Evolution Spoiler

spumoni
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Evolution Spoiler

I don't have a problem with common descent but there is serious issue with darwinism concerning the origin of DNA.  Can any of you give an explanation for the origin of DNA?


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spumoni wrote:I don't have a

spumoni wrote:

I don't have a problem with common descent but there is serious issue with darwinism concerning the origin of DNA.  Can any of you give an explanation for the origin of DNA?

We'll explain it little by little, just give us pleanty of time.

 

“Religion is regarded by the common people as true, by the wise as false, and by the rulers as useful.” Seneca


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[facepalm photo goes

[facepalm photo goes here]

Could it be that DNA means gaaaaaaawwwwwwwwwwwwwdddddddddddd?????

 


jread
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              You are not asking a question in relation to evolution. Instead, you are asking about abiogenesis and cosmological theories. Might I suggest reading Finding Darwin's God if you are having trouble understanding evolution. It is a very good source for finding answers to evolutionary questions. Just always remember that if you are asking a question about evolution, make sure that evolution is responsible for answering it.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


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I cannot give you an

I cannot give you an "answer" to the question since we don't know. But I can give you a plausible explanation. Firstly, you shouldn't actually say that there is a "serious issue" with a subject unless you are fully familiar with it. Second, you should not use archaic terms such as Darwinism.

What really is under discussion here is the origin of self-replicating molecules. Once self-replicating molecules are in place, the process of biological evolution as described kicks off. The origin of these molecules is not really of any particular concern to evolutionary biologists, that being the discipline called primordial biochemistry. No theory, after all, explains everything. To evolutionary biology, the existence of such molecules is a priori.

On the other hand, I do have a short series of notes on the matter of the origin of self-replicating molecules, if you are interested.

 The process of formation of organic autocatalysis is time consuming. It begins with Piezoelectric systems on crystallien surfaces, which form the progenitors of ribozymes. The first biological molecules on Earth may have been formed by metal based catalysis on the crystalline surface of minerals.

In principle, an elaborate system of molecular synthesis and breakdown called metabolism could have existed as such long before the first cells. Life requires molecules which catalyze reactions hsih lead directly or indirectly to replication of more molecules like themselves. Catalysts with this self promoting propertycan use raw materials to reproduce themselves and therefore divert the same materials from the production of ther substances. In modern cells the most versatile catalysts are polypeptides. However, they cannot propogate self-replication, they do not replicate. There needs to be a molecule which can act as a catalyst and guide its own replication. Such a molecule does exist: RNA

 Polynucleotides Can Both Store Information and Catalyze Chemical Reactions. RNA can propagate itself by means of complementary base pairing. However, this process without catalysis is slow, error prone and inefficient. Today, such processes are catalyzed by a massive battery of complex interactions of RNA and proteins.

In the RNA world, the RNA molecules themselves would have acted as catalysts. A pre-RNA world probably Predates the RNA One. It is unlikely RNA was the first self-replicating propogater. It is difficult to imagine that they could form through nonenzymatic means. The ribonucleotides are hard to form enzymatically, also RNA polymers entail a 5 to 3 chain which must compete with other linkages that are possible including 2 to 5 and 5 to 5. It has been suggested that RNA had another antecendant by molecules with similar properties. Candidates for pre-RNA include p-RNA and PNA (peptide nucleic acid)

The transition from pre-RNA to RNA would have occurred through the synthesis of RNA via these simpler components as template and catalyst. Laboratory experiments demonstrate this as plausible. PNA can act as a template for RNA molecules. Once the first RNA molecules had been produced, they could have outphased their antecedents leading to the RNA world. A similar process would have occured in the formation of DNA.

Single-Stranded RNA molecules can fold into highly elaborate structures Comparisons between many RNA structures reveal conserved motifs, short structural elements used over and over again as part of larger structures. Common motifs include

Single strands, double strands, single nucleotide bulges, triple nucleotide bulges, hairpin loops, symmetric internal loops, asymmetric internall loops, two stem junction, three stem junctions and four stem junctions. RNA molecules can also form common conserved interactions such as psuedoknots and “kissing hairpins” and hairpin-loop bulge contacts.

-Protein catalysts require a surface of unique countours. RNA molecules with appropriate folds can also served as enzyme. Many of the ribozymes work by positioning metal ions at the catalytic sites. Relatively few catalytic RNA exist in modern day cells, being the polypeptides work much better.

