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Author Topic:   Self-Replicating Molecules - Life's Building Blocks (Part II)
RAZD
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Message 1 of 29 (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 Handel's Messiah, 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


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Message 2 of 29 (513097)
06-24-2009 10:56 PM


Thread moved here from the Proposed New Topics forum.
  
Teapots&unicorns
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Message 3 of 29 (513177)
06-25-2009 9:21 PM


Quick question- is abiogenesis (possibly) still going on today? Or was it a one-time circumstance?
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RAZD
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Message 4 of 29 (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


we are limited in our ability to understand
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Teapots&unicorns
Member (Idle past 1354 days)
Posts: 178
Joined: 06-23-2009


Message 5 of 29 (513194)
06-26-2009 7:51 AM
Reply to: Message 4 by RAZD
06-25-2009 10:39 PM


Re: Abiogenesis now? Not likely ... imho
Ah. Thanks.
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themasterdebator
Inactive Member


Message 6 of 29 (514128)
07-03-2009 10:47 PM
Reply to: Message 1 by RAZD
06-24-2009 10:38 PM


Very impressive post. One question, has anyone been able to show these molecules turning into anything resembling a cell?
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Rahvin
Member (Idle past 138 days)
Posts: 3943
Joined: 07-01-2005


Message 7 of 29 (514170)
07-04-2009 1:11 PM
Reply to: Message 6 by themasterdebator
07-03-2009 10:47 PM


Very impressive post. One question, has anyone been able to show these molecules turning into anything resembling a cell?

That's not the point. The transition from self-replicating molecules to cells is not thought to have been the result in a change in those molecules, but rather an accident of environment much later with the addition of an early cell membrane/wall (most hypotheses I've geard of refer to a spontaneously formed bilipid layer).

For instance, see Wiki's Abiogenesis entry:

quote:
Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, a basic component of the cell membrane.

The so-called "cellular machinery" (mitochondria, etc) is yet another instance of gradual addition from a variety of pathways.

We would be identifying our proto-cell as "life" long before it looked much like a modern cell. The self-replicating molecules are the truly important step, as they allow the process of evolution through natural selection to begin.


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Mr Jack
Member
Posts: 3484
From: Leicester, England
Joined: 07-14-2003


Message 8 of 29 (514174)
07-04-2009 1:24 PM
Reply to: Message 7 by Rahvin
07-04-2009 1:11 PM


The transition from self-replicating molecules to cells is not thought to have been the result in a change in those molecules, but rather an accident of environment much later with the addition of an early cell membrane/wall (most hypotheses I've geard of refer to a spontaneously formed bilipid layer).

Two tailed lipids will spontaneously form bilayered spheres (called liposomes), yes, but one-tailed lipids (aka detergents) form micelles (little balls without an inside) instead - and here's the problem - detergents disrupt the formation of liposomes.

I'm not sure how this problem is supposed to be addressed.


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greentwiga
Member
Posts: 213
From: Santa
Joined: 06-05-2009


Message 9 of 29 (514841)
07-13-2009 9:56 AM
Reply to: Message 3 by Teapots&unicorns
06-25-2009 9:21 PM


Some events are so rare or difficult, that the first time it happens is also the last time. Conditions have changed since the first time, and even if it should happen, it will quickly be killed by life that has had billions of years to increase its efficiency. This is especially true when life needs a chain of several rare steps. For example, RNA needs to become self replicating. Then RNA needs to learn to make RNA that makes protein. Next, RNA needs to make the bilipid layer. Finally, DNA needs to take over some functions that RNA did. Each of these steps could have taken untold millions of years to accomplish. One argument that it only happened once is that all life is left handed.
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RAZD
Member
Posts: 15952
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 1.8


Message 10 of 29 (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.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

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Coragyps
Member
Posts: 5143
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 1.7


Message 11 of 29 (547789)
02-22-2010 8:50 PM
Reply to: Message 10 by RAZD
02-22-2010 8:17 PM


Re: New study - self replicating evolving RNA
Has this been peer reviewed yet?

