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Author Topic:   Converting raw energy into biological energy
jar
Member (Idle past 395 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 121 of 314 (419565)
09-03-2007 3:37 PM
Reply to: Message 119 by Rob
09-03-2007 2:45 PM


Re: a la Behe
Common ancestry could be a result of theorized evolutionary processes, or it could be the result of the theology of the common creator working within His created common environment using common materials.
Except there is evidence, abundant evidence of the "theorized evolutionary processes" and so far absolutely NO evidence of the common creator.

Aslan is not a Tame Lion

This message is a reply to:
 Message 119 by Rob, posted 09-03-2007 2:45 PM Rob has replied

Replies to this message:
 Message 123 by Rob, posted 09-03-2007 3:43 PM jar has not replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 122 of 314 (419566)
09-03-2007 3:40 PM
Reply to: Message 120 by Chiroptera
09-03-2007 3:16 PM


Ciroptera:
I don't buy this. Some people claim this, but I don't believe it, if for no other reason than I have never come across a definition of "supernatural" or "spiritual" (as opposed to the "natural" or "material") that didn't have some sort of inherent problems. Something either exists or it does not.
What about a photon? What about the laws of physics? What about energy? Is everything material?
Sidelined has a very interesting link to his homepage. And in that homepage is Feynman's definition of energy as, 'the capacity to do work'. Is it purely another coincidence that, Jesus said to them, "My Father is always at his work to this very day, and I, too, am working." (John 5:17)
When you combine that with the elusive character of light photons, and His comments about being 'the light of the world', and just consider the coherence with modern understandings of physics, it truely boggles the mind. How in the name of Stephen Hawking is that possible?
One of the biggest shocks to me after my conversion was to realize how 'natural' (if I can put it that way) the 'spiritual' is... It was there all the time, I just didn't percieve it as such.
As for bias chiroptera, we all have one. Mine was completely subconscious to me until my conversion. Your conscious will agree. You may not like to think about it, but you do have a motive. We all do... but like you said, it's only the creationists who admit it.
We're getting off topic, but I appriciate your honesty in mentioning these issues. I defer to my reply 119 to Percy for answering some of your other questions.
I know that many people have invested enormous resources to the cause of explaining things materially. And I agree with Behe and any other reasonable person that science has made some tremedous advances and discoveries that have been beneficial to mankind. However, that does not mean that material explanations are our savior all of the time. There are non material forces in our universe, and they require another method of understanding to engage them besides methodological naturalism.
There are times when no matter what the investment, we must give up the ghost. Dean Kenyon certainly did. Irrespective of the cost to him personally. He followed his conscious.

This message is a reply to:
 Message 120 by Chiroptera, posted 09-03-2007 3:16 PM Chiroptera has replied

Replies to this message:
 Message 125 by Chiroptera, posted 09-03-2007 4:01 PM Rob has not replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 123 of 314 (419567)
09-03-2007 3:43 PM
Reply to: Message 121 by jar
09-03-2007 3:37 PM


Re: a la Behe
jar:
Except there is evidence, abundant evidence of the "theorized evolutionary processes" and so far absolutely NO evidence of the common creator.
That evidence can be interpreted either way jar. And each of those creatures you refer to contain a quaternary digital code. Find one without that code that wasn't manufactured (which would defeat the point) in a test tube, and I'll convert to the jar brotherhood.
Why don't you just let Percy handle this one...
Edited by Rob, : No reason given.

This message is a reply to:
 Message 121 by jar, posted 09-03-2007 3:37 PM jar has not replied

molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 124 of 314 (419570)
09-03-2007 4:00 PM
Reply to: Message 104 by Rob
09-03-2007 11:39 AM


