Coupling of small molecules led to complex life

[Memammal]

As reported on the Wits University website: Complex life evolved out of the chance coupling of small molecules

“Life was a chance event, there is no doubt about that,” says Dr Pierre Durand from the Evolution of Complexity Laboratory in the Evolutionary Studies Institute at Wits University, who led a project to find out how exactly these molecules linked up with each other. Their results are published today in the journal Royal Society OS, in a paper entitled "Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life”.

Very simple ribonucleic acid (RNA) molecules (compounds similar to Deoxyribonucleic acid (DNA)) can join other RNA molecules to themselves though a chemical reaction called ligation. The random joining together of different pieces or RNA could give rise to a group of molecules able to produce copies of themselves and so kick start the process of life. 

[jimmydasaint]

Hi mate,

I am  a bit puzzled about this article.  It does not come from a journal and is, IMO, decades old as a theory for the production of complex molecules from simple precursors.  I don't think it is news and would advise you to update it with a new article which is from a recent peer=reviewed publication.

Cheers

[Area54]

Hi Jimmy,

I am a bit puzzled by your post. Which part of " Their results are published today in the journal Royal Society OS, in a paper entitled "Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life” did you not understand. (i.e. it is current and it is in a journal.) The published article, in the Royal Society's open access can be accessed here.

That said, I'm still studying the article to determine what they think they are saying is new. In that regard I share your puzzlement.

[Memammal]

I stand corrected, but afaik the RNA world hypothesis has been more theory and less evidential. This study claims to have demonstrated how small non-living molecules may have given rise to larger molecules that were capable of reproducing themselves, which according to them would have been a key event for life to take hold...in short: life from non-life (which probably would have been a more attention-grabbing title). Furthermore, apparently the size matters....the smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. This very basic form of RNA also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself (although its catalytic efficiency was the lowest).

Area54, if you learned anything more about it from studying the published article, please let us know.

[Area54]

17 minutes ago, Memammal said:

Area54, if you learned anything more about it from studying the published article, please let us know.

I certainly shall, but thus far the Real World has intruded on the RNA World.

[jimmydasaint]

On 25/09/2017 at 0:16 PM, Area54 said:

Hi Jimmy,

I am a bit puzzled by your post. Which part of " Their results are published today in the journal Royal Society OS, in a paper entitled "Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life” did you not understand. (i.e. it is current and it is in a journal.) The published article, in the Royal Society's open access can be accessed here.

That said, I'm still studying the article to determine what they think they are saying is new. In that regard I share your puzzlement.

Don't be so patronising and sarcastic.  Try to be positive and helpful instead of displaying your arrogance.  I hope that your summary of the article will show knowledge instead of sneering at people.

To help things along let's examine some evidence.  The bibliography section will inform all of us about the date of the theory:

Quote

References  ↵Gilbert W. 1986 Origin of life: the RNA world. Nature 319, 618. (doi:10.1038/319618a0)CrossRefGoogle Scholar ↵Joyce GF. 2007 Forty years of in vitro evolution. Angew. Chem. 46, 6420–6436. (doi:10.1002/anie.200701369)CrossRefPubMedWeb of ScienceGoogle Scholar

 

Edited October 1, 2017 by jimmydasaint

[Area54]

2 minutes ago, jimmydasaint said:

Don't be so patronising and sarcastic.  Try to be positive and helpful instead of displaying your arrogance.  I hope that your summary of the article will show knowledge instead of sneering at people.

Don't be so bloody minded. You misread a clearly written post, making two errors. I thought to birng that to your attention (and simultaneously defend Memammal) by a lighthearted post mimicing your style. To indicate that it was offered in humour and not sarcasm I noted that I shared your puzzlement. I'm sorry you feel that pointing out errors is negative and unhelpful. I'll keep that in mind for the future.

[jimmydasaint]

Point out mistakes  as much as possible, as long as you cite evidence. Just don't patronise a Scotsman, we don't take this well. I was not attacking Memammal.  I thought he made a mistake .  This theory is decades old - I presented the evidence using the References. Let's go forward by referring to the paper and I will show my openness and intellectual honesty in admitting my errors. Both of us should read the paper first and make comments later. 

