Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 78 (8905 total)
Current session began: 
Page Loaded: 04-24-2019 9:57 AM
32 online now:
1.61803, DrJones*, DWIII, edge, Heathen, kjsimons, Percy (Admin), Theodoric, vimesey (9 members, 23 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 850,146 Year: 5,183/19,786 Month: 1,305/873 Week: 201/460 Day: 17/29 Hour: 6/3


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Prev1
...
56
7
89
...
21NextFF
Author Topic:   Converting raw energy into biological energy
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 91 of 314 (419477)
09-03-2007 12:56 AM
Reply to: Message 90 by Rob
09-03-2007 12:40 AM


Re: ATP Synthase Did Not Exist 3.5 bya
Here. Start with these. There are 95 others.

Unrau, P. J. & Bartel, D. P. RNA-catalysed nucleotide synthesis. Nature 395, 260-263 (1998).

Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E. & Bartel, D. P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292, 1319-1325 (2001).

Zhang, B. & Cech, T. R. Peptide bond formation by in vitro selected ribozymes. Nature 390, 96-100 (1997).

von Kiedrowski, G. A self-replicating hexadeoxynucleotide. Angew. Chem. 25, 932-935 (1986).

Gilbert, W. The RNA world. Nature 319, 618 (1986).

Joyce, G. F. RNA evolution and the origins of life. Nature 338, 217-224 (1989).

Ferris, J. P., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis III. Synthesis of pyrimidines from cyanoacetylene and cyanate. J. Mol. Biol. 33, 693-704 (1968).

Robertson, M. P. & Miller, S. L. An efficient prebiotic synthesis of cytosine and uracil. Nature 375, 772-774 (1995).


This message is a reply to:
 Message 90 by Rob, posted 09-03-2007 12:40 AM Rob has responded

Replies to this message:
 Message 95 by Rob, posted 09-03-2007 1:12 AM molbiogirl has not yet responded

jar
Member
Posts: 30936
From: Texas!!
Joined: 04-20-2004


Message 92 of 314 (419478)
09-03-2007 12:59 AM
Reply to: Message 89 by Rob
09-03-2007 12:39 AM


Re: What is so funny about Rob's position
What in the world does it have to do with ATP production by organic processes?

The relevance is that wholly natural processes can create complex molecules; molecules that combine, divide, reproduce, evolve; simple chemistry and physics. Organic is not even necessary.

Organic is just a label of convenience, denoting carbon based chemical reactions we classify as live. However, the more we learn the less the distinction between living and non-living forms appears.

In addition, plasma states happen to be pretty common. One example is lightning. Others are produced during meteor or comet strikes, also fairly common particularly during the early period of Earth's existence.


Aslan is not a Tame Lion
This message is a reply to:
 Message 89 by Rob, posted 09-03-2007 12:39 AM Rob has responded

Replies to this message:
 Message 93 by Rob, posted 09-03-2007 1:05 AM jar has responded

Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 93 of 314 (419479)
09-03-2007 1:05 AM
Reply to: Message 92 by jar
09-03-2007 12:59 AM


Re: What is so funny about Rob's position
jar:
In addition, plasma states happen to be pretty common. One example is lightning. Others are produced during meteor or comet strikes, also fairly common particularly during the early period of Earth's existence.

Life in plasma eh? Who knows?

Perhaps the Burning Bush wasn't such a far fetch after all...


This message is a reply to:
 Message 92 by jar, posted 09-03-2007 12:59 AM jar has responded

Replies to this message:
 Message 96 by jar, posted 09-03-2007 1:13 AM Rob has responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 94 of 314 (419480)
09-03-2007 1:09 AM
Reply to: Message 80 by molbiogirl
09-03-2007 12:00 AM


Re: ATP Synthase Did Not Exist 3.5 bya
Rob: Correct me if I am wrong... please...

But wasn't Doddy specifically describing the theoretical making of these materials in a laboratory?

molbiogirl: No. He was not.

