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Author Topic:   Converting raw energy into biological energy
molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 136 of 314 (419590)
09-03-2007 6:14 PM
Reply to: Message 135 by Rob
09-03-2007 5:58 PM


their 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.

Let me ask you this, Rob.

What is the simplest form of life?

A bacterium?

In that case, you're right. We haven't created life from simple precursors. We're close, but there's work to do.

We have, however, the bits and pieces that are necessary:

Polymerization, RNA ligases, RNA capping, RNA phosphorylation, RNA cleavage, ribose formation, nucleoside formation, peptide bond formation, amide bond formation, membrane formation.

Remember. Amide and peptide bonds are the only thing standing between a puddle of chemicals and a protein. Sugars and nucleosides are the only things standing between that very same puddle and a quaternary code.

And, contrary to your assertion that we've only "postulated" "insufficient" components, I would remind you that a virus is nothing more than a tiny package of DNA encapsulated in an envelope. And a prokaryote isn't much more complicated than a virus: some DNA, some RNA, some plasma and a membrane.

Hardly the millions of components you seem to think necessary for an "organism".


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 158 of 314 (419623)
09-03-2007 8:54 PM
Reply to: Message 143 by Rob
09-03-2007 7:48 PM


It's still a highly theoretical excercise at this point (thank you Leslie Orgel).

Horse feathers.

First, Orgel's review of abiogenesis was simply that ... a review. It summarized what we knew (and what we didn't) in 2004.

And I'm certain Orgel would be horrified to find his work being used as justification for your creo claptrap.

Second, that research is 3 years old ... dog years in a field like abiogenesis ... as I've demonstrated by dropping 4 cites in your lap after only half an hour's research.

DNA, RNA, ATP, ADP, etc do not an organism make... It's a whole system.

Really.

From the article in your OP:

Experts expect an announcement within three to 10 years from someone in the now little-known field of "wet artificial life."

"It's going to be a big deal and everybody's going to know about it," said Mark Bedau, chief operating officer of ProtoLife of Venice, Italy, one of those in the race.

It's like the race that produced the human genome.

From the Protolife website:

ProtoLife is developing automated, high-throughput methods for designing complex chemical systems. We have developed proprietary statistical learning and automated design technology that optimize the benefit from each experiment in a high-throughput scan.

ProtoLife is a participant in PACE, an integrated project funded by the European Commission under the EU 6th Framework Program (FP6). PACE comprises a consortium of 14 European and USA universities and businesses that have joined together to pursue basic research related to development of artificial cells, and to set the foundations for a new generation of information technology based on using evolutionary methods to program chemical functionality.
European Center for Living Technology (ECLT)

ProtoLife is a founding member of the European Center for Living Technology in Venice, Italy, participating in multidisciplinary projects involving the study and development of living technology, i.e., technology that possesses important properties of living systems.

It isn't a question of if, but when.

Just as the bomb wasn't a question of if but when after physicists unveiled the nature of the atom.

Gentlemen, we can rebuild it. We have the tools. We have the technology. We have the capability to make the world’s first artificial life. Better than it was before. Better…stronger…faster.

What is the smallest number of components known in the smallest living, autonomous, and self replicating life form?

Are your fingers broken?

Can you no longer google?

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 165 of 314 (419636)
09-03-2007 10:40 PM
Reply to: Message 162 by Rob
09-03-2007 10:29 PM


Behe's Balderdash
"Making the molecules of life by chemical processes outside of a cell is actually rather easy. Any competent chemist can buy some chemicals from a supply company, weigh them in the correct proportion, dissolve them in an appropriate solvent, heat them in a flask for a predetermined amount of time, and purify the desired chemical produce away from unwanted chemicals produced by side reactions…

Most readers will quickly see the problem. There were no chemists four billion years ago. Neither were there any chemical supply houses, distillation flasks, nor any of the many other devices that the modern chemist uses daily in his or her laboratory, and which are necessary to get good results…"

Oh. So it's easy now.

What was with all the bitching and moaning upthread then?