An example of In vitro selection of synthetic ribozymes:

 

 

-A large pool of dsDNA each with a randomly generated sequence. Transcription and folding into randomly generated RNA molecules. Addition of ATP derivative containing a sulfer in place of oxygen Only a rare RNA has the ability to phosphorylate itself. This is captured by elution of the phosphorylated material.

These experiments and others like them have created RNAs that can catalyze a wide variety of reactions:

Peptide bond formation in protein synthesis, RNA cleavage and DNA ligation, DNA cleaving, RNA splicing, RNA polymerization, RNA and DNA phosphorylation, RNA aminoacylation, RAN alkylation, Amide bond formation, amide bond cleavage, glycosidic bond formation and porphyrin metalation, since, like proteins, ribozymes undergo allosteric conformation change

Self-Replication Molecules Undergo Natural Selection. This process is called chemical evolution:

-The 3D structure is what gives the ribozyme chemical properties and abilities. Certain polynucleotides therefore will be especially successful at self-replication. Errors inevitably occur in such processes, and therefore variations will occur over time. Consider an RNA molecule that helps catalyze template polymerization, taking any RNA as a template

-This molecule can replicate. It can also promote the replication of other RNA. If some of the other RNA have catalytic activity that help the RNA to survive in other ways, a set of different types of RNA may evolve into a complex system of mutual cooperation.

One of the crucial events leading to this must have been the development of compartments. A set of mutually beneficial RNA could replicate themselves only if the specialized others were to remain in proximity

Selection of a set of RNA molecules according to the quality of replication could not occur efficiently until a compartment evolved to contain them and therefore make them available only to the RNA that had generated them. A crude form of this may have simply been simple absorption on surfaces or particles.

The need for more sophisticated containment fulfilled by chemicals with the simple physiochemical properties of ampipathism. The bilayers they form created closed vesicles to make a plasma membrane. In vitro RNA selection experiments produced RNA molecules that can tightly bind to amino acids. The nucleotide sequence of such RNA contains a disproportionate number of codons corresponding to the amino acid. This is not perfect for all amino acids, but it raises the possibility that a limited genetic code could have arised this way. Any RNA that guided the synthesis of a useful polypeptide would have a great advantage.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

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spumoni
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jread

jread wrote:

              You are not asking a question in relation to evolution. Instead, you are asking about abiogenesis and cosmological theories. Might I suggest reading Finding Darwin's God if you are having trouble understanding evolution. It is a very good source for finding answers to evolutionary questions. Just always remember that if you are asking a question about evolution, make sure that evolution is responsible for answering it.

 

Here's my issue:  the entire premise of evolution is dependent upon a self-replicating organism.  This requires
DNA.  So which came first?


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deludedgod wrote:I cannot

deludedgod wrote:

I cannot give you an "answer" to the question since we don't know. But I can give you a plausible explanation. Firstly, you shouldn't actually say that there is a "serious issue" with a subject unless you are fully familiar with it. Second, you should not use archaic terms such as Darwinism.

What really is under discussion here is the origin of self-replicating molecules. Once self-replicating molecules are in place, the process of biological evolution as described kicks off. The origin of these molecules is not really of any particular concern to evolutionary biologists, that being the discipline called primordial biochemistry. No theory, after all, explains everything. To evolutionary biology, the existence of such molecules is a priori.

On the other hand, I do have a short series of notes on the matter of the origin of self-replicating molecules, if you are interested.

 The process of formation of organic autocatalysis is time consuming. It begins with Piezoelectric systems on crystallien surfaces, which form the progenitors of ribozymes. The first biological molecules on Earth may have been formed by metal based catalysis on the crystalline surface of minerals.

In principle, an elaborate system of molecular synthesis and breakdown called metabolism could have existed as such long before the first cells. Life requires molecules which catalyze reactions hsih lead directly or indirectly to replication of more molecules like themselves. Catalysts with this self promoting propertycan use raw materials to reproduce themselves and therefore divert the same materials from the production of ther substances. In modern cells the most versatile catalysts are polypeptides. However, they cannot propogate self-replication, they do not replicate. There needs to be a molecule which can act as a catalyst and guide its own replication. Such a molecule does exist: RNA

 Polynucleotides Can Both Store Information and Catalyze Chemical Reactions. RNA can propagate itself by means of complementary base pairing. However, this process without catalysis is slow, error prone and inefficient. Today, such processes are catalyzed by a massive battery of complex interactions of RNA and proteins.