Doddy: www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=87&m=1 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=87&m=1">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=87&m=1 First sentance...

quote:
Ok,
I'm really interested in organic chemistry, and so to brush up on my skills, I decided to see if I could find a way to build an RNA enzyme from prebiotic chemicals. Theoretically of course.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 80 by molbiogirl, posted 09-03-2007 12:00 AM molbiogirl has responded

Replies to this message:
 Message 98 by molbiogirl, posted 09-03-2007 1:18 AM Rob has not yet responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 95 of 314 (419481)
09-03-2007 1:12 AM
Reply to: Message 91 by molbiogirl
09-03-2007 12:56 AM


Re: ATP Synthase Did Not Exist 3.5 bya
molbiogirl:
Unrau, P. J. & Bartel, D. P. RNA-catalysed nucleotide synthesis. Nature 395, 260-263 (1998).

Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E. & Bartel, D. P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292, 1319-1325 (2001).

Zhang, B. & Cech, T. R. Peptide bond formation by in vitro selected ribozymes. Nature 390, 96-100 (1997).

von Kiedrowski, G. A self-replicating hexadeoxynucleotide. Angew. Chem. 25, 932-935 (1986).

Gilbert, W. The RNA world. Nature 319, 618 (1986).

Joyce, G. F. RNA evolution and the origins of life. Nature 338, 217-224 (1989).

Ferris, J. P., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis III. Synthesis of pyrimidines from cyanoacetylene and cyanate. J. Mol. Biol. 33, 693-704 (1968).

Robertson, M. P. & Miller, S. L. An efficient prebiotic synthesis of cytosine and uracil. Nature 375, 772-774 (1995).

That's nice...

So I have to read all of these to verify that the evironmental conditions were the same for the re-construction of all of the steps you listed?

Surely there is a link to the subject...

Nevermind! I'll find it myself...


This message is a reply to:
 Message 91 by molbiogirl, posted 09-03-2007 12:56 AM molbiogirl has not yet responded

  
jar
Member
Posts: 30936
From: Texas!!
Joined: 04-20-2004


Message 96 of 314 (419482)
09-03-2007 1:13 AM
Reply to: Message 93 by Rob
09-03-2007 1:05 AM


Re: What is so funny about Rob's position
Life in plasma eh? Who knows?

Perhaps the Burning Bush wasn't such a far fetch after all...

The Burning Bush is of course irrelevant and unimportant, just another nonsense attempt to bring in more of your preachifying.

The point is you have been shown examples of converting raw energy into biological energy, that complex molecules can form naturally, that there are examples of naturally occurring inorganic molecules that combine, split, recombine, evolve, form new combinations, form helixes similar to DNA.

So far all you have presented is your personal incredulity.

So other than your incredulity, what is the issue?


Aslan is not a Tame Lion
This message is a reply to:
 Message 93 by Rob, posted 09-03-2007 1:05 AM Rob has responded

Replies to this message:
 Message 97 by Rob, posted 09-03-2007 1:16 AM jar has responded

Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 97 of 314 (419483)
09-03-2007 1:16 AM
Reply to: Message 96 by jar
09-03-2007 1:13 AM


Re: What is so funny about Rob's position
jar:
The point is you have been shown examples of converting raw energy into biological energy, that complex molecules can form naturally, that there are examples of naturally occurring inorganic molecules that combine, split, recombine, evolve, form new combinations, form helixes similar to DNA.

I've been shown none of the above... what I have been shown is a bunch of theorizing and speculation.


This message is a reply to:
 Message 96 by jar, posted 09-03-2007 1:13 AM jar has responded

Replies to this message:
 Message 99 by jar, posted 09-03-2007 1:20 AM Rob has responded

  
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 98 of 314 (419484)
09-03-2007 1:18 AM
Reply to: Message 94 by Rob
09-03-2007 1:09 AM


Re: ATP Synthase Did Not Exist 3.5 bya
Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Volume 29, Number 5 / October, 1999

Theoretical, eh?


This message is a reply to:
 Message 94 by Rob, posted 09-03-2007 1:09 AM Rob has not yet responded

jar
Member
Posts: 30936
From: Texas!!
Joined: 04-20-2004


Message 99 of 314 (419485)
09-03-2007 1:20 AM
Reply to: Message 97 by Rob
09-03-2007 1:16 AM


Re: What is so funny about Rob's position
I've been shown none of the above... what I have been shown is a bunch of theorizing and speculation.

I'm sorry Rob but that is simply false. You have been provided with links and even claim to have read them. Folk can read through the thread and find the links themselves. So once again, other than your personal incredulity, what is the issue?


