Freethought & Rationalism Archive

Beer God · 05-12-2003, 04:13 PM

I have been posed a tough question by a creationist, and was wondering if an evolution here could answer it:

DNA requires ~ 75 proteins to function, but proteins are only created by the direction of DNA through RNA. How could early organisms use DNA as hereditary information if they didn't have the proteins to make DNA function??
How did DNA become the center of information for all organisms if it is useless without proteins? Did these 75 proteins also create themselves randomly and just happened to all find a DNA molecule and hang around with it and know exactly what to do with a DNA molecule?

Something tells me DNA, it's necessary proteins and RNA had to be created at the same time for life to even exist. We knoe of no life, even bacteria that doesn't have DNA. Answer that one.

?

Doubting Didymus · 05-12-2003, 04:19 PM

The first replicating entities were RNA. DNA came later. Problem solved.

johngalt · 05-12-2003, 04:22 PM

Quote:

DNA requires ~ 75 proteins to function, but proteins are only created by the direction of DNA through RNA.

My biology teacher told me my freshmen year that the atmosphere on earth was very different than the present one. He said that scientists have done tests simulating the atmosphere and made electrical charges go through it. They found out from this experiment that amino acids are created by these small charges, which means that lightning bolts could have created amino acids.

I don't know how feasible this is, but if you research this further it might help you.

caravelair · 05-12-2003, 04:52 PM

i think the fault lies in the assumption that DNA is required for "life". the first "life" could have been a self-replicating peptide molecule, which is certainly less complicated than DNA, and there are several self-replicating peptides we know of.

Dr.GH · 05-12-2003, 06:33 PM

RNA clearly preceded DNA. The idea of "first replicators" doesn't stop at RNA There are several alternates to the "RNA World" hypothesis. Some references free on the web, or at a good library:

Arcady R. Mushegian and Eugene V. Koonin
1996 A minimum gene set for cellular life derived by comparison of complete bacterial genomes, Proceedings of the National Academy of Science, USA, vol 93, p 10268

Brooks DJ, Fresco JR, Lesk AM, Singh M.
2002 Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55.

D.W. Deamer
1997 "The First Living Systems - A Bioenergetic Perspective," Microbiology and Molecular Biology Reviews, 61(2): 239; June

Dyall, Sabrina D., Patricia J. Johnson
2000 �Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.� Current Opinion in Microbiology 3:404-411

Harris, J. Kirk, Scott T. Kelley, George B. Spiegelman, and Norman R. Pace
2003 The Genetic Core of the Universal Ancestor
http://www.genome.org/cgi/content/ab...GR-6528v1?etoc

Lazcano, Antonio, Stanley L. Miller
1996 �The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time� Cell vol 85:793-798

Martin, William, Michael J. Russell
2002 "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" The Royal Society: Philosophical Transactions: Biological Sciences Volume: 358 Number: 1429 Page: 59 --85

Rasmussen, Steen, Liaohai Chen, Barbel M. R. Stadler, Peter F. Stadler
2002 �Proto-Organism Kenetics: Evolutionary Dynamocs of Lipid Aggregates with Genes and Metabolism� Santa Fe Institute Pre-print

Reader, J. S. and G. F. Joyce
2002 "A ribozyme composed of only two different nucleotides." Nature vol 420, pp 841-844.

Woese, Carl
1998 �The universal ancestor� PNAS Vol. 95, Issue 12, 6854-6859, June 9

Woese, Carl
2002 �On the evolution of Cells� PNAS Vol. 99 13:8742-8747, June 25

Basically, DNA is a later evolutionary event than RNA. RNA is capable of self replication, but for a number of known reasons, it was preceded by other molecules.

The first "Life" was not the cell, but cellular precursers. These were similar to parts of cells that we see today. In addition to peptides which have been clearly shown to be abiotic in origin, lipids (and related molecules) were also abiotically avialable. These formed the first conjoint complex molecular systems together with peptides and primitive (and probably short) polypeptides.

Enjoy.

MortalWombat · 05-12-2003, 07:36 PM

As has been indicated earlier, RNA most likely preceded DNA as a replicative molecule. Not only that, but RNA itself can be catalytic, owing to its reactive 2' hydroxyl group.

