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Author Topic:   Self-Replicating Molecules - Life's Building Blocks (Part II)
RAZD
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Message 1 of 97 (513094)
06-24-2009 10:38 PM


On the Building Blocks of Life (part I) thread I listed my thoughts on the probability of life, reviewing the status our knowledge of the development of pre-biotic chemicals. My conclusion was:

quote:
From these information sections it seems to me that the building blocks needed for beginning the creation of life were plentiful, not just on Earth but in space in general and from the earliest of times. Probably they have been around since long before even the Earth formed from the cosmic debris left behind by the life and death cycle of previous stars and planets, back to the beginning of time. These "seeds of life" no doubt extend through the far reaches of the universe as well as the depths of time (cue Crosby, Stills, Nash and Young ... "We are star dust ...").

It also seems to me that the natural processes for forming more complex structures from those basic building blocks were likely prevalent on the earth 4.5 billion years ago in a variety of forms, levels of completion and locations. We end with a scenario that has a random combination of plentiful and multitudinous organic molecules forming amino acids all over the earth, with a membranous system to contain and concentrate those molecules and their interactions within a protocell type capsule. We also see that random combination of plentiful and multitudinous amino acids into peptides and proteins is feasible, and that concentration and recombination within the membranous protocells enhances the probability that random combinations of them into the first "replicators" (the predecessors to RNA and DNA) is not as far fetched as it seemed at first. A simple building block process where the probability of a successful combination is almost inevitable: it is no longer a matter of "if" but of "when" it will occur under these conditions ... and once self replication occurs the frequency of replication will necessarily outpace the random action, and replicators that are faster and stronger will outpace their competition ... life seems inevitable when given the conditions for life.

That is my take on the probability of life on earth.


That essay is 3-1/2 years old, and progress has been made in the field of abiogenesis since then, so I would expect much more evidence can be added as reference to the essay on the formation of pre-biotic molecules. While the formation of these molecules are each fascinating in their own right, one of the questions for abiogenesis in how to get from pre-biotic molcules to a self-replicating cells. One of the element critical to that path is the formation of self-replicating molecules.

There are many known self-replicating molecules, and a brief listing of some of them is provided below. There is also a large variety of molecules that can self-replicate. Some of the more exciting research (see ref (1) below) confirmed my prediction that self-replicating molecules would compete for resources, and showing how they can dominate the population - chemical evolution: random formation plus selection of the fastest.

We can also see a hint of how DNA came to be the dominant replication system in ref (6) below:

quote:
Template-free production of RNA was completely suppressed by addition of DNA to the incubation mixture. When both DNA and RNA templates were present, transcription and replication competed, but T7 RNA polymerase preferred DNA as a template.

The DNA outcompetes the RNA production.

This does not explain all the questions of how life developed on earth over 3.5 billion years ago, but it goes a long way in showing how possible it was for life to develop from existing chemicals in the conditions that existed in the pre-biotic earth. The sheer number of possibilities also can hint that such processes were quite active, with many variations vying for resources, and that the replication system that life developed from was likely the best at self-replication - the fastest, most stable and aggressive replicators outcompeting their competitors. The likelihood is that, even if they had not existed, that another replication system would have been able to develop into life. Some initial elements of evolution - random variation and feedback selection - were evident in this pre-biotic world.

For those who want to visualize how the building blocks from the first thread and the self-replicating molecules mentioned here come together into a pre-biotic self-replicating proto-cell, see this video summary of work from Dr. Szostak:

NOTE: this starts with a review of creationist claims, and the actual science starts at about 2:40 into the video. You can move the button ahead to the 2:40 mark and not miss any of the science. You can also turn off the sound, unless you are very fond of Beethoven's 9th Symphony, as there is no narration.

Enjoy


References:

(1) - Artificial molecule evolves in the lab , 08 January 2009 by Ewen Callaway

quote:
A new molecule that performs the essential function of life - self-replication - could shed light on the origin of all living things.
...
Rather than start with RNA enzymes - ribozymes - present in other organisms, Joyce's team created its own molecule from scratch, called R3C. It performed a single function: stitching two shorter RNA molecules together to create a clone of itself.
...
To improve R3C, Lincoln redesigned the molecule to forge a sister RNA that could itself join two other pieces of RNA into a functioning ribozyme. That way, each molecule makes a copy of its sister, a process called cross replication. The population of two doubles and doubles until there are no more starting bits of RNA left.
...
Not content with achieving one hallmark of life in the lab, Joyce and Lincoln sought to evolve their molecule by natural selection. They did this by mutating sequences of the RNA building blocks, so that 288 possible ribozymes could be built by mixing and matching different pairs of shorter RNAs.

What came out bore an eerie resemblance to Darwin's theory of natural selection: a few sequences proved winners, most losers. The victors emerged because they could replicate fastest while surrounded by competition, Joyce says.


(2) - Self-Reproducing Molecules, Reported by MIT Researchers, 09 May 1990 By Eugene F. Mallove

quote:
In work recently reported in the Journal of the American Chemical Society, Professor Rebek and his coworkers, Tjama Tjivikua, a graduate student from Namibia, and Pablo Ballester, a visiting scientist from the University of Palma in Mallorca, Spain, described the creation of an extraordinary self-replicating molecular system.
...
Amazingly, the laboratory-made molecule that Professor Rebek and his colleagues have created can reproduce itself without the "outside" assistance of enzymes. As such, and because of its specific constitution, the molecule embodies some of the "template" qualities of a nucleic acid, and some of the structural qualities of a protein
...
Technically, the self-replicating compound made by the MIT group is called an amino adenosine triacid ester (AATE). This molecule was initially formed by reacting two other molecules.

The AATE replicates by attracting to one of its ends anester molecule, and to its other end an amino adenosine molecule. These molecules react to form another AATE. The "parent" and "child" AATE molecules then break apart and can go on to build still more AATE molecules.


(3) - Self-Replicating Molecules and the Meaning of Life, interview with Dr M Reza Ghadiri, 29 October 1999 by Cliff Walker

quote:
He mentioned three specific groups of scientists, including his group, that have created self-replicating molecules, and indicated that there are others. I asked him if these were derived from naturally occurring self-replicating molecules, and he said that none of the molecules were derived from naturally occurring molecules.

