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Biologists Replicate Key Evolutionary Step

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Simpler Times: Did an Earlier Genetic Molecule Predate DNA and RNA?

According to Chaput, one interesting contender for the role of early genetic carrier is a molecule known as TNA, whose arrival on the primordial scene may have predated its more familiar kin. A nucleic acid similar in form to both DNA and RNA, TNA differs in the sugar component of its structure, using threose rather than deoxyribose (as in DNA) or ribose (as in RNA) to compose its backbone.

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Strange Cousins: Molecular Alternatives to DNA, RNA Offer New Insight Into Life’s Origins

The group demonstrates for the first time that six of these unnatural nucleic acid polymers are capable of sharing information with DNA. One of these XNAs, a molecule referred to as anhydrohexitol nucleic acid or HNA was capable of undergoing directed evolution and folding into biologically useful forms.

"This is a big question," Chaput says. "If the RNA world existed, how did it come into existence? Was it spontaneously produced, or was it the product of something that was even simpler than RNA?"

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Was Life Inevitable? New Paper Pieces Together Metabolism's Beginnings

". . . carbon fixation is the centerpiece of metabolism -- the basic process by which cells take in chemicals from their environments and build them into products they need to live. It's also the link between the geochemistry of Earth and the biochemistry of life."

"What started as wonky geochemical mechanisms were sequentially replaced and fortified by biological ones, the authors believe. "Think of life like an onion emerging in layers, where each layer functions as a feedback mechanism that stabilizes and improves the ability to fix carbon," says Braakman."

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First Artificial Enzyme Created by Evolution in a Test Tube

Rational enzyme design relies on preconceived notions of what a new enzyme should look like and how it should function. In contrast, directed evolution involves producing a large quantity of candidate proteins and screening several generations to produce one with the desired function. With this approach, the outcome isn't limited by current knowledge of enzyme structure.

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Molecules Assemble in Water, Hint at Origins of Life

 

Hud's group knew that they were on to something when they added a small chemical tail to a proto-RNA base and saw it spontaneously form linear assemblies with another proto-RNA base. In some cases, the results produced 18,000 nicely ordered, stacked molecules in one long structure.

 

 

Georgia Tech partnered with the Institute for Research in Biomedicine in Barcelona, Spain on the project. The proto-RNA's two-component, self-assembling system consisted of cyanuric acid (CA) and TAPAS, a derivative of triaminopyrimidine (TAP).

Edited by dream_weaver

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Yeast not only gives rise to bread, it gave rise to an answer to a question that has eluded evolutionary biologists.

 

"To understand why the world is full of plants and animals, including humans, we need to know how one-celled organisms made the switch to living as a group, as multicelled organisms," said Sam Scheiner, program director in the National Science Foundation (NSF)'s Division of Environmental Biology. "This study is the first to experimentally observe that transition, providing a look at an event that took place hundreds of millions of years ago."

Way cool! Thank you for the reference.

 

ruveyn1

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Icy Cosmic Start for Amino Acids and DNA Ingredients

 

The scientists used the National Science Foundation's Green Bank Telescope (GBT) in West Virginia to study a giant cloud of gas some 25,000 light-years from Earth, near the center of our Milky Way Galaxy. The chemicals they found in that cloud include a molecule thought to be a precursor to a key component of DNA and another that may have a role in the formation of the amino acid alanine.


 

"Finding these molecules in an interstellar gas cloud means that important building blocks for DNA and amino acids can 'seed' newly-formed planets with the chemical precursors for life," said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO).

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Origin of Life: Power Behind Primordial Soup Discovered
 

The scientists simulated the impact of such a meteorite with the hot, volcanically-active, early Earth by placing samples of the Sikhote-Alin meteorite, an iron meteorite which fell in Siberia in 1947, in acid taken from the Hveradalur geothermal area in Iceland. The rock was left to react with the acidic fluid in test tubes incubated by the surrounding hot spring for four days, followed by a further 30 days at room temperature.

 

In their analysis of the resulting solution the scientists found the compound pyrophosphite, a molecular 'cousin' of pyrophosphate -- the part of ATP responsible for energy transfer. The scientists believe this compound could have acted as an earlier form of ATP in what they have dubbed 'chemical life'.

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 How Life May Have First Emerged On Earth: Foldable Proteins in a High-Salt Environment


Another prevailing view holds that a high-temperature (thermophile) environment, such as deep-ocean thermal vents, may have been the breeding ground for the origin of life. "The halophile, or salt-loving, environment has typically been considered one that life adapted into, not started in," Blaber said. "Our study of the prebiotic amino acids and protein design and folding suggests the opposite."