Indeed, an in vitro selected RNA ribozyme has been shown to catalyze the accurate replication of another RNA product from nucleoside triphosphates, an RNA template, and a primer, with no proteins necessary:

Quote:

Science 2001 May 18;292(5520):1319-25

RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension.

Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP.

Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.

The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

RNA ribozymes have also been selected that can catalyze peptide bond formation:

Quote:

Nature 1997 Nov 6;390(6655):96-100

Peptide bond formation by in vitro selected ribozymes.

Zhang B, Cech TR.

Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.

An attractive solution to the problem of the origin of protein synthesis in an evolving 'RNA world' involves catalysis by nucleic acid without assistance from proteins. Indeed, even the modern ribosome has been considered to be fundamentally an RNA machine, and the large ribosomal subunit can carry out peptidyl transfer in the absence of most of its protein subunits. Successive cycles of in vitro selection and amplification have been used to find RNAs that perform many biochemical reactions, including transfer of an RNA-linked amino acid to their own 5'-amino-modified terminus. Here we demonstrate the in vitro selection of ribozymes (196 nucleotides) that perform the same peptidyl transferase reaction as the ribosome: that is, they can join amino acids by a peptide bond. Like ribosome substrates, one amino acid (N-blocked methionine) is esterified to the 3'(2')-O of adenosine, whereas the acceptor amino acid (phenylalanine) has a free amino group. Our best characterized ribozyme recognizes the amino-acid ester substrate by binding its adenosine moiety, and is therefore capable of utilizing Leu- and Phe- as well as Met-derived substrates. Such lack of specificity with respect to the amino acid is a feature necessary for a generalized protein-synthesizing enzyme.

And the following paper even describes the creation by in vitro selection of an RNA ligase ribozyme which is only composed of two different nucleotides (both of which are very stable):

Quote:

Nature 2002 Dec 19-26;420(6917):841-4

A ribozyme composed of only two different nucleotides.

Reader JS, Joyce GF.

Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

RNA molecules are thought to have been prominent in the early history of life on Earth because of their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, owing to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unit. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyse the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalysed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

Kosmo · 05-12-2003, 09:53 PM

Quote:

Originally posted by caravelair
... and there are several self-replicating peptides we know of.

Really? Do you mean purely self-replicating? Without DNA/RNA templates?

I was not aware of this.

Wounded King · 05-13-2003, 01:19 AM

Check out

Yao S, Ghosh I, Zutshi R, Chmielewski J. Selective amplification by auto- and cross-catalysis in a replicating peptide system.
Nature. 1998 Dec 3;396(6710):447-50.

Quote:

Self-replication has been demonstrated in synthetic chemical systems based on oligonucleotides, peptides and complementary molecules without natural analogues. However, within a living cell virtually no molecule catalyses its own formation, and the search for chemical systems in which both auto- and cross-catalysis can occur has therefore attracted wide interest. One such system, consisting of two self-replicating peptides that catalyse each other's production, has been reported. Here we describe a four-component peptide system that is capable of auto- and cross-catalysis and allows for the selective amplification of one or more of the products by changing the reaction conditions. The ability of this system selectively to amplify one or more molecules in response to changes in environmental conditions such as pH or salt concentration supports the suggestions that self-replicating peptides may have played a role in the origin of life.

Daggah · 05-13-2003, 04:18 AM

Quote:

We knoe of no life, even bacteria that doesn't have DNA.

That's not true, is it? I'm sure I remember learning about bacteria that used RNA instead of DNA in biology.

Wounded King · 05-13-2003, 05:22 AM

Are you sure you arent getting confused with Retroviruses Daggah? Although it is arguable whether viruses are alive or not there are a number of them which do not themselves contain DNA, although they still require the DNA of their host cell to replicate.

As far as I know Beer Gods statement is true but all it means, as has been pointed out, is that DNAs role almost certainly evolved before true cellularity.