Two of the three groups, his group and that of Guntr KieDrwski, have created peptides, which are similar in structure to naturally occurring molecules.


(4) - Synthetic Self-Replicating Molecules, July 1994 by Rebek, Jr

quote:
My colleagues and I at the Massachusetts Institute of Technology have designed such self-assembling molecules and crafted them in the laboratory. Our efforts are intended to illuminate the ways in which life might have arisen. Probably it began when molecules came into existence that were capable of reproducing themselves. Our organic molecules, although they operate outside of living systems, help to elucidate some of the essential principles of self-replication.

(5) - Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase., January 1975, by M Sumper and R Luce

quote:
Highly purified coliphage Qbeta replicase when incubated without added template synthesizes self-replicating RNA species in an autocatalytic reaction. In this paper we offer strong evidence that this RNA production is directed by templates generated de novo during the lag phase. ... (3) Different enzyme concentrations lead to RNA species of completely different primary structure. (4) Addition of oligonucleotides or preincubation with only three nucleoside triphosphates affects the final RNA sequence. (5) Manipulation of conditions during the lag phase results in the production of RNA structures that are adapted to the particular incubation conditions applied (e.g., RNA resistant to nuclease attack or resistant to inhibitors or even RNAs "addicted to the drug," in the sense that they only replicate in the presence of a drug like acridine orange).

(6) - Template-free generation of RNA species that replicate with bacteriophage T7 RNA polymerase. July 1996 by C K Biebricher and R Luce

quote:
A large variety of different RNA species that are replicated by DNA-dependent RNA polymerase from bacteriophage T7 have been generated by incubating high concentrations of this enzyme with substrate for extended time periods. The products differed from sample to sample in molecular weight and sequence, their chain lengths ranging from 60 to 120. The mechanism of autocatalytic amplification of RNA by T7 RNA polymerase proved to be analogous to that observed with viral RNA-dependent RNA polymerases (replicases): only single-stranded templates are accepted and complementary replica strands are synthesized. With enzyme in excess, exponential growth was observed; ... Template-free production of RNA was completely suppressed by addition of DNA to the incubation mixture. When both DNA and RNA templates were present, transcription and replication competed, but T7 RNA polymerase preferred DNA as a template.

(7) - Evolvable self-replicating molecules in an artificial chemistry, Fall 2002 by Tim J. Hutton

quote:
This paper gives details of Squirm3, a new artificial environment based on a simple physics and chemistry that supports self-replicating molecules somewhat similar to DNA. The self-replicators emerge spontaneously from a random soup given the right conditions. Interactions between the replicators can result in mutated versions that can outperform their parents. We show how artificial chemistries such as this one can be implemented as a cellular automaton. We concur with Dittrich, Ziegler, and Banzhaf that artificial chemistries are a good medium in which to study early evolution.

(8) - Catalytic chirally self-replicating molecule. Asymmetric autocatalytic reaction of a zinc alkoxide of chiral 1-ferrocenyl-2-methylpropan-1-ol, 14 December 1994 by Kenso Soai*, Tadakatsu Hayase and Kazuhisa Takai

quote:
Isopropylzinc alkoxide of 1-ferrocenyl-2-methylpropan-1-ol was found to be a catalytic chirally self-replicating molecule which produces itself with the same configuration from ferrocenyl aldehyde and diisopropylzinc with 35–39% e.e. in good yields.

(9) - Self-Replicating Molecules: A Second Generation, October 1994 by Edward A. Wintner, M. Morgan Conn, Julius Rebek Jr.

quote:
AbstractThe use of self-complementary structures in replication experiments is discussed, and a second generation of self-replicating molecules is introduced. Key design elements of the new system are described, specifically a high affinity (Ka~10^5M^-1 in CDCl3) between the two complementary reactive components and the careful placement of nucleophilic and electrophilic centers within the system. These considerations preclude intramolecular reactions within two-component complexes, thus minimizing undesirable background reactions. Autocatalysis is observed in the new systems, and by using appropriate control experiments the autcatalysis is traced to template effects

Introduction

Previous studies from these laboratories have shown how simple organic structures can catalyze their own formation.(1,2) Self-complementarity is the key to this autocatalytic behavior; by complementary it is meant that the sizes, shapes, and chemical surfaces of the structures are arranged so as to have affinity for each other. The affinity arises from weak, intermolecular forces - hydrogen bonding and aryl stacking interactions - that act on the molecular surfaces. These forces gather the reaction components and anchor them on the template surface while the intracomplex reaction takes place. The process leads to replication of the template, and the molecules are called replicators.


(10) - Self-Sustained Replication of an RNA Enzyme , 8 January 2009 by Tracey A. Lincoln 1 and Gerald F. Joyce 1*

quote:
An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other’s synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about one hour, and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.

(11) - Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world , 15 August 2006 by Wentao Ma1, 2 and Chunwu Yu3

quote:
Abstract Although there is more and more evidence suggested the existence of an RNA World during the origin of life, the scenario concerning the origin of the RNA World remains blurry. Usually it is speculated that it originated from a prebiotic nucleotide pool, during which a self-replicating RNA synthesis ribozyme may have emerged as the first ribozyme – the RNA replicase. However, there is yet no ersuasive supposition for the mechanism for the self-favouring feature of the replicase, thus the speculation remains unconvincing. Here we suggest that intramolecular catalysis is a possible solution. Two RNA synthesis ribozymes may be integrated into one RNA molecule, as two functional domains which could catalyze the copy of each other. Thus the RNA molecule could self-replicate and be referred to as “intramolecular replicase“ here. Computational simulation to get insight into the dynamic mechanism of emergence of the intramolecular replicase from a nucleotide pool is valuable and would be included in a following work of our group.