There's been work done since 2004
Orgel writes:
Molecules that stay together evolve together.
Not necessarily!
Frequency of RNA-RNA interaction in a model of the RNA World, RNA, 12:353-359, 2006.
The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations ... This low probability (of random interactions) could be overcome if the molecules capable of productive recombination were redundant, with many nonhomologous but functionally equivalent RNAs being present in a random population ... Parallel SELEX experiments showed that at least one in 106 random 20-mers binds to the P5.1 stem-loop of Bacillus subtilis RNase P RNA with affinities equal to that of its naturally occurring partner. This high frequency predicts that a single RNA in an RNA World would encounter multiple interacting RNAs within its lifetime, supporting recombination as a plausible mechanism for prebiotic RNA evolution. The large number of equivalent species implies that the selection of any single interacting species in the RNA World would be a contingent event, i.e., one resulting from historical accident.
In other words, it would be inevitable.
Orgel writes:
The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides.
As for de novo synthesis:
Possible prebiotic catalysts formed from adenine and aldehyde, Planetary and Space Science, Volume 48, Issue 11, September 2000, Pages 1139-1142
Prebiotic chemistry experiments search to explain the origins and properties of chemical structures and reactions which may have been involved in the life emergence (for recent reviews see Eschenmoser and Loewenthal, 1992; Sutherland and Whitfield, 1997; Maurel and Décout, 1999). Small molecules present in the primitive Earth atmosphere such as water, carbon monoxide, sulfur dioxide, methane, dinitrogen (but not dioxygen) could react to lead to the elementary building blocks, ammonia, hydrogen cyanide, formaldehyde, acetonitrile, acrylonitrile, cyanogen and cyanoacetylene. Cosmic rays, ionizing radiations, electric discharges and radioactive process induced ion-molecule and radical reactions which led to these building blocks. From these molecules, formation of amino acids ( Miller and Miller; Joshi and Pathak, 1975; Kobayashi et al., 1998) and nucleic acid bases ( Or and Or; Or and Kimball, 1961; Ferris and Orgel, 1966; Robertson and Miller, 1995; Miyakawa et al., 1999) such as adenine 1 (Fig. 1, C5H5N5: pentamer of hydrogen cyanide) under prebiotic conditions could be explained. Many prebiotic molecules could already have been present in comets such as adenine detected into comet Halley dust. Or suggested that comets might already have brought to the Earth biochemical precursors necessary for emergence of life (Or, 1961; Or et al., 1992). Delsemme emphasized more and more evidences support that an intense bombardment of comets has brought to the Earth all the carbon compounds present in organic molecules used by life ( Delsemme and Delsemme 2000).
In the search of chemical prebiotic routes which could lead from nucleic acid bases to building blocks capable of polymerizing to form nucleic acids strands, we are investigating reactions of adenine with different aldehydes under presumably prebiotic conditions. Such reactions could have led to nucleoside and nucleoside-like building blocks endowed with catalytic properties necessary for life. Previously, Fel'dman (1962) reported slow reactions of adenine with formaldehyde in aqueous solution at room temperature under neutral conditions to form adducts on the 6-amino group and/or the 9-nitrogen atom.
Pyruvic acid being a central intermediate in the present metabolism, we studied reactivity of the corresponding aldehyde, pyruvic aldehyde 2 (methylglyoxal), with adenine 1 (Fig. 1) and we are reporting here these results. Pyruvaldehyde could have been produced under prebiotic conditions by retroaldolization from complex mixtures of sugars formed by the formose reaction. It was detected in caramel ( Tomasik et al., 1989) and alkaline decomposition of hexoses such as Image-mannose, Image-xylose and Image-glucose which affords pyruvaldehyde hydrate (Evans, 1942; Feather and Harris, 1973). Such decompositions of sugars could have been a source of various prebiotic molecules like aldehydes and heterocycles.
Careful examination of the present metabolism and in vitro selection of various catalytic RNAs strongly support the “RNA World” hypothesis of the origin of life. However, in this scenario, the difficult prebiotic synthesis of ribose and consequently of nucleotidesnext term remain a major problem. In order to overcome this problem and obtain nucleoside analogs, we are investigating reactions of the nucleic acid base, adenine 1, with different aldehydes under presumably prebiotic conditions. In the reaction of adenine and pyruvaldehyde 2 in water, we report here the formation in high yield of two isomeric products. These compounds possessing alcohols functions as nucleosides result from condensation of two molecules of pyruvaldehyde on the 6-amino group of one adenine molecule.
And then there's this:
Nucleoside Phosphorylation by Phosphate Minerals, Journal of Biological Chemistry, Vol. 282, Issue 23, 16729-16735, 2007.
In prebiotic scenarios biopolymers can be thought of as condensation products of abiotically formed monomers. Polymers (polysaccharides, peptides, and polynucleotides) will not spontaneously form in an aqueous solution from their monomers because of the standard-state Gibbs free-energy change ... In the polymerization process of nucleic acids extant organisms activate the monomers by converting them to phosphorylated derivatives and then utilize the favorable free energy of phosphate hydrolysis to drive the reaction. Does this present day process mimic spontaneously occurring prebiotic reactions, thus representing a sort of biochemiomimesis descending from ancient pathways, or should it be considered a fully novel cellular invention? ... we report the efficient phosphorylation of nucleosides occurring in formamide on numerous phosphate minerals. Consequently, ... activated monomers can form in prebiotic conditions in a liquid, non-aqueous environment in the presence of phosphate minerals in conditions compatible with the thermodynamics of polymerization.
And this:
Protein and nucleic acid together: A mechanism for the emergence of biological selection, Journal of Theoretical Biology, Volume 240, Issue 3, 7 June 2006, Pages 337-342
Recent studies have shown how interactions of the ”RNA world’ with lipids may have been mutually beneficial for both vesicle formation and RNA replication (Chen et al., 2004). In lipid vesicles, replicating RNA molecules profit by being segregated away from non-replicating ”free-loading’ RNAs that would otherwise benefit from efficient RNA polymerase action. Conversely, the ability of RNA molecules to replicate would have allowed vesicles to grow through increased osmotic pressure (Chen et al., 2004). In this scheme, the more successful vesicle/replicating RNA combinations would expand the fastest and would thus be more likely to split into daughter vesicles, thereby fulfilling many of the key requirements for the initiation of primordial life.
Less progress has been made in showing how mutually beneficial interactions could have arisen between the RNA and early protein world. In vitro selection strategies have shown that RNA molecules are capable of carrying out several steps required for amino acid activation and peptide bond formation (Chapple et al., 2003; Ferreira and Coutinho, 1993; Huang et al., 2000; Johnston et al., 2001; Kumar and Yarus, 2001). However, it is unclear how the acquisition of these enzymic activities would have been subject to immediate selection in the primordial environment (Orgel, 1989).
Here I propose a scheme that integrates nucleic acid and protein function in a way that allows the mutual co-evolution of nucleic acid-dependent protein synthesis and nucleic acid-dependent nucleic acid replication. The model proposes a very early association between nucleic acid and protein polymers in the primordial development of life. It suggests a specific role for amyloid; a protein aggregate in which main chain -sheet interactions stabilize the formation of fibres. Predictions from the model are consistent with recently published observations.
This proposal differs from the prevailing ”RNA-world’ model of pre-biotic development because it involves proteins interacting with the nucleic acids much earlier in evolution than previously suggested. It is even possible that the first self-replicating RNA molecules evolved in association with protein/amyloid and never existed in isolation. An advantage of this model is that it suggests simple evolutionary paths from amyloid-associated elongase and replicase activities to ribosomes and RNA polymerase respectively. In particular, the elongase activity could act as a focus for incremental selective changes that were necessary for the development of template-directed peptide bond formation, without any one step being contingent on future evolutionary developments (Chapple et al., 2003; Huang et al., 2000; Johnston et al., 2001; Lohse and Szostak, 1996; Nissen et al., 2000; Yarus and Welch, 2000; Zhang and Cech, 1997).
Re: chirality
A primordial peptide cycle involving the chemical formation and degradation of peptides has recently been proposed (Huber et al., 2003). Here I argue that peptides in solution would be selectively degraded by comparison to those included in amyloid. Mixed chiral peptides are unlikely to have formed amyloid since they have a lower propensity to form -sheet structures (Brack and Barbier, 1990), thus it is likely that amyloid was homochiral and that mixed chiral peptides were selectively degraded and recycled into other random chiral combinations. Base-pairing of nucleic acids during replication has also been argued to promote homochirality (Schoning et al., 2000), leading to the proposal here that both protein and nucleic acid polymers involved in the proposed mechanism were homochiral.
There is no a priori reason to believe that any particular homochiral amyloid-nucleic acid combinations (e.g. DD, DL, LD or LL) would have had a selective advantage. Indeed RNA was found to induce the aggregation of both homo L and D poly (Lys-Leu) polypeptides with equal efficiency (Brack and Barbier, 1990). It is therefore possible that all chiral combinations co-existed and competed with each other. The later development of enzymic activities that could direct the synthesis of chiral protein and RNA precursors would then have been the key event in the genesis of the current chiral combination.