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 190 of 314 (419756)
09-04-2007 4:07 PM
Reply to: Message 188 by Percy
09-04-2007 1:38 PM


ATP Synthase and ATP
Anyway, way back in Message 6 you claimed that ATP is required to create ATP. Are you now dropping that claim?

Percy ...

I didn't bother correcting Rob earlier ... I knew what he was getting at (since he tried this exact same routine over on the ribozyme thread ... right down to the Second Law, IC, etc.).

Rob, a cell does not require ATP to produce ATP using ATP synthase.

A cell requires an proton gradient. Which is established by NADH.

When the NADH runs out, ATP synthesis stops.

Capiche?

And before ATP/NADH/GTP/etc. existed, there was thermosynthesis, i.e. free energy gain from thermal cycling.

The first organisms (what could rightfully be called life aka prokaryotic cells) obtained their energy by a first protein named pF1 that worked on a thermal variation of the binding change mechanism of today's ATP sythase enzyme.

In other words, the reactions necessary to assemble prebiotic compounds (and then protocells and then prokaryotic cells) are thermodynamically favorable.

And, no, this is not up for debate, Rob.

If there are certain reagents in a beaker (or in a prebiotic pool), they will react. Period. Full stop. It's a matter of physics. That's what thermodynamically favorable means.

I can't stress this enough, Rob.

If the reagents are there, the reaction will occur.

And, as you acknowledged last night, "making the molecules of life" is easy.

Thermodynamically favorable reactions are the reason it's easy.

All you can argue, really, is that the necessary constituents for assembling "the molecules of life" were not present on prebiotic Earth.

Because, if you admit that those elements were there, then you will have to admit that they reacted.

The elements have no choice, Rob.

Edited by molbiogirl, : No reason given.

Edited by molbiogirl, : No reason given.


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 196 of 314 (419839)
09-05-2007 1:00 AM
Reply to: Message 192 by Rob
09-04-2007 11:53 PM


Behe's Balderdash II
In fact, if we disolved in water (using the formal chemical names) ribose-5-phosphate, glutamine, asparic acid, glycine, N10-formylTHF, carbon dioxide, and energy packets of ATP and GTP- all the small molecules that are used by the cell to build AMP- and let them sit for a long time (say, a thousand or a million years) we would not get any AMP.

Wow.

You don't read anything I post, do you? C'mon. Admit it.

Prebiotic Formation of ADP and ATP from AMP, Calcium Phosphates and Cyanate in Aqueous Solution Origins of Life and Evolution of Biospheres Vol. 29, No. 5

Because we do not know what the conditions were. We only theorize based upon limited data.

The data is hardly limited, Rob. Grow a pair and dip into pubmed sometime.

And lab techs manufacturing evidence is hardly objective...

I don't mind doing additional research on pF1. Expect the cites tomorrow.

Or that they do not look anything like life as we know it. In fact, theyre not even alive...

I repeat. Behe said "the molecules of life" are easy to make.

Are you now disagreeing with Behe?


This message is a reply to:
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Replies to this message:
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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 204 of 314 (419861)
09-05-2007 2:45 AM
Reply to: Message 197 by Rob
09-05-2007 1:20 AM


I get zilch, zero, and nada, when doing a web search for your bit...

[sigh]

A man who doesn't know how to google.

Pubmed, Rob. Look in pubmed.

Or, if pubmed is too much for you to handle, try scholar.google.

Have you even tried to read the giant chunk from that paper that I posted upthread?

All I was saying is that the factory itself (in this case a chloroplast) is made in the cell by way of a process that uses ATP.

OK. Now I know you don't bother reading my posts.

One more time.

To produce ATP, a chloroplast does not use ATP. It uses NADPH and FADH.

The "factory" you are referring to runs on NADPH and FADH to set up a proton gradient and to move electrons.

(An E. coli uses NADH.)

That's on wiki. You can find wiki, can't you Rob?


