giovedì 30 giugno 2022

THE PRIMORDIAL BROTH: Recent publications

 

Post n.3 Recent publications


At the beginning of the 1980s, Mario Ageno, in Lectures on Biophysics, after examining the thought of Oparin and Haldane and the ideas of Sidney Fox, Harada, Herrera and Calvin, wrote: "What we have said so far about the so-called 'theories' of the origin of life, proposed over the last fifty years and in part still enjoying a certain amount of credit among some, is sufficient to demonstrate the futility of this race to see who is the cleverest and most brilliant in the hunt for ideas. It is clear that these ideas are always patently inadequate in the face of the complexity of the problem, even if they can sometimes help to illuminate some very particular aspect of it. In order to acquire substantial and lasting results, one must set out on a different path: that of the patient collection of clues, of the testimonies still present in today's world of life, of their critical elaboration into coherent hypotheses and of a continuous comparison of these hypotheses with the 'experiment'.

Well, one of the evidences still present is that life is asymmetrical. How did the amino acids Destro and Levo separate? Why was Ribose Right and not Ribose Levo chosen?  And why were only 20 of the many amino acids present in prebiotic times chosen and why those? And how did the genetic code originate?

Solving these problems requires years of work and so we fall back on the brilliant idea, in the hope that it might help to shed some light on some very particular aspects.

I do not know how the processes of self-promotion of molecules were discovered. I have always known that if a chemical-physical process takes place, it is because it decreases its energy (technically its free energy).

The article contains some publications  of the last 20 years. Source: Le Scienze online.

 16 March 2022

From interstellar clouds the first molecules for life on Earth

by Yasemin Saplakoglu/Quanta Magazine

A laboratory experiment has successfully reproduced a mechanism by which parts of proteins could have formed spontaneously on cosmic dust, suggesting their role in the early stages of the origin of life, on our planet or elsewhere

  18 May 2022

Perhaps at the origin of life there was a hybrid of RNA and protein

by Davide Castelvecchi/Nature

According to the standard theory, in an RNA world, life may have existed in the form of complex proto-RNA strands capable of copying themselves and competing with other strands. Later, these 'RNA enzymes' might have developed the ability to build proteins and eventually transfer their genetic information into a more stable DNA. How this could have happened was an open question, partly because catalysts made of RNA alone are much less efficient than the protein-based enzymes found in all living cells today. 'Although [RNA]-based catalysts have been discovered, their catalytic power is poor,' says Thomas Carell, an organic chemist at the Ludwig Maximilian Universität in Munich, Germany. [...]

Carell's team constructed a synthetic RNA molecule that includes two modified nucleosides by joining two pieces of RNA commonly found in living cells. At the first of the exotic sites, the synthetic molecule could bind to an amino acid, which then moved laterally to bind to the second adjacent exotic nucleoside. The team then separated the original RNA strands and inserted a new one with its own amino acid. This was in the correct position to form a strong covalent bond with the amino acid previously attached to the second strand. The process continued step by step, growing a short chain of amino acids - a mini-protein called a peptide - that attached itself to the RNA. The formation of bonds between amino acids requires energy, which the researchers provided by priming the amino acids with various reagents in the solution

Loren Williams, a chemist-biophysicist at the Georgia Institute of Technology in Atlanta, agrees. "If the origins of RNA and proteins are linked and their emergence is not independent, then the maths shifts radically in favour of an RNA-protein world and not an RNA world," he says.

18 January 2021

Primordial life and the threat of water

by Michael Marshall/Natur

Water is indispensable for survival, but for the development of early life it posed a very serious threat because it can break down DNA and other essential molecules. How was this apparent paradox overcome? The solution was small pools in which water was intermittently present.

Emerging evidence led many researchers to abandon the idea that life appeared in the oceans, and to focus instead on land-based environments, in places that were now dry and now wet. This shift in perspective is not shared by all, but scientists in favour of the idea of a beginning on land argue that it solves a long-known paradox: water is essential for life, but also destructive to its main components.

 09 June 2020

From an asteroid energy and ingredients for the origin of life

A simulation of the primordial Earth hit by an asteroid shows that fundamental compounds such as amino acids can be produced in mixtures of simple inorganic compounds such as iron, nickel, water, as well as nitrogen and carbon dioxide, thanks to the energy released by the impact (Red.)