This message is a reply to:
 Message 104 by Rob, posted 09-03-2007 11:39 AM Rob has replied

Replies to this message:
 Message 127 by Rob, posted 09-03-2007 5:00 PM molbiogirl has replied

Chiroptera
Inactive Member


Message 125 of 314 (419571)
09-03-2007 4:01 PM
Reply to: Message 122 by Rob
09-03-2007 3:40 PM


As for bias chiroptera, we all have one.
Sure, depending on what you mean by "bias". If you mean that we all have presumptions about the way the world is, then I agree. But if by "bias" you mean that everyone has unshakeable convictions that no amount of evidence will change, then, no, I don't buy it. Some people do, some don't. Some exhibit this in some areas in their lives, but not in others.
In particular, it has yet to be demonstrated that the vast majority of people working in the biological and geological sciences are so biased toward some sort of "materialistic worldview" that they cannot or will not admit that the data with which they work speak against their materialistic assumptions.
The people who are working research biologists and geologists, including those doing abiogenesis research, come from a variety of different social and cultural backgrounds, have a variety of different religious and philosophical beliefs, and work for a variety of independent institutions and organizations. I have a hard time believing that the reason they all find a natural explanation for the origin of life on earth plausible and likely is because they are so biased that they cannot be swayed by clear evidence otherwise.