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 208 of 314 (419865)
09-05-2007 3:02 AM
Reply to: Message 199 by Rob
09-05-2007 2:08 AM


Re: Behe's Balderdash II
I found this little gem by Orgel (a real scientist). And it is from 2004.

From the paper you claim to have read:

Nucleoside 2 or 3 phosphates sometimes give nucleoside 2 or 3 cyclic phosphates in good yield in this way. More recently it has
been shown that AMP can be converted to ADP and ATP by cyanate in the presence of insoluble calcium phosphates (Yamagata, 1999).

Yamagata, 1999. That's the paper I cited, Rob.


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 209 of 314 (419866)
09-05-2007 3:08 AM
Reply to: Message 205 by Rob
09-05-2007 2:52 AM


And was that article Kuresu found on adenosine or adenine? Because Behe was talking about adenine.

Adenosine IS adenine.

How is the factory built? that was the point... Not what it runs on...

A chloroplast is irrelevant to abiogenesis.

Protocells don't generate energy using chloroplasts.

Edited by molbiogirl, : expletive deleted


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 217 of 314 (419894)
09-05-2007 11:17 AM
Reply to: Message 213 by Rob
09-05-2007 9:29 AM


Re: Behe's Balderdash II
Behe's point is that adenine is added unnaturally by chemists, and that in that case, yes AMP is easy to synthesize.

Oh, you are going to be disappointed!

Prebiotic Adenine Revisited: Eutectics and Photochemistry, Leslie Orgel, Origins of Life and Evolution of Biospheres, Volume 34, Number 4, August, 2004

Orgel writes:

Recent studies support an earlier suggestion that, if adenine was formed prebiotically on the primitive earth, eutectic freezing of hydrogen cyanide solutions is likely to have been important. Here we revisit the suggestion that the synthesis of adenine may have involved the photochemical conversion of the tetramer of hydrogen cyanide in eutectic solution to 4-amino-5-cyano-imidazole. This would make possible a reaction sequence that does not require the presence of free ammonia. It is further suggested that the reaction of cyanoacetylene with cyanate in eutectic solution to give cytosine might have proceeded in parallel with adenine synthesis.

Behe's point is that adenine is added unnaturally by chemists, and that in that case, yes AMP is easy to synthesize.

Orgel disagrees!

Edited by molbiogirl, : No reason given.


This message is a reply to:
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Replies to this message:
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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 218 of 314 (419926)
09-05-2007 2:55 PM
Reply to: Message 213 by Rob
09-05-2007 9:29 AM


Re: Behe's Balderdash II
Behe writes:

All roads lead to Rome, it is said, and similarly there are many ways to synthesize AMP. A book for chemists on my shelf lists eight different ways to make adenine (which is the top part of AMP without the foundation); the remainder of the molecule can be put together in a variety of ways also. Chemists who want to synthesize adenine, however, use completely different routes from that used by cells. Because they involve reactions in oily liquids at extremes of acidity, these conditions would cause the quick demise of any known organism.

Btw, Rob.

AMP = Adenosine Mono Phosphate

That means (pay close attention now) Adenine + Ribose + Phosphate

Behe is talking about the synthesis of AMP, not just the synthesis of adenine. My earlier cite (re: aqueous solution) stands.

And Orgel liked the study I cited too!


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 219 of 314 (419973)
09-05-2007 6:50 PM


Thermosynthesis For Dummies
Thermosynthesis as energy source for the RNA World: A model for the bioenergetics of the origin of life, Anthonie W.J. Muller, Biosystems, Volume 82, Issue 1, October 2005, Pages 93-102

Since you seem to have trouble finding the appropriate cites, I will be generous with my snippets:

The postulated molecular heat engines produced the same ATP as contemporary ATP synthase, but with much less power (energy produced per unit time) because the enzyme turnover time equaled the long thermal cycle time of a convection cell (Fig. 1). The latter constituted the inanimate self-organizing dissipative structure that any origin of life model requires. In this context, it is relevant that according to rRNA sequences, the niche of the last common ancestor of all living organisms was a – plausibly convecting – hot spring (Woese, 1987).