 29 June 2020

Did life originate from a genetic hybrid?

by Andy Extance/Scientific American

A new experiment that attempted to recreate conditions on the primordial Earth suggests that RNA and DNA, the molecules that contain genetic information, may have formed at the same time. The result contrasts with the 'RNA world' hypothesis, according to which RNA was the precursor to DNA, a popular theory but one that has yet to be fully convinced.

 09 July 2020

Cosmic rays and the shape of life

by Charlie Wood/Quanta Magazine

It is one of the great unsolved mysteries of biology: why in all living organisms are the DNA and RNA helices always wound only to the right? According to two astrophysicists, it may have been cosmic rays in the early stages of life's history that gave an evolutionary advantage to this particular structure of the molecules containing the genetic information

 04 November 2020

The origins of metabolism at the dawn of life

by John Rennie/Quanta Magazine

The chemical reactions that characterise cell metabolism today are extremely complex. A study has now found that their ancestral, much simpler versions could have taken place as early as the 'primordial soup' from which life originated, to become progressively more sophisticated over the course of evolution

Even Mansy, despite his enthusiasm for this work, is cautious about interpretation. 'Metabolism,' he explains, 'is not just about the formation of constituent parts. Rather, it is a kind of energy flow that maintains the low entropy state of a cell'. According to him, evidence that some form of proto-metabolism helped the precursors of cells to survive better (even if, strictly speaking, those precursors were not really alive) is still lacking, among other things. 'Until we start to understand how these kinds of chemical reactions can give a selective advantage to one encapsulated chemical system over another,' he comments, 'I don't know where this is leading us.

 11 October 2019

An artificial primordial soup to support the RNA world

by Davide Castelvecchi/Nature

A laboratory experiment has demonstrated a chemical pathway that produces the four bases of ribonucleic acid under conditions similar to those on the primordial Earth, reinforcing the hypothesis that the first life forms on the planet were based on this molecule

 06 June 2019

An alternative hypothesis on the origin of life

by Martina Saporiti

The oceans would not have been the crucible of chemical reactions from which life arose, but small bodies of water. New research reinforces a hypothesis already put forward by Darwin

 05 December 2018

A new ingredient fundamental to life

  


                                                   (Science Photo Library / AGF)

The composition of the earliest RNAs that marked the transition from the simplest chemicals to the earliest forms of life on Earth may have been slightly different than that of current RNAs(red)

 18 May 2018

RNA and the origin of life

 


                                          © Science Photo Library / AGF

Created for the first time is a ribozyme - an RNA strand that functions like an enzyme - capable of self-replication, as it can also make a copy of folded RNAs, and not just linear ones. A point in favour of the hypothesis that life originated in an 'RNA world'(red)

 New hypothesis on the composition of the primordial soup at the origin of life

by Milena Castigli September 8, 2017

The primordial soup that gave rise to life on Earth did not need any 'flaming' to form the first proteins, but only the continuous bubbling of hundreds of precursor molecules, joined together by reactions very common in those primitive environmental conditions.

The researchers recreated the primordial soup in the laboratory using mainly amino acids and hydroxy acids, the most abundant ingredients at that time.

The scientists were thus able to observe that against all odds the elements came together like bricks, spontaneously forming the precursors of proteins: the depsipeptides. Their evolution was then accelerated by 'drying' them at 85 degrees and throwing them back into the broth, in order to simulate the cyclical process that depsipeptides might have undergone when the puddles on Earth dried out and filled with water again.

Without any effort, the first peptides were thus obtained whose chains, joined and folded, go on to form proteins. The study was published in the journal of the American Academy of Sciences (Pnas). Source: Ansa.

