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Author Topic:   Self-Replicating Molecules - Life's Building Blocks (Part II)
New Cat's Eye
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(1)
Message 61 of 73 (743893)
12-05-2014 12:19 PM
Reply to: Message 60 by GDR
12-05-2014 11:25 AM


Re: News to Chiral you up
I mean the question that remains open which is whether or not the process itself has an intelligent root cause or not.

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.

From a scientific POV I completely agree. However if a god does exist then we should all care as presumably there would be a point to our existence and IMHO it would be helpful to know just what that point was.

But we shouldn't care as it pertains to our science experiments.

I go to church and I work in a lab.

I don't bring the beakers to the church and I don't bring the missals to the lab. That's how it should be.


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RAZD
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Message 62 of 73 (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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AZPaul3
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Message 63 of 73 (743903)
12-05-2014 1:03 PM
Reply to: Message 57 by RAZD
12-05-2014 8:37 AM


Re: News to Chiral you up -- back to the topic
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.

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

The first can be tested, the second carries an additional ontological entity and cannot.

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.

Defining OR as "choosing which is simpler" is common but incorrect. OR is a process of stripping away unnecessary or (as in this case) non testable ontological entities.

Cutting away the Prime Mover ontological entity from hypothesis 2 leaves the more ontologically parsimonious (common: simpler) hypothesis 1. Hypothesis 1 is therefore more likely to be correct. Hypothesis 1 is not shown to be true, OR is not a truth table analyitic, just more likely to be correct.

I stand by my correct use of OR and the result achieved in this specific case.

Why should this unnecessary and non testable entity be considered? By what logic or evidence does this religious whim gain any credence?

So now you've made your standard atheist argument for the absence of god/s based on your perceived absence of evidence ...

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.

can we get back to the topic?

Now back to your regularly scheduled topic.

Edited by AZPaul3, : clarity, I hope


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GDR
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Message 64 of 73 (743905)
12-05-2014 1:08 PM
Reply to: Message 61 by New Cat's Eye
12-05-2014 12:19 PM


Re: News to Chiral you up
Cat Sci writes:

But we shouldn't care as it pertains to our science experiments.

I am in complete agreement with your post. I'm going to have to learn to write more clearly.


He has told you, O man, what is good ; And what does the LORD require of you But to do justice, to love kindness, And to walk humbly with your God.

Micah 6:8


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New Cat's Eye
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Message 65 of 73 (743908)
12-05-2014 1:11 PM
Reply to: Message 64 by GDR
12-05-2014 1:08 PM


Re: News to Chiral you up
I'm going to have to learn to write more clearly.

You already are, and you've come to the right place


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Tangle
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Message 66 of 73 (743913)
12-05-2014 1:40 PM
Reply to: Message 58 by New Cat's Eye
12-05-2014 9:36 AM


Re: News to Chiral you up
Cat Sci writes:

Think about it the other way: What if we could not come up with an explanation that works that didn't require a god?

Wouldn't you take that as a indication that a god may be necessary?

That is, of course, what got us into this mess in the first place.


Life, don't talk to me about life - Marvin the Paranoid Android

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


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RAZD
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(1)
Message 67 of 73 (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


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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Replies to this message:
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AZPaul3
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Posts: 3427
From: Phoenix
Joined: 11-06-2006
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Message 68 of 73 (743925)
12-05-2014 5:23 PM
Reply to: Message 67 by RAZD
12-05-2014 4:04 PM


The Side Street
No, it just suggests starting with the simple one first. Period.

Why is that RAZD? Because unburdened of its excess baggage the more parsimonious hypothesis is "more likely" to be correct. Period.

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.

Oh, come on RAZD. Peoples perceptions as evidence? You should know better.

The plural of anecdote is not data.

There is indeed a total, glaring, demonstrable lack of evidence (objective, recognizable, repeatable evidence not some flaky spiritual emotion-centered perception masquerading as "lets pretend it qualifies as" evidence) for any flavor, kind or style of supernatural anything.

If my "perception" of this absolute lack of evidence for anything supernatural is in error then show me. I'm willing to revise my stand.

No, don't answer. I know. Wrong thread. This is a good one. I will stop throwing sand in it.


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AZPaul3
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Posts: 3427
From: Phoenix
Joined: 11-06-2006
Member Rating: 7.5


(1)
Message 69 of 73 (743928)
12-05-2014 7:39 PM
Reply to: Message 67 by RAZD
12-05-2014 4:04 PM


Re: News to Chiral you up -- back to the topic
does this explanation for chirality link the two threads together or are there other steps\blocks that need to be filled in?

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.

This is critical if we are going to have the materials required to produce those first simple self-catalyzing, reproducing, short-chain RNAs.

[ABE]

Found something interesting. From 2011, Dr. David Deamer

Pretty much the state of the discipline for abiogenesis as of then. Nicely detailed.

Edited by AZPaul3, : add link


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ringo
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Posts: 13026
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(1)
Message 70 of 73 (743972)
12-06-2014 11:51 AM
Reply to: Message 68 by AZPaul3
12-05-2014 5:23 PM


Re: The Side Street
AZPaul3 writes:

Because unburdened of its excess baggage the more parsimonious hypothesis is "more likely" to be correct.


No. Because the simpler hypothesis is easier to investigate.
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RAZD
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Message 71 of 73 (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, : .


we are limited in our ability to understand
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RAZD
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Joined: 03-14-2004
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Message 72 of 73 (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 73 (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.

Enjoy


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