Looks like - in Science:

http://www.sciencemag.org/cgi/content/abstract/1167856

(as always, I can email pdf's of Science papers on request - PM me. This one will be open access in another week, anyway.)


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finalsky 
Suspended Junior Member (Idle past 1260 days)
Posts: 1
Joined: 01-20-2011


Message 12 of 29 (601513)
01-20-2011 10:54 PM
Reply to: Message 1 by RAZD
06-24-2009 10:38 PM


DataExport
I have read your passage, I find that it's very useful in application. While there is another way, "Spam.DataSpam", it's fast and stable. Now it's free for everyone, I think it may help. More information:
http://www.spam.spam

Edited by Adminnemooseus, : Fix link.


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Hunter
Junior Member (Idle past 1194 days)
Posts: 1
Joined: 04-18-2011


Message 13 of 29 (612770)
04-18-2011 5:01 PM
Reply to: Message 1 by RAZD
06-24-2009 10:38 PM


Probability
You say that you think it’s very possible that there was debris left behind from the life cycle of previous stars and planets, but have you ever really looked into or calculated the probability of one protein molecule forming from such debris or mineral like material. The probability of one single protein molecule randomly forming on its own is 2.02 in 10^321. This doesn't even touch the probability of thousands of these protein molecules forming into DNA strands; which turns out to be 1 in 10^40,000.

Setting aside the improbability of protein molecules and DNA strands forming on their own, the chance that our universe could/would be laid out the way it is, is extremely improbable. It's 1 in 10^133, to be exact.

The theory you laid out in your second paragraph was nicely done, but it’s only a theory. No one has ever seen this complete process take place. Why would we base our beliefs on the origin of life on a theory?

It doesn't seem like life is inevitable from the statistics above.

Sources:

Peterson, Reichenbach, Hasker & Basinger (2007). Philosophy of Religion Selected Readings (Third Edition). Oxford university press, NY

Edited by Hunter, : No reason given.


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fearandloathing
Member (Idle past 612 days)
Posts: 990
From: Burlington, NC, USA
Joined: 02-24-2011


Message 14 of 29 (612776)
04-18-2011 5:11 PM
Reply to: Message 13 by Hunter
04-18-2011 5:01 PM


Re: Probability
Hi hunter,

If you could provide a link to your sources I would appreciate it as I can only find reference's to the book and not its content. I am interested to know how they came up with the numbers you cited.


"I hate to advocate the use of drugs, alcohol, violence, or insanity to anyone, but they always worked for me." - Hunter S. Thompson

Ad astra per aspera


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subbie
Member
Posts: 3358
Joined: 02-26-2006


Message 15 of 29 (612787)
04-18-2011 5:55 PM
Reply to: Message 13 by Hunter
04-18-2011 5:01 PM


Re: Probability
The probability of one single protein molecule randomly forming on its own is 2.02 in 10^321.

No.

Of course, it's difficult to tell exactly what, if anything, you've calculated since you didn't give us the calculation. But I suspect that, if you've calculated anything, it's the odds of a protein molecule coming together in one fell swoop, rather than a step by step combining over a long period of time.

Now, if you'd care to actually provide the calculations, I'd be willing to look at them as see if I'm wrong. But I don't think I am.


Ridicule is the only weapon which can be used against unintelligible propositions. -- Thomas Jefferson

We see monsters where science shows us windmills. -- Phat

It has always struck me as odd that fundies devote so much time and effort into trying to find a naturalistic explanation for their mythical flood, while looking for magical explanations for things that actually happened. -- Dr. Adequate

...creationists have a great way to detect fraud and it doesn't take 8 or 40 years or even a scientific degree to spot the fraud--'if it disagrees with the bible then it is wrong'.... -- archaeologist


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