I've done everything the Bible says, even the stuff that contradicts the other stuff! -- Ned Flanders

This message is a reply to:
 Message 122 by Rob, posted 09-03-2007 3:40 PM Rob has not replied

Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 126 of 314 (419575)
09-03-2007 4:59 PM
Reply to: Message 119 by Rob
09-03-2007 2:45 PM


Re: a la Behe
Rob writes:
As you said Percy:
So it is not a problem if the designer cannot be directly detected as long as we may detect him by his works.
Well?
So let's design a test that would detect the designer by his works. Let us say that me and a Greek from ancient Athens observe lightning in a thunder storm. I claim the lightning is a natural phenomenon caused by the discharge of electricity between clouds and ground which have become oppositely charged due to the storm. The ancient Athenian says the lightning bolt was cast by Zeus. What test could we make to tell who is right?
If you think about this for a while you'll see that no such test can be devised, but let me take you through a little of the discussion between me and the Athenian to make clear why this is so.
I set up charge meters on the ground and in an airplane in the clouds to measure the electrical charge, and I place an ammeter between an iron post and the ground to measure the electrical current of the lightning. After lightning strikes the pole I show the results to the Athenian. I have charts showing the gradual buildup of opposite charges in the clouds and on the ground that suddenly disappear at the exact time of the lightning strike. And I have another chart of the amount of current flowing between the steel pole and the ground that indicates no current was flowing until the exact time of the lightning strike, at which time a huge amount of current flowed for an extremely short time period. In other words, there was a large current spike when the lightning bolt struck the steel pole.
The Athenian replies that that might all be true, but that it was Zeus who caused the buildup of opposite charges on the ground and in the clouds.
Now what? I could make more detailed measurements showing the flow of charge in the clouds and on the ground and claim that the flow of charge was due to the motion of water droplets in the air, but the Athenian could then claim that Zeus made the water droplets move as they did. So I could then make detailed meteorological measurements showing that it was the wind that caused the water droplets to move as they did, but the Athenian could then claim that Zeus made the wind blow as it did.
Do you see the problem? And look at how difficult it was for me to gather my data. I had to send planes up in the clouds during storms, and I had to buy a special ammeter that could handle a huge flow of current, and I had to make detailed meteorological measurements probably by sending up hundreds of weather balloons. The fact of the matter is that if someone wants to attribute divine causes to a natural phenomenon, no amount of evidence will convince him otherwise.
If you find the lightning example a bit strained, since no one today doubts that lightning is a natural phenomenon, keep in mind that there are still flat-earthers out there (The Flat Earth Society).
So, given that no test can be devised to definitively show one way or the other whether lightning is a natural phenomenon or comes from Zeus, how are you going to devise a test for the much more complicated phenomenon of evolution to definitively show whether it is a natural or divine phenomenon?
No such test is possible, and that's why supernatural causes are not part of science. Supernatural causes are the postulate of spirituality and religion, and not the result of evidence. They are not constrained by reality, and anyone who resorts to supernatural explanations is free to postulate whatever contingency is required. They're just not free to call it science. Science is not in the business of postulating untestable questions.
--Percy

This message is a reply to:
 Message 119 by Rob, posted 09-03-2007 2:45 PM Rob has replied

Replies to this message:
 Message 130 by Rob, posted 09-03-2007 5:30 PM Percy has replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 127 of 314 (419576)
09-03-2007 5:00 PM
Reply to: Message 124 by molbiogirl
09-03-2007 4:00 PM