In the RNA world, the RNA molecules themselves would have acted as catalysts. A pre-RNA world probably Predates the RNA One. It is unlikely RNA was the first self-replicating propogater. It is difficult to imagine that they could form through nonenzymatic means. The ribonucleotides are hard to form enzymatically, also RNA polymers entail a 5 to 3 chain which must compete with other linkages that are possible including 2 to 5 and 5 to 5. It has been suggested that RNA had another antecendant by molecules with similar properties. Candidates for pre-RNA include p-RNA and PNA (peptide nucleic acid)

The transition from pre-RNA to RNA would have occurred through the synthesis of RNA via these simpler components as template and catalyst. Laboratory experiments demonstrate this as plausible. PNA can act as a template for RNA molecules. Once the first RNA molecules had been produced, they could have outphased their antecedents leading to the RNA world. A similar process would have occured in the formation of DNA.

Single-Stranded RNA molecules can fold into highly elaborate structures Comparisons between many RNA structures reveal conserved motifs, short structural elements used over and over again as part of larger structures. Common motifs include

Single strands, double strands, single nucleotide bulges, triple nucleotide bulges, hairpin loops, symmetric internal loops, asymmetric internall loops, two stem junction, three stem junctions and four stem junctions. RNA molecules can also form common conserved interactions such as psuedoknots and “kissing hairpins” and hairpin-loop bulge contacts.

-Protein catalysts require a surface of unique countours. RNA molecules with appropriate folds can also served as enzyme. Many of the ribozymes work by positioning metal ions at the catalytic sites. Relatively few catalytic RNA exist in modern day cells, being the polypeptides work much better.

An example of In vitro selection of synthetic ribozymes:

 

 

-A large pool of dsDNA each with a randomly generated sequence. Transcription and folding into randomly generated RNA molecules. Addition of ATP derivative containing a sulfer in place of oxygen Only a rare RNA has the ability to phosphorylate itself. This is captured by elution of the phosphorylated material.

These experiments and others like them have created RNAs that can catalyze a wide variety of reactions:

Peptide bond formation in protein synthesis, RNA cleavage and DNA ligation, DNA cleaving, RNA splicing, RNA polymerization, RNA and DNA phosphorylation, RNA aminoacylation, RAN alkylation, Amide bond formation, amide bond cleavage, glycosidic bond formation and porphyrin metalation, since, like proteins, ribozymes undergo allosteric conformation change

Self-Replication Molecules Undergo Natural Selection. This process is called chemical evolution:

-The 3D structure is what gives the ribozyme chemical properties and abilities. Certain polynucleotides therefore will be especially successful at self-replication. Errors inevitably occur in such processes, and therefore variations will occur over time. Consider an RNA molecule that helps catalyze template polymerization, taking any RNA as a template

-This molecule can replicate. It can also promote the replication of other RNA. If some of the other RNA have catalytic activity that help the RNA to survive in other ways, a set of different types of RNA may evolve into a complex system of mutual cooperation.

One of the crucial events leading to this must have been the development of compartments. A set of mutually beneficial RNA could replicate themselves only if the specialized others were to remain in proximity

Selection of a set of RNA molecules according to the quality of replication could not occur efficiently until a compartment evolved to contain them and therefore make them available only to the RNA that had generated them. A crude form of this may have simply been simple absorption on surfaces or particles.

The need for more sophisticated containment fulfilled by chemicals with the simple physiochemical properties of ampipathism. The bilayers they form created closed vesicles to make a plasma membrane. In vitro RNA selection experiments produced RNA molecules that can tightly bind to amino acids. The nucleotide sequence of such RNA contains a disproportionate number of codons corresponding to the amino acid. This is not perfect for all amino acids, but it raises the possibility that a limited genetic code could have arised this way. Any RNA that guided the synthesis of a useful polypeptide would have a great advantage.

Can you provide the experiments for RNA self-replication or enzyme catalytic activity?  It was my understanding that amino acids require DNA to exist.