From my brief reading of the paper, I can back up Memammal's conclusions that larger functional ligases occur from the smaller ligases. However, the researchers admit that the efficiency is low. 

Quote

 Conclusion: implications for RNA evolution at the origin of life

Ligases (and related polymerases) have primarily been explored with the aim of evolving a self-replicating enzyme (2).  The results indicate that, in the early stages of the RNA world, molecular size could have increased in a modular, stepwise fashion via the reactions of small ligases with a range of oligomers, albeit with a relatively poor efficiency. It supports the computational and theoretical predictions that assembly of larger functional molecules resulted from short RNA ligases [26,27]. The derived larger and more complex ligases developed specificity and efficiency for the kinds of substrates ligated. This trade-off could have contributed to building molecular complexity and the generation of a pool of functionally specialized molecules, which were necessary for the emergence of a self-sustained replicating system.

was small.  Earlier,the same researchers asserted the following statement: 

Quote

The largest ribozyme, R18, self-ligated only 7 out of 24 different substrates and was most selective in its function. and also: " With increased molecular size in larger ribozymes, the degree of folding and self-pairing increased (as determined by the Gibbs free energy: R18-T4 (−3 kcal mol⁻¹), R18-T3 (−18 kcal mol⁻¹), R18-T2 (−31.2 kcal mol⁻¹), R18-T1 (−46.7 kcal mol⁻¹), R18 (−67.3 kcal mol⁻¹))".

http://rsos.royalsocietypublishing.org/content/4/9/170376#sec-2

Previously, other researchers have had to address the following issues raised by other scientists:: 

Quote

However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteins first’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/

Edited October 1, 2017 by jimmydasaint

[Memammal]

The next bit of news seems to fit nicely with the above:

Quote

Scientists find potential 'missing link' in chemistry that led to life on earth

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. Yet, no one has ever found a phosphorylating agent that was plausibly present on early Earth and could have produced these three classes of molecules side-by-side under the same realistic conditions.

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."

The study, reported today in Nature Chemistry, is part of an ongoing effort by scientists around the world to find plausible routes for the epic journey from pre-biological chemistry to cell-based biochemistry.

Other researchers have described chemical reactions that might have enabled the phosphorylation of pre-biological molecules on the early Earth. But these scenarios have involved different phosphorylating agents for different types of molecule, as well as different and often uncommon reaction environments.

...postdoctoral research associates at TSRI, showed first that DAP could phosphorylate each of the four nucleoside building blocks of RNA in water or a paste-like state under a wide range of temperatures and other conditions.

With the addition of the catalyst imidazole, a simple organic compound that was itself plausibly present on the early Earth, DAP's activity also led to the appearance of short, RNA-like chains of these phosphorylated building blocks.

Moreover, DAP with water and imidazole efficiently phosphorylated the lipid building blocks glycerol and fatty acids, leading to the self-assembly of small phospho-lipid capsules called vesicles--primitive versions of cells.

DAP in water at room temperature also phosphorylated the amino acids glycine, aspartic acid and glutamic acid, and then helped link these molecules into short peptide chains (peptides are smaller versions of proteins).

 

[Mike Smith Cosmos]

If it is of any help ! 

This weeks New Scientist , ( 4th November  2017 ) lead article is: BEFORE THE BEGINNING 

here is discussed the action of " reading the genetic code contained in the DNA  and its function in constructing Proteins, as CELLULAR ROBOTS , building the " stuff " that makes cells tick . 

Ref :- https://en.m.wikipedia.org/wiki/Ribosome

 Bob Holms . Edmonton Canada .

Mike 

 

Edited November 7, 2017 by Mike Smith Cosmos

[Memammal]

Thanks Mike. I would love to read the rest of this.

[Mike Smith Cosmos]

Here is a bit more , continuing . Sorry I am in bed, with a sick dog and a bit cramped . 

If its not clear enough to read , I will send it again in " daylight " ,

plus the last page , that I have not sent yet ! 

 

mike 

Edited November 7, 2017 by Mike Smith Cosmos

[Memammal]

Thanks again Mike. The first page that you published is readable (together with the intro that I found), but the second one not. Don't worry too much as I think I got the gist of it. Also, the New Scientist Facebook page has a very good diagram/image relating to this article (plus the same intro) where they summarised their findings.