(12) - A self-replicating ligase ribozyme, 2002 by Natasha Paul and Gerald F. Joyce

quote:
A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 min−1, whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 × 10−11 M⋅min−1. Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

(13) - A self-replicating peptide, 8 August 1996 by David H. Lee, Juan R. Granja, Jose A. Martinez, Kay Severin & M. Reza Ghadiri

quote:
THE production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known1,2. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally3−6. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-root of initial template concentration.

(14) - Approaching Exponential Growth with a Self-Replicating Peptide, 22 May 2002 by Roy Issac and Jean Chmielewski

quote:
Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.

(15) - A Self-Replicating Peptide under Ionic
Control
, 1998 by Shao Yao, Indraneel Ghosh, Reena Zutshi, and Jean Chmielewski

quote:
Recent examples of designed molecular systems capable of self-replication include nucleotide-based oligomers,[2] conjugates of adenine and Kemps triacid,[3] peptides,[4] and micelles.[5] The production of a self-replicating molecule from a large molecular pool has been a more elusive target.[6] Recent work of Lee et al. demonstrated that peptides from the GCN4 leucine zipper domain self-replicate in an autocatalytic cycle.[4] We sought a peptidic self-replicating system that would be sensitive to environmental conditions and reproduce only under extreme conditions. We now describe a peptide that reproduces autocatalytically in an environmentally dependent manner.

(16) - Kinetic Analysis of Self-Replicating Peptides: Possibility of Chiral Amplification in Open Systems , 3 November 2004 by Jesús Rivera Islas1, Jean-Claude Micheau2 and Thomas Buhse1

quote:
Abstract A simplified kinetic model scheme is presented that addresses the main reactions of two recently reported peptide self-replicators. Experimentally observed differences in the autocatalytic efficiency between these two systems - caused by variations in the peptide sequences - and the possible effect of chiral amplification under heterochiral reaction conditions were evaluated. Our numerical simulations indicated that differences in the catalytic performance are exclusively due to pronounced variations in the rate parameters that control the reversible and hydrophobic interactions in the reaction system but neither to alterations in the underlying reaction network nor to changes in the stoichiometry of the involved aggregation processes. Model predictions further demonstrated the possible existence of chiral amplification if peptide self-replication is performed under heterochiral reaction conditions. Pointing into the direction of a possible cause for biomolecular homochirality, it was found that in open flow reactors, keeping the system under non-equilibrium conditions, a remarkable amplification of enantiomeric excess could be achieved. According to our modeling, this is due to a chiroselective autocatalytic effect and a meso-type separation process both of which are assumed to be intrinsic for the underlying dynamics of heterochiral peptide self-replication.

I also ran across this:

http://www.asa3.org/archive/evolution/200011/0202.html

quote:
>>>>Chris: Self-replicating molecules are not exactly uncommon.
>>>>DNAunion: I am unaware of any known natural self-replicating molecule(they are very uncommon in nature, if they exist at all). Note the even DNA is not self-replicating (I bring this up because it is sometimes incorrectly stated that DNA replicates itself)
>>Susan: I happen to have just posted material on this subject to another list.
go to www.google.com and type in "self-replicating molecules"

Which is what I did. Oldtimers will recognize DNAUnion from this forum.

And that's just the start of the 196,000 google hits for "self-replicating molecules".

Also see

(A) - Did life begin in ice?, 9 August 2005 by Anon.

quote:
Reporting their results in the May 25, 2004 issue of the journal Nucleic Acids Research, the researchers noted that the broken-up RNAs still could carry out some of the same functions as normal RNAs, but only in ice or sometimes other extreme conditions, such as dehydration.

These activities included grabbing other pieces of RNA and attaching them together, an activity called “ligation” that is similar to self-replication.

To fully self-replicate, a molecule must attach other molecules together in such a way as to match the sequence of chemical pieces that characterize the first molecule. This process is called “template-directed” ligation.

But the ligation alone—even without the self-replication—can build up ever larger and more complex RNA molecules, which according to the RNA world hypothesis could eventually develop self-replicating abilities.


(B) - The RNA World, undated by Brig Klyce

quote:
Virtually all biologists now agree that bacterial cells cannot form from nonliving chemicals in one step. If life arises from nonliving chemicals, there must be intermediate forms, "precellular life." Of the various theories of precellular life, the most popular contender today is "the RNA world."

RNA has the ability to act as both genes and enzymes. This property could offer a way around the "chicken-and-egg" problem. (Genes require enzymes; enzymes require genes.) Furthermore, RNA can be transcribed into DNA, in reverse of the normal process of transcription. These facts are reasons to consider that the RNA world could be the original pathway to cells. James Watson enthusiastically praises Sir Francis Crick for having suggested this possibility (1): ...
...
Today, research in the RNA world is a medium-sized industry. Scientists in this field are able to demonstrate that random sequences of RNA sometimes exhibit useful properties. For example, in 1995, a trio at the Whitehead Institute for Biomedical Research reported "Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences" (4). (Ligases are enzymes that splice together other molecules such as DNA or RNA.) The results are interesting—they suggest that randomness can produce functionality. The authors interpret the results to mean that "the number of distinct complex functional RNA structures is very large indeed."
...
At the Salk Institute for Biological Studies, in 1994, Leslie Orgel observes, "Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule..." (9).


(C) - DNA-like Molecule Replicates Without Help, 11 June 2009 by Robert F. Service

quote:
In hopes of finding something simpler, Leman and colleagues did away with the sugar-phosphate backbones altogether. Instead, they turned to amino acids, protein building blocks that have been shown to assemble under prebiotic conditions. The researchers report online today in Science Express that when they combined just two amino acids, a backbone readily assembled without the need for additional enzymes. They then found that DNA bases could bind to a sulfur group in one of the amino acids, cysteine, creating a protein-DNA hybrid strand. But because the nucleic acid bases attach weakly to the cysteines--think Velcro instead of glue--the bases can jump on and off in solution. As a result, when the researchers placed their hybrids in solution with single strands of DNA and RNA, the hybrids were able to rearrange their nucleic acid makeup to form complementary strands that would bind to the DNAs and RNAs. The researchers discovered that the hybrids could also form strands that would bind to other complementary hybrids, which shows that such molecules have the potential to copy themselves.