Aslan is not a Tame Lion
This message is a reply to:
 Message 97 by Rob, posted 09-03-2007 1:16 AM Rob has responded

Replies to this message:
 Message 100 by Rob, posted 09-03-2007 1:29 AM jar has not yet responded

Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 100 of 314 (419486)
09-03-2007 1:29 AM
Reply to: Message 99 by jar
09-03-2007 1:20 AM


Re: What is so funny about Rob's position
jar:
So once again, other than your personal incredulity, what is the issue?

There's something very wrong with this picture...

I intend to show that molbiogirl's assertion that the same environmental conditions in the lab led to the reproduction of all of those different properties is false. That it would in fact, take completely different atmospheric conditions to produce subsequent changes in the prebiotic matter. And that her assertion assumes the survivability of said matter in the mean time.

Be patient. Don't cover me with dirt quite yet...

Edited by Rob, : No reason given.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 99 by jar, posted 09-03-2007 1:20 AM jar has not yet responded

  
Percy
Member
Posts: 18375
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.9


Message 101 of 314 (419487)
09-03-2007 2:41 AM


Request for More Info
This thread is mostly comprised of a bunch of tiny exchanges with little specific information. For example, if someone asked me, "Please explain how ATP forms naturally using just the information provided in this thread, not including any provided links or references," I'm pretty sure I couldn't do it.

--Percy


Replies to this message:
 Message 102 by molbiogirl, posted 09-03-2007 3:52 AM Percy has not yet responded
 Message 108 by Chiroptera, posted 09-03-2007 11:59 AM Percy has not yet responded

  
molbiogirl
Member (Idle past 751 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 102 of 314 (419489)
09-03-2007 3:52 AM
Reply to: Message 101 by Percy
09-03-2007 2:41 AM


Re: Request for More Info
Doddy outlined one method in the ribozyme thread.

Here's another:

Here, novel experimental results are reported that ATP are synthesized from adenosine-5-diphosphate (ADP) and ADP from adenosine-5-monophosphate (AMP) by spontaneous phosphorylation in aqueous solution containing calcium phosphate and cyanate. The phosphorylation reactions proceeded only when cyanate was used as a condensing reagent. This recyclable molecule is observed in cosmic clouds, suggesting it was present in prebiotic times.

The reaction is strongly dependent on the pH, and a pH of 5.5–6.0 is the most effective. We must ask, is this pH range likely to have existed in primitive Earth conditions. Miller and Orgel (1974) have suggested that pH of the primitive ocean was weakly basic between 8.0–8.5 similar to that of the present ocean. However, the early primitive Earth would have been covered with an atmosphere of relatively high partial pressure of carbon dioxide (Rubey, 1955; Abelson, 1966; Kasting and Ackerman, 1987). In that case, the sea water would have been weakly acidic. This was actually checked in a laboratory experiment. A fresh sea water (from Sea of Japan at the sea shore of Kanazawa) showed a pH of 8.26. When carbon dioxide was poured over the sea water in the Erlenmeyer flask (not bubbling), the pH stayed at a value of 4.95 after decreasing gradually. Then, calcium carbonate (1.0% of the sea water) was added in the flask still pouring carbon dioxide. In this case, the pH increased to a value of 6.03.

It was reported that AMP was constantly synthesized by the phosphorylation of adenosine in a long-term discharge experiment, which simulated the recycling system of the water and the other volatile substances on the primitive Earth surface (Yamagata et al., 1979, 1981). The condensation was demonstrated to be due to the formation of cyanate (Yamagata and Mohri, 1982). Cyanate is a condensing reagent that can be hydrolyzed to the gaseous components, carbon dioxide and ammonia. The recyclability would be a necessary condition imposed on prebiotic condensing reagents, because the prebiotic evolution had to continue through the geologic time. Cyanic acid or isocyanic acid would be a true prebiotic condensing reagent, since the latter molecule that is the tautomer of cyanic acid has been observed in the interstellar clouds (Rank et al., 1971).