In the model, we apply the rule of parsimony (Benner et al., 1989) to primordial enzymes (Black, 1970) and enzyme mechanisms: in addition to broadly specific phosphorylations – that yield NMPs, NDPs, NTPs and phospholipids – pF1 also condensed amino acids and peptides to new peptide bonds. In this way, thermosynthesis effected the endergonic synthesis of high-energy products, enabling the modeling of a simple but powerful primordial metabolism. The basic primordial energy generating mechanism is therefore suggested to have been the binding of a substrate in a dehydrated local environment, followed by its conversion into a product with similar free energy in that environment, but a higher free energy in water. The higher free energy made direct release impossible; this release required a temperature change.

The genetic machinery is hypothesized to have emerged in seven stages (Fig. 5). Protocells, a suitable starting point for the origin of life (Morowitz et al., 1988), are assumed to have been stabilized by membrane lipid phosphorylation by pF1 in stage 1. There are many protocell candidates, some composed of lipids or material found in meteorites (Mautner et al., 1995, Dworkin et al., 2001, Hanczyc et al., 2003 and Chen et al., 2004). In stage 2, a proposed early pF1 synthesized by thermosynthesis a library of proteins of which a tiny fraction had multiple substrate condensing ability. In this way, pF1 propagated functionally, making daughters with similar capability but not necessarily identical composition. Such compositional replication is implausible for proteins (Orgel, 1987): a few small proteins cannot be expected to recognize and copy during peptide bond synthesis the many possible different combinations of amino acid residues. Random synthesis of a specific long protein sequence is also implausible (Orgel, 1987). The pF1 protein must have had a short motif sequence that is frequent in a long random sequence. The amino acid residue motif contained only a dehydration pocket and glycine hinges that enabled a lobe to cover a substrate in the dehydrated pocket. The lobe resembled the lobe of ATP-using enzymes that consist of the G(X)4KT/S(X)6I/V motif (Walker et al., 1982).

The NTPs generated in stage 3 of the mode were used for RNA synthesis (Joyce and Orgel, 1993). The self-replicating RNA-replicase of stage 4 is the key theoretical entity of the RNA World. A version that can replicate up to 14 nt has been found (Johnston et al., 2001). It is assumed that RNA replication resembled the DNA amplification by PCR demonstrated in a convection cell (Krishnan et al., 2002). RNA that enhanced the synthesis rate of pF1 was selected.

The emergence of ribozymes with aminoacylation ability constituted stage 5. Predicted already in 1958 (Crick, 1958), these ribozymes were found in the 1990s (Illangasekare et al., 1995, Illangasekare and Yarus, 1999, Yarus and Illangasekare, 1999, Lee et al., 2000, Schimmel and Kelley, 2000 and Saito et al., 2001). In stage 6 of the model, charged tRNAs increased the overall, still random, protein synthesis rate by their enhanced reactivity (Fig. 6a) that was catalysed by pF1 or ribozymes (Zhang and Cech, 1997); such ribozymes were progenitors of rRNA.

Other implications of thermosynthesis were discussed extensively previously (Muller, 1995). In addition, we refer to recent studies on nucleic acid polymerisation by convection (Krishnan et al., 2002, Braun et al., 2003, Braun and Libchaber, 2003 and Braun, 2004). We identify in pF1 a plausible component of the pre-RNA World (Orgel, 2003), describe this proposed pre-RNA World (Crick, 1993 and Dworkin et al., 2003) and illustrate how a protein could have supported the RNA World (Schuster, 1993) by yielding the free energy (Mehta, 1986 and Jeffares et al., 1998). We agree with the suggestion that only a few proteins were present during the emergence of the genetic code (Trevors and Abel, 2004).

Hey! Lookee! Your favorite real scientist! Leslie Orgel!

More pF1 research to come ...

Oh. Btw, Rob.

Percy writes:

Please don't feel the need to respond by quoting my text and highlighting the words "possible" and "may". Just remind yourself that science is tentative.