Re: There's been work done since 2004
Molbiogirl, I just wanted to repost and highlight some of your sources for the blind among us:
Orgel writes:
Molecules that stay together evolve together.
Not necessarily!
Frequency of RNA-RNA interaction in a model of the RNA World, RNA, 12:353-359, 2006.
The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations ... This low probability (of random interactions) could be overcome if the molecules capable of productive recombination were redundant, with many nonhomologous but functionally equivalent RNAs being present in a random population ... Parallel SELEX experiments showed that at least one in 106 random 20-mers binds to the P5.1 stem-loop of Bacillus subtilis RNase P RNA with affinities equal to that of its naturally occurring partner. This high frequency predicts that a single RNA in an RNA World would encounter multiple interacting RNAs within its lifetime, supporting recombination as a plausible mechanism for prebiotic RNA evolution. The large number of equivalent species implies that the selection of any single interacting species in the RNA World would be a contingent event, i.e., one resulting from historical accident.
In other words, it would be inevitable.
Orgel writes:
The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides.
As for de novo synthesis:
Possible prebiotic catalysts formed from adenine and aldehyde, Planetary and Space Science, Volume 48, Issue 11, September 2000, Pages 1139-1142
Prebiotic chemistry experiments search to explain the origins and properties of chemical structures and reactions which may have been involved in the life emergence (for recent reviews see Eschenmoser and Loewenthal, 1992; Sutherland and Whitfield, 1997; Maurel and Décout, 1999). Small molecules present in the primitive Earth atmosphere such as water, carbon monoxide, sulfur dioxide, methane, dinitrogen (but not dioxygen) could react to lead to the elementary building blocks, ammonia, hydrogen cyanide, formaldehyde, acetonitrile, acrylonitrile, cyanogen and cyanoacetylene. Cosmic rays, ionizing radiations, electric discharges and radioactive process induced ion-molecule and radical reactions which led to these building blocks. From these molecules, formation of amino acids ( Miller and Miller; Joshi and Pathak, 1975; Kobayashi et al., 1998) and nucleic acid bases ( Or and Or; Or and Kimball, 1961; Ferris and Orgel, 1966; Robertson and Miller, 1995; Miyakawa et al., 1999) such as adenine 1 (Fig. 1, C5H5N5: pentamer of hydrogen cyanide) under prebiotic conditions could be explained. Many prebiotic molecules could already have been present in comets such as adenine detected into comet Halley dust. Or suggested that comets might already have brought to the Earth biochemical precursors necessary for emergence of life (Or, 1961; Or et al., 1992). Delsemme emphasized more and more evidences support that an intense bombardment of comets has brought to the Earth all the carbon compounds present in organic molecules used by life ( Delsemme and Delsemme 2000).
In the search of chemical prebiotic routes which could lead from nucleic acid bases to building blocks capable of polymerizing to form nucleic acids strands, we are investigating reactions of adenine with different aldehydes under presumably prebiotic conditions. Such reactions could have led to nucleoside and nucleoside-like building blocks endowed with catalytic properties necessary for life. Previously, Fel'dman (1962) reported slow reactions of adenine with formaldehyde in aqueous solution at room temperature under neutral conditions to form adducts on the 6-amino group and/or the 9-nitrogen atom.
Pyruvic acid being a central intermediate in the present metabolism, we studied reactivity of the corresponding aldehyde, pyruvic aldehyde 2 (methylglyoxal), with adenine 1 (Fig. 1) and we are reporting here these results. Pyruvaldehyde could have been produced under prebiotic conditions by retroaldolization from complex mixtures of sugars formed by the formose reaction. It was detected in caramel ( Tomasik et al., 1989) and alkaline decomposition of hexoses such as Image-mannose, Image-xylose and Image-glucose which affords pyruvaldehyde hydrate (Evans, 1942; Feather and Harris, 1973). Such decompositions of sugars could have been a source of various prebiotic molecules like aldehydes and heterocycles.
Careful examination of the present metabolism and in vitro selection of various catalytic RNAs strongly support the “RNA World” hypothesis of the origin of life. However, in this scenario, the difficult prebiotic synthesis of ribose and consequently of nucleotidesnext term remain a major problem. In order to overcome this problem and obtain nucleoside analogs, we are investigating reactions of the nucleic acid base, adenine 1, with different aldehydes under presumably prebiotic conditions. In the reaction of adenine and pyruvaldehyde 2 in water, we report here the formation in high yield of two isomeric products. These compounds possessing alcohols functions as nucleosides result from condensation of two molecules of pyruvaldehyde on the 6-amino group of one adenine molecule.
And then there's this:
Nucleoside Phosphorylation by Phosphate Minerals, Journal of Biological Chemistry, Vol. 282, Issue 23, 16729-16735, 2007.
In prebiotic scenarios biopolymers can be thought of as condensation products of abiotically formed monomers. Polymers (polysaccharides, peptides, and polynucleotides) will not spontaneously form in an aqueous solution from their monomers because of the standard-state Gibbs free-energy change ... In the polymerization process of nucleic acids extant organisms activate the monomers by converting them to phosphorylated derivatives and then utilize the favorable free energy of phosphate hydrolysis to drive the reaction. Does this present day process mimic spontaneously occurring prebiotic reactions, thus representing a sort of biochemiomimesis descending from ancient pathways, or should it be considered a fully novel cellular invention? ... we report the efficient phosphorylation of nucleosides occurring in formamide on numerous phosphate minerals. Consequently, ... activated monomers can form in prebiotic conditions in a liquid, non-aqueous environment in the presence of phosphate minerals in conditions compatible with the thermodynamics of polymerization.
And this:
Protein and nucleic acid together: A mechanism for the emergence of biological selection, Journal of Theoretical Biology, Volume 240, Issue 3, 7 June 2006, Pages 337-342
Recent studies have shown how interactions of the ”RNA world’ with lipids may have been mutually beneficial for both vesicle formation and RNA replication (Chen et al., 2004). In lipid vesicles, replicating RNA molecules profit by being segregated away from non-replicating ”free-loading’ RNAs that would otherwise benefit from efficient RNA polymerase action. Conversely, the ability of RNA molecules to replicate would have allowed vesicles to grow through increased osmotic pressure (Chen et al., 2004). In this scheme, the more successful vesicle/replicating RNA combinations would expand the fastest and would thus be more likely to split into daughter vesicles, thereby fulfilling many of the key requirements for the initiation of primordial life.
Less progress has been made in showing how mutually beneficial interactions could have arisen between the RNA and early protein world. In vitro selection strategies have shown that RNA molecules are capable of carrying out several steps required for amino acid activation and peptide bond formation (Chapple et al., 2003; Ferreira and Coutinho, 1993; Huang et al., 2000; Johnston et al., 2001; Kumar and Yarus, 2001). However, it is unclear how the acquisition of these enzymic activities would have been subject to immediate selection in the primordial environment (Orgel, 1989).
Here I propose a scheme that integrates nucleic acid and protein function in a way that allows the mutual co-evolution of nucleic acid-dependent protein synthesis and nucleic acid-dependent nucleic acid replication. The model proposes a very early association between nucleic acid and protein polymers in the primordial development of life. It suggests a specific role for amyloid; a protein aggregate in which main chain -sheet interactions stabilize the formation of fibres. Predictions from the model are consistent with recently published observations.
This proposal differs from the prevailing ”RNA-world’ model of pre-biotic development because it involves proteins interacting with the nucleic acids much earlier in evolution than previously suggested. It is even possible that the first self-replicating RNA molecules evolved in association with protein/amyloid and never existed in isolation. An advantage of this model is that it suggests simple evolutionary paths from amyloid-associated elongase and replicase activities to ribosomes and RNA polymerase respectively. In particular, the elongase activity could act as a focus for incremental selective changes that were necessary for the development of template-directed peptide bond formation, without any one step being contingent on future evolutionary developments (Chapple et al., 2003; Huang et al., 2000; Johnston et al., 2001; Lohse and Szostak, 1996; Nissen et al., 2000; Yarus and Welch, 2000; Zhang and Cech, 1997).
Re: chirality
A primordial peptide cycle involving the chemical formation and degradation of peptides has recently been proposed (Huber et al., 2003). Here I argue [insert: -as opposed to showing emperically-]that peptides in solution would be selectively degraded by comparison to those included in amyloid. Mixed chiral peptides are unlikely to have formed amyloid since they have a lower propensity to form -sheet structures (Brack and Barbier, 1990), thus it is likely that amyloid was homochiral and that mixed chiral peptides were selectively degraded and recycled into other random chiral combinations. Base-pairing of nucleic acids during replication has also been argued to promote homochirality (Schoning et al., 2000), leading to the proposal here that both protein and nucleic acid polymers involved in the proposed mechanism were homochiral.
There is no a priori reason to believe that any particular homochiral amyloid-nucleic acid combinations (e.g. DD, DL, LD or LL) would have had a selective advantage. [Insert: -and no a priori reason that they would not have either-]Indeed RNA was found to induce the aggregation of both homo L and D poly (Lys-Leu) polypeptides with equal efficiency (Brack and Barbier, 1990). It is therefore possible that all chiral combinations co-existed and competed with each other. The later development of enzymic activities that could direct the synthesis of chiral protein and RNA precursors would then have been the key event in the genesis of the current chiral combination.