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How Life Began: New Research Suggests Simple Approach

 

A possible candidate for Shapiro's driver reaction might have been recently discovered in an undersea microbe, Methanosarcina acetivorans, which eats carbon monoxide and expels methane and acetate (related to vinegar).

 

Biologist James Ferry and geochemist Christopher House from Penn State University found that this primitive organism can get energy from a reaction between acetate and the mineral iron sulfide. Compared to other energy-harnessing processes that require dozens of proteins, this acetate-based reaction runs with the help of just two very simple proteins.

 
Miller–Urey experiment

 

After Miller's death in 2007, scientists examining sealed vials preserved from the original experiments were able to show that there were actually well over 20 different amino acids produced in Miller's original experiments. That is considerably more than what Miller originally reported, and more than the 20 that naturally occur in life.

 

ome evidence suggests that Earth's original atmosphere might have had a different composition from the gas used in the Miller–Urey experiment.

 

Thanks.

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Untangling Life's Origins

 

Contact order is the ability of a protein to establish links between segments of the polypeptide chain. When points that are close together on the chain come together, they generally form helical structures; when distant points come together, they form beta strands that interact with each other and form sheets. Contact order measures how many of the connections are local and how many are distant. Experimental studies have shown that it is correlated with folding speed. The measure is normalized (size modified) to take protein length, which affects folding speed, into account.

 

They saw a peculiar pattern in the results.

 

"What we see is an hourglass," said Caetano-Anollés. "At the beginning, proteins seem not to be folding so fast. And then, as time progresses, there's a tendency to fold faster and faster. And then it reaches a critical point, and at this point we have a tendency that reverses, that seems to go back again to slow folding." However, the tendency toward higher speed dominates.

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Billion-Year-Old Water Could Hold Clues to Life On Earth and Mars

 

We've found an interconnected fluid system in the deep Canadian crystalline basement that is billions of years old, and capable of supporting life. Our finding is of huge interest to researchers who want to understand how microbes evolve in isolation, and is central to the whole question of the origin of life, the sustainability of life, and life in extreme environments and on other planets.'

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Origins of Life: In Early Earth, Iron Helped RNA Catalyze Electron Transfer

 

The study shows that RNA is capable of catalyzing electron transfer under conditions similar to those of the early Earth. Because electron transfer, the moving of an electron from one chemical species to another, is involved in many biological processes -- including photosynthesis, respiration and the reduction of RNA to DNA -- the study's findings suggest that complex biochemical transformations may have been possible when life began.

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Excited, but Cold: Scientists Unveil the Secret of a Reaction for Prebiotic Synthesis of Organic Matter


Using diverse computational-chemistry methods, the team has arrived at astonishing conclusions: For example that the reaction does not take place in the hot spot created by the solar radiation. "This has nothing to do with heat, but with electrons," says Mario Barbatti.

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Some evidence that a small DNA change does not necessarily equate to a small, incremental downstream difference.

 

Two Mutations Triggered an Evolutionary Leap 500 Million Years Ago

 

"Changes in just two letters of the genetic code in our deep evolutionary past caused a massive shift in the function of one protein and set in motion the evolution of our present-day hormonal and reproductive systems," said Joe Thornton, PhD, professor of human genetics and ecology & evolution at the University of Chicago, who led the study.

 

"Our findings show that new molecular functions can evolve by sudden large leaps due to a few tiny changes in the genetic code," Thornton [also] said

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Natural Affinities -- Unrecognized Until Now -- May Have Set Stage for Life to Ignite

 

"In testing one of the fatty acids representative of those found before life began -- decanoic acid -- the scientists discovered that the four bases in RNA bound more readily to the decanoic acid than did the other seven bases tested. By concentrating more of the bases and sugar that are the building blocks of RNA, the system would have been primed for the next steps, reactions that led to RNA inside a bag."

 

"The researchers found that several sugars also give protective benefit but the sugar from RNA, ribose, is more effective than glucose or even xylose, a sugar remarkably similar to ribose, except its components are arranged differently. The ability of the building blocks of RNA to stabilize the fatty acid bags simplifies one part of the puzzle of how life started, Keller said."

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Biochemists Resurrect 'Molecular Fossils': Findings Challenge Assumptions About Origins of Life

 

Our genetic code is translated by two super-families of modern-day enzymes. Carter's research team created and superimposed digital three-dimensional versions of the two super-families to see how their structures aligned. Carter found that all the enzymes have virtually identical cores that can be extracted to produce "molecular fossils" he calls Urzymes -- Ur meaning earliest or original. The other parts, he said, are variations that were introduced later, as evolution unfolded.
 
These two Urzymes are as close as scientists have gotten to the actual ancient enzymes that would have populated Earth billions of years ago.
 