05-12-2003, 04:13 PM	#1
Beer God Junior Member Join Date: Apr 2003 Location: USA Posts: 67	Can an Evolutionist answer this? I have been posed a tough question by a creationist, and was wondering if an evolution here could answer it: DNA requires ~ 75 proteins to function, but proteins are only created by the direction of DNA through RNA. How could early organisms use DNA as hereditary information if they didn't have the proteins to make DNA function?? How did DNA become the center of information for all organisms if it is useless without proteins? Did these 75 proteins also create themselves randomly and just happened to all find a DNA molecule and hang around with it and know exactly what to do with a DNA molecule? Something tells me DNA, it's necessary proteins and RNA had to be created at the same time for life to even exist. We knoe of no life, even bacteria that doesn't have DNA. Answer that one. ?

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05-12-2003, 04:19 PM	#2
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	The first replicating entities were RNA. DNA came later. Problem solved.

05-12-2003, 04:52 PM	#4
caravelair Regular Member Join Date: Apr 2003 Location: toronto Posts: 420	i think the fault lies in the assumption that DNA is required for "life". the first "life" could have been a self-replicating peptide molecule, which is certainly less complicated than DNA, and there are several self-replicating peptides we know of.

05-12-2003, 06:33 PM	#5
Dr.GH Veteran Member Join Date: Jul 2001 Location: Dana Point, Ca, USA Posts: 2,115	RNA clearly preceded DNA. The idea of "first replicators" doesn't stop at RNA There are several alternates to the "RNA World" hypothesis. Some references free on the web, or at a good library: Arcady R. Mushegian and Eugene V. Koonin 1996 A minimum gene set for cellular life derived by comparison of complete bacterial genomes, Proceedings of the National Academy of Science, USA, vol 93, p 10268 Brooks DJ, Fresco JR, Lesk AM, Singh M. 2002 Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55. D.W. Deamer 1997 "The First Living Systems - A Bioenergetic Perspective," Microbiology and Molecular Biology Reviews, 61(2): 239; June Dyall, Sabrina D., Patricia J. Johnson 2000 �Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.� Current Opinion in Microbiology 3:404-411 Harris, J. Kirk, Scott T. Kelley, George B. Spiegelman, and Norman R. Pace 2003 The Genetic Core of the Universal Ancestor http://www.genome.org/cgi/content/ab...GR-6528v1?etoc Lazcano, Antonio, Stanley L. Miller 1996 �The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time� Cell vol 85:793-798 Martin, William, Michael J. Russell 2002 "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" The Royal Society: Philosophical Transactions: Biological Sciences Volume: 358 Number: 1429 Page: 59 --85 Rasmussen, Steen, Liaohai Chen, Barbel M. R. Stadler, Peter F. Stadler 2002 �Proto-Organism Kenetics: Evolutionary Dynamocs of Lipid Aggregates with Genes and Metabolism� Santa Fe Institute Pre-print Reader, J. S. and G. F. Joyce 2002 "A ribozyme composed of only two different nucleotides." Nature vol 420, pp 841-844. Woese, Carl 1998 �The universal ancestor� PNAS Vol. 95, Issue 12, 6854-6859, June 9 Woese, Carl 2002 �On the evolution of Cells� PNAS Vol. 99 13:8742-8747, June 25 Basically, DNA is a later evolutionary event than RNA. RNA is capable of self replication, but for a number of known reasons, it was preceded by other molecules. The first "Life" was not the cell, but cellular precursers. These were similar to parts of cells that we see today. In addition to peptides which have been clearly shown to be abiotic in origin, lipids (and related molecules) were also abiotically avialable. These formed the first conjoint complex molecular systems together with peptides and primitive (and probably short) polypeptides. Enjoy.

05-13-2003, 05:22 AM	#10
Wounded King Veteran Member Join Date: Mar 2003 Location: Edinburgh Posts: 1,211	Are you sure you arent getting confused with Retroviruses Daggah? Although it is arguable whether viruses are alive or not there are a number of them which do not themselves contain DNA, although they still require the DNA of their host cell to replicate. As far as I know Beer Gods statement is true but all it means, as has been pointed out, is that DNAs role almost certainly evolved before true cellularity.

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