(D) - Scripps Research Team Creates Simple Chemical System that Mimics DNA, 2009 by Keith McKeown

quote:
A team of Scripps Research scientists has created a new analog to DNA that assembles and disassembles itself without the need for enzymes. Because the new system comprises components that might reasonably be expected in a primordial world, the new chemical system could answer questions about how life could emerge.
...
One of the theory's challenges is that RNA is still so complex that many researchers believer something still simpler must have preceded it. "I have been working for years to learn what replicators and genetic systems might have come before the advent of the RNA World," says team leader of the new research Professor Reza Ghadiri, a Scripps Research chemist.
...
The resulting new system involves two main component types. The backbone units are peptides linked in a set pattern with the amino acid cysteine exposed and available to react. These peptides interact with the same nucleobases found in DNA, but each nucleobase is bound to an organic compound known as a thioester.

Thioester bonds reversibly with the cysteine on the peptides to form thioester peptide nucleic acid (tPNA). This allows the nucleobases to attach and disassemble on their own without enzymes, so that a given peptide strand will hold a shifting array of nucleobases. This process is something like soldiers walking around a field achieving a certain formation then moving into a new formation.
...
The Ghadiri team was also able to show that a strand of tPNA can act as a template, causing complementary tPNA formation and strand pairing, though they have not yet achieved self-replication for tPNA, an ultimate goal.


(E) - Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, 14 May 2009 by Matthew W. Powner1, Béatrice Gerland1 & John D. Sutherland1

quote:
Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis—cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate—are plausible prebiotic feedstock molecules12, 13, 14, 15, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

(F) - Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world, 15 August 2006 by Wentao Ma1, 2 and Chunwu Yu3

quote:
Abstract Although there is more and more evidence suggested the existence of an RNA World during the origin of life, the scenario concerning the origin of the RNA World remains blurry. Usually it is speculated that it originated from a prebiotic nucleotide pool, during which a self-replicating RNA synthesis ribozyme may have emerged as the first ribozyme – the RNA replicase. However, there is yet no ersuasive supposition for the mechanism for the self-favouring feature of the replicase, thus the speculation remains unconvincing. Here we suggest that intramolecular catalysis is a possible solution. Two RNA synthesis ribozymes may be integrated into one RNA molecule, as two functional domains which could catalyze the copy of each other. Thus the RNA molecule could self-replicate and be referred to as “intramolecular replicase“ here. Computational simulation to get insight into the dynamic mechanism of emergence of the intramolecular replicase from a nucleotide pool is valuable and would be included in a following work of our group.


Admin: either as another Columnist article, or in Links and Information?

Edited by RAZD, : slight title modification

Edited by RAZD, : .


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RAZD
Member
Posts: 20036
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Message 4 of 97 (513179)
06-25-2009 10:39 PM
Reply to: Message 3 by Teapots&unicorns
06-25-2009 9:21 PM


Abiogenesis now? Not likely ... imho
Hi Teapots&unicorns,

Quick question- is abiogenesis (possibly) still going on today? Or was it a one-time circumstance?

I think it could still be going on, if it were not for one thing - existing life eating up all the resources. Everywhere you look the are living organisms, sucking up nutrients = amino acids = building blocks.

I read once about a microbiologist that sailed across the atlantic, and every day he scooped up some water and looked at it (only a microbiologist would take a lab on a sailboat ...) and every day he discovered new organisms and viruses.

Secondly, if it was occurring it would show up in genetic studies as not related to anything. Curiously, there are viruses that attack each of the three main domains of life, with viruses specific for each domain, but which carry common protein markers that show the wear and tear of 3.5 billion years of evolution, and that show they are related. This implies they existed before the three domains.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=419632
Hot new virus, deep connections

quote:
... This is where detailed structural similarities like the ones described in the previous paragraph come to the rescue. The assumption is that the structural similarities in the capsid proteins of adenovirus, phage PRD1, algal virus PBCV-1, and now archaeal virus STIV imply a common ancestry for those viruses (or strictly speaking, for the genes responsible for capsid structure), despite the absence of any surviving sequence similarity. In addition, there are two other groups of large viruses for which similar ancestral connections can be inferred across domains of life. ...

The simplest interpretation of these observations, and my own personal favorite, is that there were already viruses resembling modern adenoviruses, herpesviruses, and reoviruses active before the divergence of cellular life into the contemporary domains of Bacteria, Archaea, and Eukarya, ≈3 billion years ago. In this view, different lines of each of these virus types diverged in parallel with the cellular forms, with each viral line coevolving with one of the three cellular domains down to the present. The main alternative views are that the similar structures and assembly mechanisms arose independently and therefore do not imply common ancestry, or that each virus type arose more recently in one of the three domains and spread horizontally to the others. Which of these views (or which combination of them) is right can only become clearer as we isolate and characterize more new viruses and learn more about the viruses already in hand. ...


More at:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=419672
The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life

Personally I think they are the remnants of the RNA world. Some people think they should be classified as a fourth domain ...

See http://en.wikipedia.org/wiki/Non-cellular_life.

quote:
The issue of life without cellular structure came to the fore with the 2003 discovery that the large and complex Mimivirus can make some proteins that are involved in the synthesis of proteins.[1] This discovery suggests the possibility that some viruses may have evolved from earlier forms that could produce proteins independent of a host cell.[2] If so, there may at one time have been a viral domain of life.

ie - RNA world.

Enjoy.

Edited by RAZD, : last quote


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RAZD
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Message 10 of 97 (547784)
02-22-2010 8:17 PM


New study - self replicating evolving RNA
From To catch a creationist...

http://www.cosmosmagazine.com/.../life-evolution-a-test-tube

quote:
For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes - that can replicate themselves without the help of any proteins or other cellular components.

What’s more, these simple nucleic acids can act as catalysts and continue the process indefinitely.

The researchers began with ribozymes known to occur naturally, and put these in a growth medium, heated them and allowed the ribozymes to replicate until they had exhausted their fuel – usually within an hour.

The team then extracted a random subset, and put them in a new medium: ribozymes then competed with each other to consume as much of the medium as possible.

