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Author Topic:   coded information in DNA
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Message 331 of 334 (512967)
06-22-2009 9:34 PM


Closing Time Soon: Please Post Summations
This thread is way past 300 messages, so it's time to post summations. I'll allow 2 or 3 days for this.

Please do not post replies. Only post summations.

Please do not reply to any summation.


--Percy
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Message 332 of 334 (512970)
06-22-2009 10:30 PM
Reply to: Message 329 by WordBeLogos
06-22-2009 8:52 PM


Summary
Back in post #306 I wrote:

quote:
If you're doing a summary post, you left out "Amen."

Because that's what you're doing is presenting us with your religious beliefs (witnessing?) wrapped up in any science that you feel supports those beliefs, while ignoring the vast majority of science that contradicts them.


In post #307 you took issue with this:

quote:
My religious / theological beliefs have nothing to do with this argument.

Which brings us to your post #310, in which you wrote:

quote:
There is no logical choice other than the information came from outside the material universe; that it came from an uncaused cause; and that the cause itself is both code and a designer. Which brings us to

John 1:1: "In the beginning was the WORD and the Word was with God and the Word was God. He was in the beginning with God. And through Him all things were made. Everything we know about DNA leads us to Jesus Christ."

Joh 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.
Joh 1:2 The same was in the beginning with God.
Joh 1:3 All things were made by him; and without him was not any thing made that was made.

Joh 1:14 And the Word (information) was made flesh, and dwelt among us, and we beheld his glory, the glory as of the only begotten of the Father, full of grace and truth.

Heb 1:3 Who being the brightness of his glory, and the express image of his person, and upholding all things by the word (information) of his power, when he had by himself purged our sins, sat down on the right hand of the Majesty on high;

Joh 1:5 And the light shineth in darkness; and the darkness comprehended it not.
Joh 1:10 He was in the world, and the world was made by him, and the world knew him not.



You are witnessing! You are not presenting scientific data.

You are cherry picking creationist misrepresentations of scientific data and bringing that tripe to us in support of your religious beliefs.

And you are ignoring refutations of your posts, just as you are ignoring any evidence that contradicts your religious beliefs. This much is very clear from your posts.

In short, you are presenting us with creation "science" in a forum devoted to real science.

The sum total of your efforts can only be described as witnessing; you are practicing religious apologetics, not science.

(I'm not impressed.)


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
This message is a reply to:
 Message 329 by WordBeLogos, posted 06-22-2009 8:52 PM WordBeLogos has not yet responded

RAZD
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Posts: 19811
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Message 333 of 334 (512971)
06-22-2009 10:58 PM
Reply to: Message 328 by WordBeLogos
06-22-2009 7:57 PM


Many simple codes, many simple answers.
Hi again, WordBeLogos. Still struggling with reality eh?

RAZD, you are making a huge error here. There are no self-replicating molecules of any kind, outside of the realm of life.

I challenge you to show us one that does not already come from a living thing.

Before you provide a link of something you claim does, please read it carefully and see if it actually replicates at all.

Get ready to put on your denial helmet:

(1)

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)

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)

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)

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)

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).

Note - Q beta Replicase: is an enzyme that catalyzes the replication of the RNA of coliphage Q beta, and Q beta, Coliphage: is a bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the longer version of the genome and have no separate cell lysis gene. This is from a virus.

(6)

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)

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)

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)

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)

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)

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.

(11)

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.

(12)

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.

(13)

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.

(14)

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.

(15)

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)

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)

quote:
The RNA World

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)

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)

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)

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)

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.

And finally,

As I said before - you have it backwards, DNA is a result of the natural coded behavior of simpler self-replicating molecules, including RNA, peptides and other organic molecules.

Enjoy

ps - it took me longer to assemble this post than it did to find the articles.

Edited by RAZD, : fixed

Edited by RAZD, : ps

Edited by RAZD, : Qbeta info


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This message is a reply to:
 Message 328 by WordBeLogos, posted 06-22-2009 7:57 PM WordBeLogos has not yet responded

Percy
Member
Posts: 18369
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


Message 334 of 334 (513035)
06-24-2009 10:05 AM


Summation
I've already had my say, more times than I would have thought necessary. It would be nice to have a successor thread with some real back and forth. An actual discussion about naturally produced information and codes would be welcome.

--Percy


  
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