 03 November 2017

A new theory on the origin of life

It would have been the combined action of peptides and ribonucleic acid (RNA) that triggered the processes from which life on Earth originated. This is supported by a new theory that challenges the so-called RNA world hypothesis, according to which ribonucleic acid alone was sufficient to trigger life. (Red)

 

28 July 2015

Self-replication and the origin of life

 

A new model explains how increasingly complex polymers capable of self-replication may have developed from simple molecules. The model may fill gaps in the explanation of how life arose from the primordial soup in which the first organic molecules formed

 

9 September 2014

A step forward in explaining the origin of life

 


                                         © Robert Postma/First Light/Corbis

Sophisticated computer simulations of Stanley Miller's classic experiments on the formation of complex organic compounds from simple molecules in the 'primordial soup' of the ancient Earth have shown the central role of electric fields in the environment. The result indirectly strengthens the 'RNA world' theory and has interesting implications for the search for extraterrestrial life forms(red)

Particularly significant is the explanation for the formation of formamide, as it has recently been shown that this molecule, when subjected to UV irradiation, allows the formation of guanine. Guanine was the only one of the four nucleotide bases that could not be produced merely by providing heat to the 'primordial soup', so much so that scholars of the origin of life had dubbed guanine 'the missing G'.

 22 March 2011

An even richer 'primordial soup



 The amino acids produced in Miller's historic experiment were similar in structure and ratio to those found in meteorites

 Jeffrey Bada, rediscovered samples of the results of Miller's 1958 experiments, and subjected them to new analysis, first in 2008, already finding more amino acids than originally identified by Miller, and then again recently, obtaining results that indicate that the variety of organic compounds present in Earth's distant past was much greater than previously thought, and also found that the amino acids produced in Miller's hydrogen sulphide experiment are similar in structure and ratio to those found in meteorites, a result that supports the hypothesis that processes such as those in these experiments are widespread in the universe.

03 February 2010

A theory against the 'primordial soup




Thermodynamic constraints imply that chemosynthesis is strictly necessary for carbon and energy metabolism in all organisms growing from simple chemical compounds, and presumably it was also necessary in the first cells capable of autonomous life. The textbooks recite that life originated from the primordial soup in which the first cells formed by fermenting the organic substances present therein to generate energy in the form of ATP; we provide an alternative theory that life originated from gases, H2, CO2, N2, and H2S, and that the energy for the earliest forms of life came from exploiting the geochemical gradients present in the ocean floor in hydrothermal springs, probably interconnected by a myriad of compartments or pores.

 14 September 2005

Was the primordial atmosphere reducing?

Experiments with chondrites suggest that the atmosphere of the early Earth was devoid of oxygen and rich in methane and ammonia

Using primitive meteorites (chondrites) as a model, a team of geophysicists and planetary scientists at Washington University in St. Louis performed outgassing calculations and showed that Earth's primordial atmosphere was reductive, full of methane, ammonia, hydrogen and water vapour

 12 January 2004

Did life originate from a mineral?

Some of the initial processes that helped form life on Earth are said to be due to a mineral containing borax

 09 March 2019

Life flourishing at the bottom of the oceans

by Cindy Lee Van Dove/Nature

The importance of microbial chemosynthesis near hot springs also prompts us to rethink our ideas about the extreme conditions life can adapt to, the origin of life on this planet and also the potential for life elsewhere in the universe.

 01 April 2001

Life from rocks

The first living beings formed from the only available raw materials: air, water and rock.

A series of fascinating experiments is revealing that minerals play a crucial part in the basic chemical reactions from which life must have originated.

 20 February 2001

The left hand of life

Life's preference for left-handed molecules could be the result of its own self-promotion

In a study published in the journal 'Nature', researchers describe their experiment in which they used peptides, chains made up of a few amino acids, to understand why life is dominated by homochirality. The peptides used in the experiments could be combined to give rise to four different products, two homochiral, composed only of left or right-handed amino acids, and two heterochiral, composed of peptides of different orientations.

After mixing their peptides, the researchers almost always obtained homochiral products and observed that this occurs because homochiral molecules, once produced, tend to stimulate the production of those similar to them, a behaviour not observed in heterochiral molecules.

 01 February 2001

Life-bearing giants

Only solar systems like ours, where giant planets are found, can harbour life

According to the results of a recent study, the search for life on other worlds should focus on solar systems similar to our own with giant planets. In fact, it seems that it was Jupiter that 'shipped' the water necessary for carbon-based life to Earth.

 

Next Post: Life beyond the Earth. (end of october-november)


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