In conclusion, the present phosporylation reactions are summarized as follows:
NMP + Pi + Ca2+ + cyanate → NDP
NDP + Pi + Ca2+ + cyanate → NTP
NMP + hydroxyapatite[or Ca3 (PO4 )2 or CaHPO4 ·2H2 O] + cyanate → NDP
NDP + hydroxyapatite[or Ca3 (PO4 )2 or CaHPO4 ·2H2 O] + cyanate → NTP

Recently, it was found that water-soluble phosphate and polyphosphates were produced through the volcanic activity (Yamagata et al., 1991). Most of the phosphates from volcanoes eventually would have been converted into water-insoluble calcium phosphate by the reaction with calcium ion in the ocean. Rocks on the Earth as well as meteorites contain most phosphate in the form of apatite. In the weathering of the rocks the apatite would have been released into the ocean from the rocks. These conditions on the primitive Earth have been simulated in the present experiments. Probable low temperature and weakly acidic conditions of the primitive ocean would have made it possible to survive and to accumulate the essential prebiotic molecules. Miller and Parris (1964) reported the formation of pyrophosphate from hydroxyapatite and cyanate. The present reactions are closely related to their reaction.

Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Volume 29, Number 5 / October, 1999


This message is a reply to:
 Message 101 by Percy, posted 09-03-2007 2:41 AM Percy has not yet responded

Doddy
Member (Idle past 4019 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 103 of 314 (419492)
09-03-2007 5:57 AM
Reply to: Message 78 by Rob
09-02-2007 11:57 PM


Re: ATP Synthase Did Not Exist 3.5 bya
Rob writes:

But wasn't Doddy specifically describing the theoretical making of these materials in a laboratory?

Ok, it was theoretical. I wasn't following along in my Erlenmeyer.

Also, I was hardly going to wait half a billion years to see if I had the correct environment and concentrations. That's why you have to guide the reactions along by providing the best catalysts you can find and the optimum environments. Of course, nobody can (yet) physically make ATP like you would out of Lego (join this atom to that atom...), so the reactions done by the organic chemists that I cited still have to show self-assembly. All they did is provide the optimum conditions.

Take golf as an example: You seem to imply we are driving the ball into the hole, but rather we are just accelerating the relevant powers of the wind, water and earth to see if they will do it. If we didn't, it would take billions of years, and few research agencies will fund that.


Help to inform the public - contribute to the EvoWiki today!

What do you mean "You can't prove a negative"? Have you searched the whole universe for proofs of a negative statement? No? How do you know that they don't exist then?!


This message is a reply to:
 Message 78 by Rob, posted 09-02-2007 11:57 PM Rob has responded

Replies to this message:
 Message 104 by Rob, posted 09-03-2007 11:39 AM Doddy has not yet responded

  
Rob 
Suspended Member (Idle past 3958 days)
Posts: 2297
Joined: 06-01-2006


Message 104 of 314 (419510)
09-03-2007 11:39 AM
Reply to: Message 103 by Doddy
09-03-2007 5:57 AM


Leslie Orgel
I found some interesting comments on this subject (in general) by Orgel. I have some questions for you Doddy, since I cannot seem to find what it is I am looking for and cannot recall where I got the information I have forgotten. Perhaps you can answer them.

Conclusion

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. Many individual steps that might have contributed to the formation of nucleotides on the primitive Earth have been demonstrated, but few of the reactions give high yields of products, and those that do tend to produce complex mixtures of products. It should also be realized that any prebiotic synthesis of a nucleotide would yield a racemic product, not the biologically important D-nucleotide. Recent publications, particularly those of Zubay and his coworkers (cited above), suggest that the search for a convincing prebiotic synthesis of the nucleotides is not hopeless. However, the difficulties remain so severe that alternatives to the de novo appearance of RNA on the primitive Earth deserve serious consideration. The succeeding sections of this review, in addition to discussing possible routes to RNA from a hypothetical source of prebiotic nucleotides, will also consider other ways in which the RNA World could have appeared.

( http://www.crbmb.com/cgi/content/full/39/2/99#SEC2 )

Forgetting the problem of racemic molecules and chiralty for now(second bolded section), in the first bolded section above; 'are the environmental factors necessary for formation of nucleotides in differing experiments compatable'?

Or, in other words, would it take necessarily different environments to produce individual components that would have to merge and cohere at some single point in time to spontaneously create life?

And do you think this is one reason why the de novo approach is effetively being abandoned even though it is not addressed in this aritcle?

