypothesis by studying the evolution of molecular functions in organisms representing all realms of life. For 249 organisms, their genomes -- or complete set of genes -- were available in a searchable database. What's unique about this particular resource, known as the Gene Ontology (GO) database, is the fact that for each gene product -- a protein or RNA molecule -- a set of terms describing its function goes with it.

The experiment:

The team used the information and advanced computational methods to construct a tree that traced the most likely evolutionary path of molecular functions through time. At the base of the tree, close to its roots, were the most ancient functions. The most recent were close to the crown.

The observation:

At the base of the tree, corresponding to the origin of life on Earth, were functions related to metabolism and binding. "It is logical that these two functions started very early because molecules first needed to generate energy through metabolism and had to interact with other molecules through binding," Caetano-Anollés explains.

The next major advancements were functions that made the rise of macromolecules possible, which is when RNA might have entered the picture. Next came the machinery that integrated molecules into cells, followed by the rise of functions allowing communication between cells and their environments. "Finally, as you move toward the crown of the tree, you start seeing functions related to highly sophisticated processes involving things like muscle, skin, or the nervous system," Caetano-Anolles says.

Of course if you search for and stack your molecular functions from simplest to most complex, is it a reflection of the order of chronological precedence, or a sorting based on expectation that the most ancient functions and most recent go according to the rules that were written in the computer program?

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Another article citing the RNA study two posts back on Science magazine's website:

Chemists may be zeroing in on chemical reactions that sparked the first life

. . . A handful of simple steps transformed the aldehyde into two compounds resembling adenine- and guanine-containing nucleotides, they report today in Nature Communications. The resemblance wasn’t perfect: In the base of each, a carbon atom was bound to an oxygen atom instead of a hydrogen atom as in the familiar purines.  

“It’s nice chemistry,” says Nicholas Hud, an RNA chemist at Georgia Institute of Technology in Atlanta. However, he says, that wayward oxygen atom is a key stumbling block. There’s no simple way to exchange it for hydrogen. And the unconventional purines might have been unable to form RNA analogs with the properties needed to spark life. Powner says he and his colleagues are now looking for solutions. If they succeed, the path from simple chemicals to life will be a whole lot clearer. 


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Did life begin on land rather than in the sea?

A paradigm-shifting hypothesis could reshape our idea about the origin of life

Date: July 18, 2017

Source: University of California - Santa Cruz

Summary: A new discovery pushes back the time for the emergence of microbial life on land by 580 million years and also bolsters a paradigm-shifting hypothesis that life began, not in the sea, but on land.

While there is still debate about whether life began on land or in the sea, the discovery of ancient microbial fossils in a place like the Pilbara shows that these geothermal areas -- full of energy and rich in the minerals necessary for life -- harbored living microorganisms far earlier than believed.


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Was the primordial soup a hearty pre-protein stew?
The evolutionary path to first proteins may have been paved with relatively easy, small steps

Date: September 5, 2017

Source: Georgia Institute of Technology


How proteins evolved billions of years ago, when Earth was devoid of life, has stumped many a scientist. A little do-si-do between amino acids and their chemical lookalikes may have done the trick. Evolutionary chemists tried it and got results by the boatload.

More developments referencing the RNA, this time with depsipeptides.

The new study joins similar work about the formation of RNA precursors on prebiotic Earth, and about possible scenarios for the formation of the first genes.

. . .

To identify the more than 650 depsipeptides that formed, the researchers used mass spectrometry combined with ion mobility, which could be described as a wind tunnel for molecules. Along with mass, the additional mobility measurement gave the researchers data on the shape of the depsipeptides.

Algorithms created by Georgia Tech researcher Anton Petrov processed the data to finally identify the molecules.

To illustrate how potentially bountiful depsipeptides could have been on prebiotic Earth: The researchers had to limit the number of amino acids and hydroxy acids to three each. Had they taken 10 each instead, the number of theoretical depsipeptides could have climbed over 10,000,000,000,000.


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On a related note, it appears that Earth had some form of life from near the current accepted formation of the planet.

Earth Had Life From Its Infancy

In a rock formation called the Saglek Block, Yuji Sano and Tsuyoshi Komiya from the University of Tokyo found crystals of the mineral graphite that contain a distinctive blend of carbon isotopes. That blend suggests that microbes were already around, living, surviving, and using carbon dioxide from the air to build their cells. If the two researchers are right—and claims about such ancient events are always controversial—then this Canadian graphite represents one of the earliest traces of life on Earth.

The Earth was formed around 4.54 billion years ago. If you condense that huge swath of prehistory into a single calendar year, then the 3.95-billion-year-old graphite that the Tokyo team analyzed was created in the third week of February. By contrast, the earliest fossils ever found are 3.7 billion years old; they were created in the second week of March.

(links removed)

3.95-3.7 would leave 0.25 billion years between these two stages.

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Did life on Earth start due to meteorites splashing into warm little ponds?

Date: October 2, 2017

Source: McMaster University


Life on Earth began somewhere between 3.7 and 4.5 billion years ago, after meteorites splashed down and leached essential elements into warm little ponds, say scientists. Their calculations suggest that wet and dry cycles bonded basic molecular building blocks in the ponds' nutrient-rich broth into self-replicating RNA molecules that constituted the first genetic code for life on the planet.

Not quite sure what is meant by calculations here, but between this:

The researchers base their conclusion on exhaustive research and calculations drawing in aspects of astrophysics, geology, chemistry, biology and other disciplines. Though the "warm little ponds" concept has been around since Darwin, the researchers have now proven its plausibility through numerous evidence-based calculations.

"Because there are so many inputs from so many different fields, it's kind of amazing that it all hangs together," Pudritz says. "Each step led very naturally to the next. To have them all lead to a clear picture in the end is saying there's something right about this."

and this:

Pearce and Pudritz plan to put the theory to the test next year, when McMaster opens its Origins of Life laboratory that will re-create the pre-life conditions in a sealed environment.

"We're thrilled that we can put together a theoretical paper that combines all these threads, makes clear predictions and offers clear ideas that we can take to the laboratory," Pudritz says.

the suggestion near the beginning of this ongoing thread that someone be able to piece many of the various inputs together appears to be coming to fruition from what is cited from this article.

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Potential 'missing link' in chemistry that led to life on Earth discovered

Date: November 6, 2017

Source: Scripps Research Institute


Chemists have found a compound that may have been a crucial factor in the origins of life on Earth, explains a new report.

Origins-of-life researchers have hypothesized that a chemical reaction called phosphorylation may have been crucial for the assembly of three key ingredients in early life forms: short strands of nucleotides to store genetic information, short chains of amino acids (peptides) to do the main work of cells, and lipids to form encapsulating structures such as cell walls. ...

TSRI chemists have now identified just such a compound: diamidophosphate (DAP).

"We suggest a phosphorylation chemistry that could have given rise, all in the same place, to oligonucleotides, oligopeptides, and the cell-like structures to enclose them," said study senior author Ramanarayanan Krishnamurthy, associate professor of chemistry at TSRI. "That in turn would have allowed other chemistries that were not possible before, potentially leading to the first simple, cell-based living entities."

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Meteroites' mechanical energy might have created building blocks of life on Earth

Researchers in Germany are now arguing that a meteorite impact could have created the molecules that gave life its big break. Their experiments are the first to show that the mechanical energy released during an impact could have transformed simple chemicals into amino acids.1


‘I was standing in front of the Coliseum. Everybody was taking pictures but I was looking at the floor and saw these very round stones,’ he recounts. He took a few of them back to Germany and found that they could replace metal milling balls in his mechanochemical experiments.2

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