"Once we identified the core part of the enzyme, we cloned it and expressed it," Carter said. "Then we wanted to see if we could stabilize it and determine if it had any biochemical activity." They could and it did

 

RNA World Hypothesis: Primordial Soup May Need A New Recipe
 

The study leaves open the question of exactly how those primitive systems managed to replicate themselves — something neither the RNA World hypothesis nor the Peptide-RNA World theory can yet explain. Carter, though, is extending his research to include polymerases — enzymes that actually assemble the RNA molecule. Finding an Urzyme that serves that purpose would help answer that question.

Edited by dream_weaver

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Scientists Discover Cosmic Factory for Making Building Blocks of Life

 

The researchers discovered that when a comet impacts on a world it creates a shock wave that generates molecules that make up amino acids. The impact of the shock wave also generates heat, which then transforms these molecules into amino acids.
 
The team made their discovery by recreating the impact of a comet by firing projectiles through a large high speed gun. This gun, located at the University of Kent, uses compressed gas to propel projectiles at speeds of 7.15 kilometres per second into targets of ice mixtures, which have a similar composition to comets. The resulting impact created amino acids such as glycine and D-and L-alanine.

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Clay May Have Been Birthplace of Life On Earth, New Study Suggests

 

To make the process useful for producing large quantities of proteins, as in drug manufacturing, you need a lot of hydrogel, so the researchers set out to find a cheaper way to make it. Postdoctoral researcher Dayong Yang noticed that clay formed a hydrogel. Why consider clay? "It's dirt cheap," said Luo. Better yet, it turned out unexpectedly that using clay enhanced protein production.

 

An 'accidental' discovery driven by the "unseen hand" of economics.

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RNA Controls Splicing During Gene Expression, Further Evidence of 'RNA World' Origin in Modern Life

 

The team found that the U6 RNA subunit directly controls catalytic function -- effectively acting as the blade of the spliceosome. This is the first experimental proof that RNA is the key functional component of this critical biological mechanism.

 

"In modern life, protein enzymes catalyze most biological reactions," Piccirilli said. "The finding that a system like the spliceosome, which contains more protein than RNA, uses RNA for catalysis and has a molecular ancestor composed entirely of RNA suggests that the spliceosome's reaction center may be a molecular fossil from the 'RNA World.'"

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Theory on origin of animals challenged: Some animals need extremely little oxygen

 

One of science's strongest dogmas is that complex life on Earth could only evolve when oxygen levels in the atmosphere rose to close to modern levels. But now studies of a small sea sponge fished out of a Danish fjord shows that complex life does not need high levels of oxygen in order to live and grow.

 

The origin of complex life is one of science's greatest mysteries. How could the first small primitive cells evolve into the diversity of advanced life forms that exists on Earth today? The explanation in all textbooks is: Oxygen. Complex life evolved because the atmospheric levels of oxygen began to rise app. 630 -- 635 million years ago.

 

"But nobody has ever tested how much oxygen animals need -- at least not to my knowledge. Therefore we decided to find out," says Daniel Mills.

 

"When we placed the sponges in our lab, they continued to breathe and grow even when the oxygen levels reached 0.5 per cent of present day atmospheric levels," says Daniel Mills.

Edited by dream_weaver

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Origins of life: In early Earth, iron helped RNA catalyze electron transfer

 

The study shows that RNA is capable of catalyzing electron transfer under conditions similar to those of the early Earth. Because electron transfer, the moving of an electron from one chemical species to another, is involved in many biological processes -- including photosynthesis, respiration and the reduction of RNA to DNA -- the study's findings suggest that complex biochemical transformations may have been possible when life began.

 

"Our study shows that when RNA teams up with iron in an oxygen-free environment, RNA displays the powerful ability to catalyze single electron transfer, a process involved in the most sophisticated biochemistry, yet previously uncharacterized for RNA," said Loren Williams, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology.

 

Free oxygen gas was almost nonexistent in Earth's atmosphere more than 3 billion years ago. When free oxygen began entering the environment as a product of photosynthesis, it turned Earth's iron to rust, forming massive banded iron formations that are still mined today. The free oxygen produced by advanced organisms caused iron to be toxic, even though it was -- and still is -- a requirement for life. Williams believes the environmental transition caused a slow shift from the use of iron to magnesium for RNA binding, folding and catalysis.

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Thanks for keeping this thread running. 

 

Thanks for finding this thread of value.  From yeast, to meteorites, and oxygen thin environments; all touch on the complexity of the variables involved. Galileo  started with a chandelier osculating in a church cathedral  I can only bring together items that resonate along a single axis as I read them. May they contribute to a soul that harmonizes with the universe along a frequency I've not yet detected.

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