Orgel seems to hint at the question here, but in the sense of 'environment'. in terms of encapsulation by a cell wall:

Molecules that stay together evolve together. This sums up the arguments in favor of compartmentalization. There are two important and distinct aspects of this generalization, one concerning small-molecule metabolites, etc., and the other concerning macromolecules. Evolution is at a severe disadvantage in enhancing the performance of an organism's metabolic enzymes unless the small molecules that they synthesize are retained long enough to be utilized by the producing macromolecules (or their near relatives). There is no place in evolution for charity, and to synthesize a useful molecule and hand it over to an unrelated competitor would constitute molecular charity.

She even appears to hint at the other double-stranded structures kind of like the article jar brought to bear:

The prebiotic synthesis of nucleotides in a sufficiently pure state to support RNA synthesis cannot be achieved using presently known chemistry. Each of the steps needed to assemble a nucleotide from very simple starting materials was demonstrated early in the development of prebiotic chemistry, but the reactions were inefficient, nonspecific, or both. Some progress has been made in developing more specific prebiotic syntheses, but formidable difficulties remain. This has led some researchers to explore a major new approach to the problem of molecular evolution—the search for polymers that could function as alternative genetic systems.

It is now clear that there are numerous double-stranded structures with backbones very different from that of RNA but held together by Watson-Crick base pairing. Investigation of these structures is a novel and fruitful branch of organic chemistry (and Astrobiology) regardless of whether it turns out to be relevant to the origin of life on the Earth. It also seems possible that there are pairing structures much simpler than RNA in the sense that their monomeric components can be synthesized much more easily than nucleotides. The discovery of TNA is encouraging, but structures that are independent of Watson-Crick base pairing are as yet unknown.

I like the honesty in her final statement. Some of you (not you Doddy) could learn a lesson from her:

FUTURE DIRECTIONS

Prebiotic chemistry remains so diverse a field that it is by no means clear where the next important advances will occur. It seems likely that adsorption on and catalysis by minerals was essential for the origin of the RNA World, so increasing efforts to study heterogeneous reactions are to be anticipated. Since minerals are so varied in composition and structure, combinatorial methods will be required. It will be necessary to study each potentially important reaction in parallel on tens or hundreds of different mineral samples. Whether or not this approach will lead to the discovery of a plausible prebiotic route to the nucleotides, as the believers in the Molecular Biologists' Dream hope, remains to be seen, but it is likely that many novel mineral catalysts will be discovered in this way.

The search for pairing structures based on monomeric components that can be synthesized much more easily than nucleotides and, hopefully, that polymerize more readily has just begun. No doubt it will remain an active and expanding field. Whether or not it leads to a plausible scenario for a simple pre-RNA World, as advocates of "RNA late" hope, it is likely to generate some novel organic chemistry.

One must recognize that, despite considerable progress, the problem of the origin of the RNA World is far from being solved.

Doddy, in your opinion, how relevant to this debate is the issue of chiralty?

Edited by Rob, : No reason given.

Edited by Rob, : chiralty not chiralry


This message is a reply to:
 Message 103 by Doddy, posted 09-03-2007 5:57 AM Doddy has not yet responded

Replies to this message:
 Message 105 by CK, posted 09-03-2007 11:47 AM Rob has responded
 Message 110 by Wounded King, posted 09-03-2007 12:12 PM Rob has responded
 Message 124 by molbiogirl, posted 09-03-2007 4:00 PM Rob has responded

  
CK
Member (Idle past 2237 days)
Posts: 3221
Joined: 07-04-2004


Message 105 of 314 (419515)
09-03-2007 11:47 AM
Reply to: Message 104 by Rob
09-03-2007 11:39 AM


Re: Leslie Orgel
What is "chiralry"? none of the academic sources I can access have heard of such a term and it doesn't appear in any general web searches I do.
This message is a reply to:
 Message 104 by Rob, posted 09-03-2007 11:39 AM Rob has responded

Replies to this message:
 Message 106 by Rob, posted 09-03-2007 11:54 AM CK has not yet responded
 Message 107 by Rob, posted 09-03-2007 11:57 AM CK has not yet responded
 Message 109 by jar, posted 09-03-2007 12:02 PM CK has not yet responded

Prev1
...
56
7
89
...
21NextFF
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019