This message is a reply to:
 Message 124 by molbiogirl, posted 09-03-2007 4:00 PM molbiogirl has replied

Replies to this message:
 Message 128 by Percy, posted 09-03-2007 5:13 PM Rob has replied
 Message 132 by molbiogirl, posted 09-03-2007 5:41 PM Rob has replied

Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 128 of 314 (419578)
09-03-2007 5:13 PM
Reply to: Message 127 by Rob
09-03-2007 5:00 PM


Re: There's been work done since 2004
Rob, all you've done is highlight in bold phrases that include the typically tentative phrasing of scientific papers. We've been over this ground before. Science is tentative.
So when a scientific paper says that something "could" have occurred in such-and-such a way, it only means that it is a possibility as opposed to a definite fact. What those papers are describing are possible natural pathways for the formation of ATP. That such pathways exist does not mean that they are the ones that nature actually took advantage of, it only means that we understand some of the ways ATP could have formed naturally. After billions of years there may be too little evidence left to reach any definitive conclusions.
What you require in order to keep open the possibility of divine intervention is for scientists to never discover any natural pathways for the formation of ATP. Unfortunately for you, scientists have already uncovered such pathways.
--Percy

This message is a reply to:
 Message 127 by Rob, posted 09-03-2007 5:00 PM Rob has replied

Replies to this message:
 Message 129 by Chiroptera, posted 09-03-2007 5:21 PM Percy has not replied
 Message 131 by Rob, posted 09-03-2007 5:38 PM Percy has replied

Chiroptera
Inactive Member


Message 129 of 314 (419579)
09-03-2007 5:21 PM
Reply to: Message 128 by Percy
09-03-2007 5:13 PM


Re: There's been work done since 2004
So when a scientific paper says that something "could" have occurred in such-and-such a way, it only means that it is a possibility as opposed to a definite fact....
What you require in order to keep open the possibility of divine intervention is for scientists to never discover any natural pathways for the formation of ATP. Unfortunately for you, scientists have already uncovered such pathways.
Which is what I already tried to say. We seem to be getting confused whether we are trying to conclude that a process cannot happen, or to conclude that we process could very well happen, even if we don't yet know all the details.
The coulds demonstrate that the processes, um, could have happened. So if the desired conclusion is that there is no possibility of natural explanations, these quotes undermine that.
If the desired conclusion is that we don't know all the answers yet, then, um, okay, so what? No one claims to have all the answers.