Ditto.


molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 226 of 314 (419998)
09-05-2007 9:27 PM
Reply to: Message 224 by kuresu
09-05-2007 9:19 PM


Re: Behe's Balderdash II
And do you realize you are only quoting the abstract to the whole article?

Kuresu, I'll tell you why Rob hasn't moved beyond the abstract.

He's too cheap to register with the publisher.

Rob writes:

Where'd you get the adenine? That comes in my next response...

Read Orgel's article! Or don't you have $32?


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Replies to this message:
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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 227 of 314 (420001)
09-05-2007 9:29 PM
Reply to: Message 221 by Rob
09-05-2007 9:05 PM


Re: Behe's Balderdash II
He said, if it was formed prebiotically... Do you know wahat the word if means. Or is it like the word is that some folks in high positions seem to have trouble with?

eee hee hee!

Yeah, Rob, I know wahat (sic) "if" means.

That the best you got?


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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 239 of 314 (420019)
09-05-2007 10:25 PM
Reply to: Message 228 by Rob
09-05-2007 9:38 PM


Evidence, Comin' Right Up!
Sulphate metabolism among thermophiles and hyperthermophiles in natural aquatic systems, A.N. Roychoudhury, Biochemical Society Transactions (2004) Volume 32, part 2

Thermophiles, a class of extremophile that has a temperature optimum for growth at around 70◦ C or higher [3], are of particular interest. Within the domains Archaea and Bacteria, thermophiles are among the most deeply branching organisms on the phylogenetic tree, based on 16 S rRNA. Thus they are the most primitive group of organisms known on this planet and possibly are closely similar to the common ancestor.

Although clear evidence of autotrophic CO2 fixation into the biomass by 3.8 bya ago is present in the sedimentary record, the specific metabolic pathways employed by the archaic organisms are still unclear. Sulphur isotope studies have provided the earliest evidence of a specific metabolic pathway – sulphate reduction – from a 3.47 bya- old barite mineral.

In order for the nascent life to sustain and proliferate, metabolic energy is essential. Therefore, to reconstruct the history of life on Earth, an inquiry of possible respiration pathways utilized by thermophilic organisms is required ... Prevalence of sulphate respiration among modern thermophiles and hyperthermophiles is now well known [13–18]. Microbiological results further suggest that it is possible that sulphate reduction was prevalent even before the divergence of the three domains of living organisms [19].

The kinetic data from hydrothermal environments suggest that the thermophilic sulphate reducers respond to the environmental determinants in a similar fashion to the microbes found in less hostile modern aquatic environments. In other words, if it is assumed that archaic microbes were similar to thermophiles in modern hydrothermal systems, then they were well advanced in adapting to environmental extremes and were capable of surviving and proliferating by utilizing sulphate respiration as one of the metabolic pathways.

Sulphate reduction.

Hmmmmm.

The Bacteria of the Sulphur Cycle [and Discussion], N. Pfennig, F. Widdel, J. R. Postgate, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 298, No. 1093, Sulphur Bacteria (Sep. 13, 1982), pp. 433-441

The bioenergetics of sulphate reduction have been shown to be quite different in the two most extensively studied genera of these basteria, Desulfovibrio and Desulfotomaculum. The major enzymes, ATP sulphurylase, adenylyl sulphate (APS) reductase, and bisulphate reductase, and intermediate bisulphite, APS and PPi are shown: H2 + SO4 --> S + 4H2O

ATP.

Now where could I get my hands on some prebiotic ATP?

More cites to come!


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Replies to this message:
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molbiogirl
Member (Idle past 806 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 243 of 314 (420023)
09-05-2007 10:32 PM
Reply to: Message 240 by Rob
09-05-2007 10:26 PM


Rob's Balderdash XCII
Why do you assume that there were prebiotic organisms?

Now, hold on a second here, Kuresu. I don't think we have Rob on record re: the origins of life.

Rob. I think we all know by now that abiogenesis isn't your cup of tea.

So. In your opinion. How exactly did we get here?


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