Eventually more successful ribozymes came to dominate the culture, and as the process continued, the ribozymes – undergoing evolution - grew in complexity, blindly finding solutions that made them more successful.


Has this been peer reviewed yet?

Enjoy.


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RAZD
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Message 28 of 97 (725260)
04-25-2014 7:37 AM
Reply to: Message 24 by Ed67
04-24-2014 1:04 PM


So you haven't explained how the complex, specified information could have been generated. Your sources simply state:

Curiously I can't explain how something could have been generated that does not exist in reality.

Please explain what "complex, specified information" means to you ... I've explained what it means to me, based on common understanding of the english words involved ... Semiotic argument for ID, Message 148:

quote:
So we have something too complex and mysterious for the average person to understand or explain, specified by and unspecified specifier to specifically accomplish the specific task of inserting the unspecified specifier, that acts to inform someone\thing and implying a communicator and a receiver.

In other words ... gigo. Words thrown together with connotations intended to imply something that isn't necessarily there, something with no metric to determine how to measure it. Pseudo-terminology: word jumbles with no real meaning for the purpose of fooling the gullible.


So until you tell me what this word salad "complex, specified information" means to you, I can't answer your question.

Now I expect you'll lay down another insulting string of words so that you can pretend that you know what it means (as you have done in response to others) or you can answer the question.

Until you answer what "complex, specified information" means to you, I (and likely everyone else) will continue to assume that you have no idea what it means.

"Evolution did it - POOF". That's, again, a statement of faith, not supported by any of the facts you presented.

Which is, of course, a lie. "POOF"ing is your belief department, not the way evolution works, if we are dealing with evolution at this point (which we can't be as this thread is about how life develops - a point I thought you had conceded ... ).

"Signature in the Cell", by Stephen Meyer, p. 312

Wishful thinking in a book, by Stephen Meyer ... hope you weren't suckered into buying the book ...


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(1)
Message 30 of 97 (743721)
12-03-2014 6:01 PM


News to Chiral about
New Twist Found in the Story of Life’s Start
By: Emily Singer
Quanta Magazine
November 26, 2014

quote:
For 30 years, Gerald Joyce has been trying to create life. As a graduate student in the 1980s, he studied how the first RNA molecules — chemical cousins to DNA that can both store and transmit genetic information — might have assembled themselves out of simpler units, a process that many scientists believe led to the first living things.

Unfortunately, he had a problem. At a chemical level, a deep bias permeates all of biology. The molecules that make up DNA and other nucleic acids such as RNA have an inherent “handedness.” These molecules can exist in two mirror image forms, but only the right-handed version is found in living organisms. Handedness serves an essential function in living beings; many of the chemical reactions that drive our cells only work with molecules of the correct handedness. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules?

Joyce was able to build RNA out of right-handed building blocks, as others had done before him. But when he added in left-handed molecules, mimicking the conditions on the early Earth, everything came to a halt. “Our paper said if you have [both] forms in the same place at the same time, you can’t even get started,” Joyce said.

His findings, published in Nature in 1984, suggested that in order for life to emerge, something first had to crack the symmetry between left-handed and right-handed molecules, an event biochemists call “breaking the mirror.” ...

Three decades later, Joyce’s latest research has shown that perhaps life came first after all. Joyce, now at the Scripps Research Institute in La Jolla, Calif., and Jonathan Sczepanski, a postdoctoral researcher, created an RNA enzyme — a substance that copies RNA — that can function in a soup of left- and right-handed building blocks, providing a potential mechanism for how some of the first biological molecules might have evolved in a symmetrical world. The new experiment, published in the November 20 issue of Nature, is reinvigorating the discussion over how life first arose. ...

... Joyce thought that this assembly process might generate a crack in the mirror. A reaction that selectively plucked right-handed building blocks from the primordial soup would quickly start to create only right-handed molecules, just as a machine that selects only red or only blue Legos from a mixed box would create single-colored towers.

Such a process would simultaneously solve two problems in the origins of life: It would create complex biological molecules while breaking the mirror. ...

So last year, Joyce and Sczepanski decided to start from scratch. They unleashed a pool of random right-handed RNA molecules and let them react in a test tube with left-handed building blocks. They hoped that within that random pool of RNA molecules was a ribozyme capable of stringing the building blocks together. They then isolated the best candidates — ribozymes that could copy RNA of the opposite handedness — replicated them, and subjected the new pool to the same trial over and over again.

In just a few short months, they had a surprisingly effective ribozyme. The right-handed version binds to a left-handed RNA template and produces a left-handed copy. The left-handed copy can then go on to produce a right-handed version. “It’s amazing what they did,” said John Chaput, a biochemist at Arizona State University in Tempe. “It really does get to the heart of the question of the origins of chirality and provides some solid evidence to move things forward.”

Perhaps even more exciting is how well the enzyme works. ... Joyce’s ribozyme could produce a range of sequences — including its own. And it’s still getting better. The ribozyme in the paper emerged after just 16 rounds of evolution, a shockingly short run for this kind of experiment. ...

... it binds based on the molecule’s shape rather than its sequence, an approach that turns out to be much more flexible. “They found something completely novel,” Lehman said. “It goes to show there’s a lot out there we don’t know.”

Scientists now have an enzyme that doesn’t need a chiral world. ...

If chirality emerged sometime after the origins of life, the question remains: Why did right-handed RNA win? Left- and right-handed molecules have chemically identical properties, so there’s no obvious reason for one to triumph.

Joyce and others suspect it’s simply chance. Say a ribozyme capable of transforming a pool of mixed nucleic acids into left- and right-handed RNAs appeared on the early Earth. It would produce two distinct groups, lefties and righties, which in turn might have functioned like competing populations. “If the right hand stumbles on useful mutations and runs away with the game, then the other side of the mirror can go dark,” Joyce said. ...


More studies are underway on this new approach, but at this point it looks like it may explain the mirror problem.

And we are another step closer on the building blocks of life.