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It depends on your

It depends on your definition of "organism". Obviously, DNA is the antecedant to cells, but the antecedant to cellular structure, which are lipid vesicles that form spherical membranes which enclose self-replicating molecular systems are the antecedant to cells too, and they were active before DNA, playing an important part in the RNA world. Life arose in the ocean. Water has left a permanent stamp on our biology. If you define organisms in terms of "cells", DNA came first. If you define an organism as "life", and any set of self-replicating molecules that encode information, as "life", then organisms came before DNA. Organisms do not require DNA in principle. DNA is simply the self-replicating molecule that is employed by all of todays organisms because they are descended from ancestry with DNA. But the first DNA based organisms would have been so simple and primitive as to have arose very gradually from a transition from RNA. The "transition" from RNA is more of an addition process, since the pre-DNA world would already have included autocatalysis, ribozymes, some form of transcription and replication, and of course, mutation and recombination. Elaborate biomolecular systems were certainly present before DNA become the bookkeeping molecule of life. It is difficult to imagine anything to the contrary of that statement. This process is called chemical evolution.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

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deludedgod
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You will need online access

You will need online access to journals so you can see the whole paper, not just the abstract. Just enter a scientific database like NCBI or AAAS and type in "elution and "chromatography".I am unsure where you came across the idea that "amino acids" need DNA to exist. Amino acids are a large family of small organic molecules consisting of a carboxyl group, a hydrogen group, an alpha carbon, a side chain and an amine group. This chemical family is unrelated to DNA, which stands for Deoxyribonucleic acid, and is hence part of the nucleic acid family, consisting of purine and pyrimidine rings, not chemically related to amino acids.

Perhaps you mean "polypeptides" need DNA to exist since DNA holds the codons which are transcribed into RNA which are translated into protein. You would still be incorrect, however. Modern organisms do require this. However, this is because the system has been in place for so long and is so universal that is essentially an irreversible system short of catastrophic destruction of life on this planet. It is important to remember that the first biological life would not have used amino acids at all, but ribozymes in catalysis. Ribozymes are not as good as polypeptides at catalysis, but they are ancient and a very old part of life on this planet, and despite being almost wholly outphased by proteins, they are enormously important even in biological life today. The ribosome is 2/3 rRNA. The snRNA and snoRNA are autocatalytic as well. Other forms of RNA reflect what is now a median process in the step between DNA and protein but used to be the immediate step. Transcription. mRNA, miRNA, siRNA, all work on the principle of base pairing and complementary bonding that DNA works on. DNA did eventually outphase RNA. But the first polypeptides arose before DNA-based organisms. There was a reason for this:

-DNA is obviously a more advantegous molecule to use. It is more stable, but more importantly, it can form larger double-strands. The double-strand is enormously important in biology. It allows the information in DNA to be kept in two templates, the one holding the base pairs in question, and the one that can retrieve them via templated polymerization.

Whenever we examine the requisites for certain systems in biological life, it is important to remember that because of the process of coevolution, their antecedants did not start out that way. The modern mitochondria and eukaryota both need each other because they have been in symbiosis for so long that mtDNA has ingrained itself in the nuclear genome hence making it an irreversible addition to the Eukaryota. Without it, the organelle dies. WIthout the organelle, the cell dies. But their antecedants, as they had not evolved "into" each other yet, did not require this relationship. THis is true of many complex interlocking systems in biology, and the concept of mutual interlocking dependancy is an enormous topic on evolutionary biology

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


jread
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spumoni wrote:jread

spumoni wrote:

jread wrote:

              You are not asking a question in relation to evolution. Instead, you are asking about abiogenesis and cosmological theories. Might I suggest reading Finding Darwin's God if you are having trouble understanding evolution. It is a very good source for finding answers to evolutionary questions. Just always remember that if you are asking a question about evolution, make sure that evolution is responsible for answering it.

 

Here's my issue:  the entire premise of evolution is dependent upon a self-replicating organism.  This requires
DNA.  So which came first?

 

Again, your question does not apply to evolution. The evidence that evolution is happening exists. How evolution began is another field of scientific research. Of course, being a theist, how evolution began or how what precluded DNA came into existence can be a point of inserting the hand of God. However, justifying faith based on science's (current) lack of understanding or ability to provide an explanation is a problematic approach. If faith in God's existence rests in the gaps of science, then where does that leave your faith in God when the gaps are filled? I would recommend following deludedgod's advice. Searching for the answer to your questions is never a bad thing. And what you'll come to find out, is that science is actually very modest and humble in their claims. Scientists are passionate about their research, but neglect positing "Truth" claims in relation to their discoveries. The self-checking mechanisms of science are an excellent method of insuring that evidentiary support is priority number one. The origin of DNA is something that I am trying to understand as well. My understanding is far below what should accompany such an endeavor, but I've found that the information I've come upon thus far is both exciting and humble.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat