Paradox DNA Codes for Proteins Which It Needs for Survival

[oBWhat]

Ok tough question or a nice paradox.

How can DNA (same for RNA) require proteins which it encodes to maintain its integrity and replicate? And if this is the case, how could they both (DNA and associated proteins) be created from scratch i.e without outside influence?

Even the most basic of life contain DNA, RNA and protein.....so how could that basic life have formed?

[danfive]

I believe most of those maintenance proteins evolved to accomodate bigger and more sophisticated genomes. In other words they did not originate at the same time.

As to basic lifeforms now, even they are products of evolution, and are more complex than what the actual beginnings of life would look like. Evolutionary theory books I've read postulate that more basic lifeforms were mostly RNA based where RNA encoded hereditary info and catalyzed reactions within a micelle-like membrane. This is called the RNA world hypothesis and you can read about it in wikipedia --> [Only registered users see links. ]

[danfive]

That wiki entry is really worth reading, here's part of the intro:

The RNA world hypothesis proposes that a world filled with RNA (ribonucleic acid) based life predates current DNA (deoxyribonucleic acid) based life. RNA, which can store information like DNA and catalyze reactions like proteins (enzymes), may have supported cellular or pre-cellular life. Some hypotheses as to the origin of life present RNA-based catalysis and information storage as the first step in the evolution of cellular life.

The RNA world is proposed to have evolved into the DNA and protein world of today. DNA, through its greater chemical stability, took over the role of data storage while protein, which is more flexible in catalysis through the great variety of amino acids, became the specialized catalytic molecules. The RNA world hypothesis suggests that RNA in modern cells, in particular rRNA (RNA in the ribosome which catalyzes protein production), is the evolutionary remnant of the RNA world.

[danfive]

Here's another entry from wikipedia, its the outline for Major Transitions in Evolution, (the book I was thinking about in an earlier post):

Transitions described in the book

1. Replicating molecules to Populations of molecules in compartments Can't observe
2. Independent replicators (probably RNA) to Chromosomes
3. RNA as both genes and enzymes to DNA as genes, proteins as enzymes
4. Prokaryotes to Eukaryotes Can observe
5. Asexual clones to sexual populations — evolution of sex
6. Protists to multicellular organisms — animals, plants, fungi; evolution of multicellularity
7. Solitary individuals to colonies with non-reproductive castes
8. Primate societies to Human societies with language, enabling memes

Maynard Smith and Szathmary identified several properties common to the transitions:

1. Smaller entities have often come about together to form larger entities. e.g. Chromosomes, eukaryotes, sex multicellular colonies.
2. Smaller entities often become differentiated as part of a larger entity. e.g. DNA & protein, organelles, anisogamy, tissues, castes
3. The smaller entities are often unable to replicate in the absence of the larger entity. e.g. Organelles, tissues, castes
4. The smaller entities can sometimes disrupt the development of the larger entity e.g. Meiotic drive (selfish non-Mendelian genes), parthenogenesis, cancers, coup d’état
5. New ways of transmitting information have arisen.e.g. DNA-protein, cell heredity, epigenesis, universal grammar.

And the link --> [Only registered users see links. ]

[danfive]

Originally Posted by oBWhat

And if this is the case, how could they both (DNA and associated proteins) be created from scratch i.e without outside influence?

Concerning things created from scratch, check out ---> [Only registered users see links. ] Contains summaries of all models and hypotheses on the subject.

[oBWhat]

Originally Posted by danfive

That wiki entry is really worth reading, here's part of the intro:

The RNA world hypothesis proposes that a world filled with RNA (ribonucleic acid) based life predates current DNA (deoxyribonucleic acid) based life. RNA, which can store information like DNA and catalyze reactions like proteins (enzymes), may have supported cellular or pre-cellular life. Some hypotheses as to the origin of life present RNA-based catalysis and information storage as the first step in the evolution of cellular life.

The RNA world is proposed to have evolved into the DNA and protein world of today. DNA, through its greater chemical stability, took over the role of data storage while protein, which is more flexible in catalysis through the great variety of amino acids, became the specialized catalytic molecules. The RNA world hypothesis suggests that RNA in modern cells, in particular rRNA (RNA in the ribosome which catalyzes protein production), is the evolutionary remnant of the RNA world.

Thanks for your input Danfive very interesting discussion. The problem is even viruses of RNA have protein caps and many other protein structures.

This is even true for bacteriophages which infect the oldest prokaryotes including bacteria.

I am not exactly sure how RNA enzymes alone could replicate RNA in order for it to survive or even how they would have been created along with RNA strands. There would even have to be an abundance of nucleotides for it to continue to exist which in a world of "new" compounds this would not be the case. Also, there is no evidence that there exists an RNA-based transcription enzyme.

Furthermore, in a harsh hot, environment hell even on a pretty "sterile" benchtop RNA degrades. Back then there may not have been RNAses however, UV light, pH and the chemical environment would have quickly destroyed any miracle molecules.

Even the ribosome which conducts translation is partly RNA but a great deal protein. I know there are RNA enzymes out there however they are not at the complexity of protein enzymes such as transcriptosomes.

More interesting is that life is the complete opposite of entropy. When you drop ink into a pool in spreads.
Lets jump to cells. Why and what purpose would possess a bag of lipids, or cells to keep a membrane potential?

Good discussion

[oBWhat]

Just of note:

"A puzzle piece that we lack for the RNA world is the demonstration that RNA
can copy itself. The as-yet-undiscovered "RNA-dependent RNA autoreplicase" remains
a Holy Grail for origins-of-life research."

for more on this:
[Only registered users see links. ]

[danfive]

Originally Posted by oBWhat

The problem is even viruses of RNA have protein caps and many other protein structures.

This is even true for bacteriophages which infect the oldest prokaryotes including bacteria.

Viruses evolved as well that's why they are a compilation of useful biological tools, their existence and simple design doesn't support a paradox.

Originally Posted by oBWhat

I am not exactly sure how RNA enzymes alone could replicate RNA in order for it to survive or even how they would have been created along with RNA strands. There would even have to be an abundance of nucleotides for it to continue to exist which in a world of "new" compounds this would not be the case. Also, there is no evidence that there exists an RNA-based transcription enzyme.

If I'm not mistaken, the third and fourth chapters of the Transitions book goes into detail on how the mechanics of this is possible [Ch. 3 Chemical Evolution and Ch 4 The evolution of templates]. If I remember accurately that substrates, porous rocks for example, produced the pre-cell micro-environment, where such reactions would be more likely. I looked up the chapter using books.google and the section is 3.3 The hypothesis of surface metabolism and 3.4 The logical basis for autocatalysis.

Originally Posted by oBWhat

Furthermore, in a harsh hot, environment hell even on a pretty "sterile" benchtop RNA degrades. Back then there may not have been RNAses however, UV light, pH and the chemical environment would have quickly destroyed any miracle molecules.

Again I believe the microenviroments from porous substrates, or clay, or deep sea vents created micro enviroments that break the rule of harsh hostile enviroment.

Originally Posted by oBWhat

Even the ribosome which conducts translation is partly RNA but a great deal protein. I know there are RNA enzymes out there however they are not at the complexity of protein enzymes such as transcriptosomes.

I saw in wiki that the protein doesn't play any special role in the ribosome. Here's the quote from wikipedia:
In 2001, the RNA world hypothesis was given a major boost with the deciphering of the 3-dimensional structure of the ribosome, which revealed the key catalytic sites of ribosomes to be composed of RNA and for the proteins to hold no major structural role, and be of peripheral functional importance. Specifically, the formation of the peptide bond, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA: the ribosome is a ribozyme. This finding suggests that RNA molecules were most likely capable of generating the first proteins. Other interesting discoveries demonstrating a role for RNA beyond a simple message or transfer molecule include the importance of small nuclear ribonucleoproteins (SnRNPs) in the processing of pre-mRNA and RNA editing and reverse transcription from RNA in Eucaryotes in the maintenance of telomeres in the telomerase reaction.

Here's a link to google.books for Major Transitions in Evolution good read and the table of contents is a great outline of major and minor steps into understanding the molecular basis of evolution. ----> [Only registered users see links. ]

[danfive]

Originally Posted by oBWhat

Just of note:

"A puzzle piece that we lack for the RNA world is the demonstration that RNA
can copy itself. The as-yet-undiscovered "RNA-dependent RNA autoreplicase" remains
a Holy Grail for origins-of-life research."

for more on this:
[Only registered users see links. ]

I'm noting the above as FUD (FUD is generally a strategic attempt to influence public perception by disseminating negative (and vague) information).
Specifically,
1. Emotionally toned words
2. Argument in a circle
3. Putting forward a tautology as if it were a factual judgement.
4. Argument by forced analogy

[oBWhat]

Hello again

I didnt say that the guy here did that why i quoted it:
[Only registered users see links. ]

But I think its a valid point in that if one believes in RNA self replication, there needs to be evidence for the existence of an RNA autoreplisome or whatever you want to call it to maintain this "RNA World" hypothesis.

Also wikipedia is a very poor reference but many people quote it. Sometimes it is good, but most of the people on there have no idea about even basic science. However they do post some good points here:

"Storage of large amounts of information in RNA is not easy. The chemical properties of RNA make large RNA molecules inherently fragile and they can easily be broken down into their constituent nucleotides through hydrolysis. The aromatic bases also absorb strongly in the ultraviolet region, and would have been susceptible to damage and breakdown by background radiation[11] [12]."
and here:
"Since there are no known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions it may be that nucleic acids did not contain the nucleobases seen in life's nucleic acids.[13] Tellingly, the nucleoside cytosine has a half-life in isolation of 19 days at 100°C and 17,000 years in freezing water, which is still very short on the geologic time scale.[14] Others have questioned whether ribose and other backbone sugars could be stable enough to be found in the original genetic material.[15] For example, the ester linkage of ribose and phosphoric acid in RNA is known to be prone to hydrolysis.[16] Additionally, ribose must all be the same enantiomer, because any nucleotides of the wrong chirality act as chain terminators[17]."

Which is basically what I have been saying more or less.

Also I strongly disagree that proteins play no role in the ribosome. Studying translation for a long time as a PhD, protein regions on ribosomes are not only conserved throughout different species but also play an important role both enzymatically and in other processes involved in translation.

But more seriously most scientists believe the RNA World Hypothesis is a joke. There are just too many obstacles for it to be a viable hypothesis.

I mentioned a few including degradation but there are even bigger ones:
For one nucleotide isomeric impurities would block the replication of the RNA. Also there is no plausible way that primed nucleotides could be supplied to this RNA "enzyme". A good review is posted here:
[Only registered users see links. ]

And some references from other researchers:
Orgel, L. 1994. The origin of life on earth. Scientific American. 271 (4) p. 82.
Shapiro, R. 1995. The prebiotic role of adenine: a critical analysis. Orig. Life Evol. Biosph. 25: 83-98 25: 83-98.
Shapiro, R. 1999. Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life. Proc. Natl.Acad. Sci. USA 96: 4396-4401.
Shapiro, R. 2000. A replicator was not involved in the origin of life. IUBMB Life 49: 173-176.