Enjoy


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Message 38 of 97 (743733)
12-03-2014 10:53 PM
Reply to: Message 31 by GDR
12-03-2014 8:50 PM


Re: News to Chiral you up
Hi GDR

It certainly makes a case against instant creation but it does not make a case against creation itself. It is a theory of how life came into existence. It still does not answer the question of whether or not there was a prime mover behind any or all of the processes required.

I agree.

Choice two. We are the result, regardless of how many natural process were required, of an intelligent prime mover(s).

See Panspermic Pre-Biotic Molecules - Life's Building Blocks (Part I)

"We are star dust ... " (song by Joni Mitchell written for Woodstock sung by Crosby, Stills, Nash and Young)

Enjoy.


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RAZD
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Message 54 of 97 (743799)
12-04-2014 1:30 PM
Reply to: Message 42 by GDR
12-04-2014 12:42 AM


Re: News to Chiral you up, take too
Hi GDR, you seem to misunderstand me.

He says things like, ...

That's me you are quoting in my conclusion to the first building blocks thread (bbt1). It attacks\addresses the issue\question of when life formed from the beginning of the universe. This thread (bbt2) attacks\addresses the issue\question of when life formed from the other side, by working back from life to how life is formed.

Chirality is one of the "building blocks" that is\was between bbt1 and bbt2.

Your argument for the non-existence of a prime mover(s) ...

Curiously that is not and has never been my argument. As a Deist I am interested in the scientific explanation of how the universe, earth and life were created and how the various processes were set up to cause an end result (not that we are close to that yet).

But I don't pretend that this is evidence that god/s exist nor that they don't exist.

If one believes in a omnipotent omniscient all-powerful god/s creation the logical conclusion you reach is that the universe was created at the very beginning to become what we see, and what we understand of how the universe works is what we understand of how that creation was designed to work. All the natural laws and natural processes are part of the design.

If one does not believe in a omnipotent omniscient god/s creation the logical conclusion you reach is that what we understand of how the universe works is just how it happened to work.

The evidence does not persuade one either way, imho, so people see in it what they want to see.

Enjoy.

(btw -- I used to live in Victoria ... cheers)

Edited by RAZD, : ...


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(1)
Message 57 of 97 (743836)
12-05-2014 8:37 AM
Reply to: Message 56 by AZPaul3
12-04-2014 8:14 PM


Re: News to Chiral you up -- back to the topic
Don't you have an Occam'sTM Razor?

All it tells you is that if you have two (or more) systems to study and one is simpler than the other(s) that you might benefit from trying the simpler one first. It does not guarantee that the simpler one is better or more complete than the other(s) -- you don't know that until they are tested.

If you are presuming to use it to choose between two untestable concepts, then you are just using it as confirmation of your bias(es), because you can't test that your choice actually is the better one. That isn't scientific.

It seems to me that choosing either system is a "leap of faith" and that it is much more logical, imh(ysa)o, to just say that there is insufficient evidence and information to make an informed guess at this time.

So now you've made your standard atheist argument for the absence of god/s based on your perceived absence of evidence -- can we get back to the topic?

Does the mechanism for developing chirality form a link between Panspermic Pre-Biotic Molecules - Life's Building Blocks (Part I) and
Self-Replicating Molecules - Life's Building Blocks (Part II)?

Or are there still some blocks missing?

Enjoy


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Message 62 of 97 (743902)
12-05-2014 1:01 PM
Reply to: Message 61 by New Cat's Eye
12-05-2014 12:19 PM


Re: News to Chiral you up -- topic
We are able to explain the emergence of the process without needing an intelligent root cause.

From a scientific perspective, that is all that matters.

Good, so we can get back to the topic ... Does the mechanism for developing chirality form a link between Panspermic Pre-Biotic Molecules - Life's Building Blocks (Part I) and
Self-Replicating Molecules - Life's Building Blocks (Part II)?

Or are there still some blocks missing?

Enjoy


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(1)
Message 67 of 97 (743920)
12-05-2014 4:04 PM
Reply to: Message 63 by AZPaul3
12-05-2014 1:03 PM


Re: News to Chiral you up -- back to the topic
Just a coupla quick quibbles:

While you are right that Occam's Razor (OR) cannot choose which hypothesis is correct it does tell you which hypothesis is "more likely" correct.

No, it just suggests starting with the simple one first. Period. If that doesn't work you fall back on the more complex one, and if that doesn't work you start over.

We have two competing hypotheses. Evolution works because the natural processes work vs evolution works because the Prime Mover created it to work.

Not really. What you have is "it appears that evolution works by natural processes, whether god/s set up those processes or not." You can test the first part, but you cannot test the second part, so it becomes irrelevant to the discussion on how evolution works.

No, not a perceived absence of evidence but an actual, demonstrable and total lack of evidence. Unless, of course, you are holding something back from the rest of us.

So you perceive. Unless, of course you are omniscient or that you can demonstrate that you have looked everywhere inside and out of the universe and every subatomic particle. Many people will tell you they have perceived god/s, and they would disagree with your perception, so no, there is not a total lack of evidence.

Now back to your regularly scheduled topic.

Thanks. So to the question -- does this explanation for chirality link the two threads together or are there other steps\blocks that need to be filled in?

Enjoy


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Message 71 of 97 (773454)
12-02-2015 9:13 AM


Updated from the Life - an Unequivicol Definition thread
Update from Message 160 on the Life - an Unequivicol Definition thread:

RAZD writes:

(1) It doesn't address the issue of viral life, which is increasingly being accepted as life forms as more is found out (self replication without host, metabolism and making of proteins used to encase it, etc)

You have claimed this several times now. Admittedly, I am totally unaware of this. Evidence Please! Hopefully papers I can access on the web. Not journalistic articles I hope.+

Rather than go back to old posts to find this material I did a search on this topic to also see what the current status is. My original information involved the first paper\article, and I am pleased to see that further progress has been made on this.

Start with these two articles (bold added for emphasis):

Astrobiology: Test-Tube RNA, 2001

quote:
A new RNA enzyme, or ribozyme, synthesized by David Bartel, Wendy Johnson and colleagues at MIT’s Whitehead Institute for Biomedical Research, opens a door to create a path for the earliest evolution to have happened without either DNA or proteins in the primordial soup. Since first described in the journal Science, the Whitehead ribozyme, or RNA catalyst, has filled in the picture of early chemical evolution and how life might have arisen.