I've done everything the Bible says, even the stuff that contradicts the other stuff! -- Ned Flanders

This message is a reply to:
 Message 128 by Percy, posted 09-03-2007 5:13 PM Percy has not replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 130 of 314 (419580)
09-03-2007 5:30 PM
Reply to: Message 126 by Percy
09-03-2007 4:59 PM


Re: a la Behe
Percy:
So let's design a test that would detect the designer by his works. Let us say that me and a Greek from ancient Athens observe lightning in a thunder storm. I claim the lightning is a natural phenomenon caused by the discharge of electricity between clouds and ground which have become oppositely charged due to the storm. The ancient Athenian says the lightning bolt was cast by Zeus. What test could we make to tell who is right?
I was expecting so much more...
There is no test for such a scenario. I agree!
But, are you telling me that a lightening bolt is the equivilant in terms of information complexity to the quaternary digital code of DNA?
I might very well say that the mathematical elegance and balance necessary for the creation of a lightening bolt does itself indicate a supremely intelligent creator who makes those laws stand firm, but I would not expect you to necessarily agree.
But in the case of DNA were not talking about electricity, we're talking about a peculiar kind of information; specified, highly complex, non-repeating digital text that instructs and directs the building of biological structures. It even contains the instructions for building the machines that do the actual work of transporting parts and such in the cell.
We know of other systems that do the same... A blueprint designed by engineers that instruct agents on how to build a specified building for example. And it is designed by intelligent agents.
And to touch on the thermodynamic problem which is always evaded with assurances of invalidity because we live in an open system; the energy to build the system must be directed. Water cannnot flow up hill simply because it flows in a thermodynamically open system. But you can use the available energy in an open system if it is converted and harnessed to create a water pump. But it is an intelligently designed system. Free undirected energy will contribute to the deterioration of the pump, hence it must also be maintained. Even the instructions will deteriorate in an open system. But the energy in the open system cannot build the pump, and it cannot make water flow uphill. if the law of thermodynamics wasn't valid in an open system, then how did we discover it and prove it here in an open system?
The same applies for cellular factories that convert energy. The energy itself cannot create them. Which gets back to a major point of the thread.
So... we know where instructions come from; intelligence. It has yet to be shown (though it is extravegantly suggested and theorized) that non-intelligent guidance and simple repetative physical laws (informationally) can be a cause and origin for this peculiar form of information that is shown emperically to be caused by intelligence elsewhere.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 126 by Percy, posted 09-03-2007 4:59 PM Percy has replied

Replies to this message:
 Message 133 by molbiogirl, posted 09-03-2007 5:50 PM Rob has replied
 Message 140 by Doddy, posted 09-03-2007 7:21 PM Rob has replied
 Message 180 by Percy, posted 09-04-2007 5:25 AM Rob has not replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 131 of 314 (419581)
09-03-2007 5:38 PM
Reply to: Message 128 by Percy
09-03-2007 5:13 PM


Re: There's been work done since 2004
Percy:
Rob, all you've done is highlight in bold phrases that include the typically tentative phrasing of scientific papers. We've been over this ground before. Science is tentative.
So when a scientific paper says that something "could" have occurred in such-and-such a way, it only means that it is a possibility as opposed to a definite fact. What those papers are describing are possible natural pathways for the formation of ATP. That such pathways exist does not mean that they are the ones that nature actually took advantage of, it only means that we understand some of the ways ATP could have formed naturally. After billions of years there may be too little evidence left to reach any definitive conclusions.
What you require in order to keep open the possibility of divine intervention is for scientists to never discover any natural pathways for the formation of ATP. Unfortunately for you, scientists have already uncovered such pathways.
Not at all Percy...
I firmly believe it is possible! I think anythings possible because of what the Bible tells me about possibility. But not all things are probable, and not all things are right.
All I am saying is that these theories offer no emperical proof of anything.
Furthermore, the creation of these systems by human manipulation only proves intelligent design (ironically for the case of proving inteligent design is not necessary).
If you want proof on how these complex systems can be made, you need only look to intelligent agents ie. human ingenuity. We can even invent stories that are so clever, that other intelligent people believe them.
You really need to read my last reply to you...

This message is a reply to:
 Message 128 by Percy, posted 09-03-2007 5:13 PM Percy has replied

Replies to this message:
 Message 138 by DrJones*, posted 09-03-2007 6:20 PM Rob has replied
 Message 181 by Percy, posted 09-04-2007 6:04 AM Rob has replied

molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 132 of 314 (419582)
09-03-2007 5:41 PM
Reply to: Message 127 by Rob
09-03-2007 5:00 PM