... When aligning the master and copy molecules upon themselves, they tested their fidelity to the original design. The key feature showed 95% accuracy.

... “The reaction must be accurate in incorporating nucleotides based on the template strand, general enough that any template can be copied, and efficient enough to add on a large number of nucleotides,” says Johnston. In fact, one complete RNA helix turn, a chain length of 14 code letters (or nucleotides) was able to replicate itself.

One key piece for a RNA World scenario is now available: a laboratory version of a master and copy molecule, 95% fidelity to the master, and independence from RNA chain length or sequence order. ...


I haven't found the Science article yet, perhaps you would like to try.

Follow up research leads to (bold added for emphasis):

The Daily Galaxy: "Evolution in a Test Tube" -Scientists Create Immortal Genetic Molecule, 2010

quote:
For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes - that can replicate themselves without the help of any proteins or other cellular components.These simple nucleic acids can act as catalysts and continue the process indefinitely.

... The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.

Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.

Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.

The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.

"This is the only case outside biology where molecular information has been immortalized," says Joyce.

The researchers then generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. ...


So as long as there was substrate (food to metabolize) the RNA enzyme\catalysts replicated, competed, evolved. In other words QED -- independent self-replicating RNA molecules.

For an overview of the RNA world current status see Wikipedia: RNA world (accessed Dec 2015) (bold in original):

quote:
RNA as an enzyme

RNA enzymes, or ribozymes, are found in today's DNA-based life and could be examples of living fossils. Ribozymes play vital roles, such as those in the ribosome, which is vital for protein synthesis. Many other ribozyme functions exist; for example, the hammerhead ribozyme performs self-cleavage[21] and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template.[22]

Among the enzymatic properties important for the beginning of life are:

Self-replication. The ability to self-replicate, or synthesize other RNA molecules; relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165-bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189-bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11 nucleotide long RNA strand from primed template strands.[23] This 189 base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self replication, but a potential lead for further investigation. The longest primer extension performed by a ribozyme polymerase was 20 bases.[24]

RNA in information storage

RNA is a very similar molecule to DNA, and only has two chemical differences. The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However RNA is less stable.

Prebiotic RNA synthesis

Nucleotides are the fundamental molecules that combine in series to form RNA. They consist of a nitrogenous base attached to a sugar-phosphate backbone. RNA is made of long stretches of specific nucleotides arranged so that their sequence of bases carries information. The RNA world hypothesis holds that in the primordial soup (or sandwich), there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another, which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, enabling them to stay together for longer periods of time. As each chain grew longer, it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down.

These chains have been proposed by some as the first, primitive forms of life.[59] In an RNA world, different sets of RNA strands would have had different replication outputs, which would have increased or decreased their frequency in the population, i.e. natural selection. As the fittest sets of RNA molecules expanded their numbers, novel catalytic properties added by mutation, which benefitted their persistence and expansion, could accumulate in the population. Such an autocatalytic set of ribozymes, capable of self replication in about an hour, has been identified. It was produced by molecular competition (in vitro evolution) of candidate enzyme mixtures.[60]

Implications of the RNA world

The RNA world hypothesis places RNA at center-stage when life originated. This has been accompanied by many studies[citation needed] in the last ten years that demonstrate important aspects of RNA function not previously known—and supports the idea of a critical role for RNA in the mechanisms of life. The RNA world hypothesis is supported by the observations that ribosomes are ribozymes: the catalytic site is composed of RNA, and proteins hold no major structural role and are of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA.


[22] Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (May 2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension" (PDF). Science 292 (5520): 1319–25. Bibcode:2001Sci...292.1319J. doi:10.1126/science.1060786. PMID 11358999.

[23] Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (May 2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension". Science 292 (5520): 1319–25. Bibcode:2001Sci...292.1319J. doi:10.1126/science.1060786. PMID 11358999.

[24] Hani S. Zaher and Peter J. Unrau, Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA (2007), 13:1017-1026

[60] Lincoln TA, Joyce GF (Feb 2009). "Self-sustained replication of an RNA enzyme". Science (American Association for the Advancement of Science) 323 (5918): 1229–32. Bibcode:2009Sci...323.1229L. doi:10.1126/science.1167856. PMC 2652413. PMID 19131595. Lay summary – Medical News Today (January 12, 2009).


[22] and [23] would be the Science articles related to the first article above; it doesn't appear that the wiki article has been updated with the information from the second article above. I'll have to look into that.

See also Science: Mirror image RNA enzymes may hold clues to origin of life:

quote:

Much as in M. C. Escher's famous lithograph, novel RNA enzymes can assemble mirror image versions of themselves.

Like a pair of hands that appear as mirror images of one another, biomolecules, such as DNA and RNA, come in left-handed and right-handed forms. Normally, enzymes that recognize one mirror image form won’t touch the other. But researchers have isolated RNA enzymes, known as ribozymes, that synthesize RNAs of the opposite handedness. As esoteric as this may sound, similar mirror image–making RNAs may have played a role in the early evolution of life.

Researchers consider RNA a likely central figure in the origin of life. That’s because, like DNA, the molecule can store genetic information, and like proteins it can act as a chemical catalyst that speeds up normally slow reactions. Many researchers believe that life likely got its start in an “RNA world” where RNAs evolved to replicate other RNA molecules. In this scenario, the more specialized DNA and proteins arose later.

Now, Joyce and his postdoc Jonathan Sczepanski have found a possible solution. Online this week in Nature, they show that by using a technique called test-tube evolution they were able to generate ribozymes capable of assembling RNA strands of the opposite handedness in the presence of a mixture of D- and L-RNA nucleotides. What’s more, when they started with a D-RNA ribozyme, they found that it preferred to work on an L-RNA template to synthesize an L-RNA complementary strand. Likewise, they prepared L-RNA ribozymes that synthesized D-RNA complementary strands from D-RNA templates. And both the D- and L-RNA ribozymes were able to make mirror image copies of themselves.