Re: There's been work done since 2004
Two things:
One. You need to edit that post so that the passages you're interested in are highlighted in color.
Two. If you haven't already noticed, a scientist argues both sides of an issue. Usually, the "could haves" and "suggests" and whatnot are his way of saying, "Well, my friend and colleague here has said thus-and-such, but I think he's full of beans and here's why." It's just a way of being polite.
Sometimes, though, the "could haves" etc. are a way of introducing an idea. For example, Dr. Schmidt said "This low probability (of random interactions) could be overcome..." and then he goes on to show exactly how it was overcome.
Furthermore, all of these quotes are from the Introduction and/or Discussion. For example, from the last paper: "Here I propose a scheme..." Are you under the impression that the author didn't test his hypothesis? That he simply suggested an alternate explanation with no data?
And sometimes, the passage you highlight as evidence of scientific waffling is answered in the very next sentence. For example, "However, in this scenario, the difficult prebiotic synthesis of ribose and consequently of nucleotides next term remain a major problem. In order to overcome this problem and obtain nucleoside analogs, we are investigating reactions of the nucleic acid base, adenine 1, with different aldehydes under presumably prebiotic conditions. In the reaction of adenine and pyruvaldehyde 2 in water, we report here the formation in high yield of two isomeric products."
What exactly are you arguing with all of this highlighting anyway?
Are you suggesting that a scientist should declare that he knows, without a shadow of a doubt, the exact prebiotic conditions 3.8 billion years ago?
Not gonna happen, chum.
Are you suggesting that unless a scientist knows, without a shadow of a doubt, the exact prebiotic conditions 3.8 billion years ago, he can't further our understanding abiogenesis?

This message is a reply to:
 Message 127 by Rob, posted 09-03-2007 5:00 PM Rob has replied

Replies to this message:
 Message 134 by Rob, posted 09-03-2007 5:50 PM molbiogirl has not replied

molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 133 of 314 (419585)
09-03-2007 5:50 PM
Reply to: Message 130 by Rob
09-03-2007 5:30 PM


You just couldn't wait to drag in the Second Law, could you?
You tried this on the ribozyme thread too.
The energy itself cannot create them.
This is biochemistry, Rob. As Percy mentioned upthread, when a reaction is thermodynamically favorable, chemical bonds form. Period. Each of the papers I've cited employ thermodynamically favorable reactions.

This message is a reply to:
 Message 130 by Rob, posted 09-03-2007 5:30 PM Rob has replied

Replies to this message:
 Message 135 by Rob, posted 09-03-2007 5:58 PM molbiogirl has replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 134 of 314 (419586)
09-03-2007 5:50 PM
Reply to: Message 132 by molbiogirl
09-03-2007 5:41 PM


Re: There's been work done since 2004
molbiogirl:
Are you suggesting that unless a scientist knows, without a shadow of a doubt, the exact prebiotic conditions 3.8 billion years ago, he can't further our understanding abiogenesis?
Not at all... though it may only show us more understanding of the complexity of biology, and other useful understandings. Unlike you, I am not assuming that abiogenesis is a fact explainable by material causes alone.
I am suggesting however that he can only infer it. And that there is a superior inference to solve the problem that has made itself available in the last decade. And science has always made inference to the best explaination. But in this case, the inference is made to that which though emperical does not provide the 'how', only the 'what'. And without a physical being to attach the 'what' to, methodological naturalism rejects the emperical evidence.
Would you as a methodological naturalist also reject an alien transmission of a quaternary digital code picked up by SETI researchers? Or even a simple set of prime numbers? I doubt it...
But in another universe (inside the vast complexity of the living cell) the alien is communicating.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 132 by molbiogirl, posted 09-03-2007 5:41 PM molbiogirl has not replied

Rob 
Suspended Member (Idle past 5849 days)
Posts: 2297
Joined: 06-01-2006


Message 135 of 314 (419588)
09-03-2007 5:58 PM
Reply to: Message 133 by molbiogirl
09-03-2007 5:50 PM


Re: You just couldn't wait to drag in the Second Law, could you?
molbiogirl:
This is biochemistry, Rob. As Percy mentioned upthread, when a reaction is thermodynamically favorable, chemical bonds form. Period. Each of the papers I've cited employ thermodynamically favorable reactions.
So what?
And none of those papers suggest anything resembling the emmense metabolisms we see today. What created them? What good is one one thousanth of a solution when you have a whole factory to account for?
You got gaps that make the Grand Canyon look like a seam between the cells of a human hair.
Have you shown me any life that exists without the known energy conversion mechanisms? Where are these precursors and transitional forms of metabolism? Those that exist today are extraordinarily complex.
All you've done is provided sources to postulated and incredibly insuficient components to produce even the simplest of conceivable cells (which have never been shown to exist but are only conceived of...). There are thousands and millions of components that not only have to be created, but brought together to form an entire organized system we call an organism even in only a single celled creature.
What you're doing is burying the public in masses of details that don't even begin to touch the survface of these problems. And yet our televisions and science classes at school would lead us to believe it is a certainty!
Let me ask you molbiogirl... is it a certainty? Or is it your deep faith that it is a certainty?
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 133 by molbiogirl, posted 09-03-2007 5:50 PM molbiogirl has replied

Replies to this message:
 Message 136 by molbiogirl, posted 09-03-2007 6:14 PM Rob has replied
 Message 139 by Chiroptera, posted 09-03-2007 6:22 PM Rob has replied
 Message 182 by Percy, posted 09-04-2007 6:16 AM Rob has replied

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