... the new work does suggest that if these cross-copying ribozymes arose early on, they could have copied both mirror versions of RNA to propel the evolution of more complex RNAs. If one of those later, more complex RNAs—say a D-RNA—proved more capable, it could have encouraged the copying of its own kind, and promoted the single-handedness in nucleotides that we see today.


A possible path to chirality.

In between self-replicating RNA and modern cell life would be self-replicating DNA molecules, with DNA viruses as 'living fossils' of their pre-cell existence.

From http://www.bioedonline.org/news/news.cfm?art=1288

quote:
Giant virus qualifies as 'living organism' - Huge genome allows mimivirus to make its own proteins.

Mimi carries about 50 genes that do things never seen before in a virus. It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses.

1. Raoult D., et al. Science, published online, doi:10.1126/science.1101485 (2004).
2. La Scola B., et al. Science, 299. 2033 (2003).

This isn't self-replication and it is inside a cell, but it is the virus acting alone to make its proteins, another step on the road to RNA world.

Enjoy

Edited by RAZD, : .


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Message 72 of 97 (773455)
12-02-2015 9:27 AM
Reply to: Message 69 by AZPaul3
12-05-2014 7:39 PM


formation of the mononucleotides still a missing block
One block that still needs a more robust explanation, unless I've missed something - again, is the formation of the mononucleotides. At present we can only artificially produce these pre-cursors to nucleic acids. We haven't been able, to my knowledge, to whip up a brew and have these things spontaneously pop out the way we can with the aminos, monomers and other organics.

Apparently still true.

Enjoy


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RAZD
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Message 73 of 97 (801095)
03-03-2017 8:49 AM


Thought I'd pop this in here for discussion
From Message 6, Here's the Nature article on the Earliest life may be up to 4.28 billion years old. thread

Here's the Nature article

quote:
Evidence for early life in Earth’s oldest hydrothermal vent precipitates

Matthew S. Dodd, Dominic Papineau, Tor Grenne, John F. Slack, Martin Rittner, Franco Pirajno, Jonathan O’Neil & Crispin T. S. Little

Nature 543, 60–64 (02 March 2017) doi:10.1038/nature21377

Received 12 November 2016 Accepted 09 January 2017 Published online 01 March 2017

Abstract

Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite–haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago.


Slightly different take ... at least 3.77 billion years old, observations "consistent with an oxidized biomass"

Because we are looking at possible byproducts of life, rather than actual fossils, it is possible imho that they could be from the pre-biotic world of self-replicating molecules and other precursors to life formation.

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RAZD
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Message 84 of 97 (815779)
07-24-2017 11:46 AM
Reply to: Message 1 by RAZD
06-24-2009 10:38 PM


Update --- have self-replicating molecules become life?
quote:
Diversification of self-replicating molecules

Abstract

How new species emerge in nature is still incompletely understood and difficult to study directly. Self-replicating molecules provide a simple model that allows us to capture the fundamental processes that occur in species formation. We have been able to monitor in real time and at a molecular level the diversification of self-replicating molecules into two distinct sets that compete for two different building blocks (‘food’) and so capture an important aspect of the process by which species may arise. The results show that the second replicator set is a descendant of the first and that both sets are kinetic products that oppose the thermodynamic preference of the system. The sets occupy related but complementary food niches. As diversification into sets takes place on the timescale of weeks and can be investigated at the molecular level, this work opens up new opportunities for experimentally investigating the process through which species arise both in real time and with enhanced detail.


This also begs the question of when "life" develops -- I would say when evolution begins, and that looks like these molecules qualify.

Enjoy


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RAZD
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From: the other end of the sidewalk
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(1)
Message 86 of 97 (816183)
07-31-2017 9:00 AM
Reply to: Message 85 by CRR
07-31-2017 1:17 AM


Re: Diversification of self-replicating molecules
Physicist Rob Sheldon ...

Do you mean this Rob Sheldon?

quote:
Discovery Institute > Multimedia Library > Center for Science and Culture > ID the Future (podcast) > Physicist Rob Sheldon on the History of Cosmological Thought, Pt. 1

Physicist Rob Sheldon on the History of Cosmological Thought, Pt. 1
Posted on December 26, 2016

On this episode of ID the Future, physicist Rob Sheldon talks with Casey Luskin about how there has been a paradigm shift in cosmological thought. Though cosmologists used to believe that the universe existed eternally in a static state, they now see a finite universe that had a beginning. Dr. Sheldon also explores the implications of this shift for theism, materialism, and intelligent design.


and

quote:
Reasonable Faith, Honolulu Chapter
Home > 2016 > 11 > Physicist Rob Sheldon: What ID is really about | Uncommon Descent

Physicist Rob Sheldon: What ID is really about | Uncommon Descent
November 5, 2016

“Einstein spent the last 40 years of his life trying to combine QM and Gravity and failed. Stephen Hawking also reported that he failed to find a theory of QM gravity. But the 21st century is discovering that the solution lies in ID, in design, in information. We haven’t got a QM theory of gravity yet, but we have a series of “standard models” with gobs and gobs of “fine tuning”, of design, of functional information. From the Higgs to the failure of SUSY, to the failure of dark matter WIMPS, to the failure of inflation, of BBN (Li-7 problem) and on up the chain to OOL, we have so much unaccounted-for information it’s embarrassing.”


Just asking ...

... made a pithy observation ...

"Pithy" because you like it and the implications of denigrating the fact that it is peptides?

... “If this paper were about anything but ‘peptides’, it would be called ‘crystallization’.” ...

Which becomes a meaningless statement because we are talking about peptides ... this is known as a "red herring" fallacy.

So the questions remain:

  1. do we have self-replicating molecules? Yes No ...
  2. did they "evolve" and diversify into two different types of self-replicating molecules? Yes No
  3. does this "evolution" show the possibility of life's beginning? Yes No

Inquiring minds want to know ...

The origin of abiotic species: Seven epic fails

Can you pick your best one?

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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Replies to this message:
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