locutus7 wrote:This is one bizarre thread. Rather than proffering a disjointed critique of Cali's paper, why doesn't Rainbow offer HIS explanation of the beginnings of life?

OgreMkV wrote:I've answered the question about whether I have read the paper.

locutus7 wrote:This is one bizarre thread. Rather than proffering a disjointed critique of Cali's paper, why doesn't Rainbow offer HIS explanation of the beginnings of life?

rainbow wrote:

locutus7 wrote:This is one bizarre thread. Rather than proffering a disjointed critique of Cali's paper, why doesn't Rainbow offer HIS explanation of the beginnings of life?

What perhaps you should realise that the person opening a thread decides on the format of that thread.
This gives a three options:
1) Accept the way I've set it up.
2) Ignore the thread.
3) Open a new thread with the format you prefer.

OK?

Rumraket wrote:Wow... 29 pages of a useless discussion regarding the definition of "directed" chemical reactions. Not much mention of abiogenesis at all.

Rainbow, you have previously (on RD.net) erected valid criticisms(not to be mistaken for refutations) of *some* abiogenesis models and papers. But this entire charade about whether water boils or not or if "artificial agents" are part of the picture just isn't one of them.
I'd much rather see this discussion steer in the direction of actual contemporary abiogenesis research, specifically steps which are yet to be fully explored.

It seems to me, from what I have gathered over the last 6-12 months of interest in the subject, that a number of steps have been presented as being abiotically plausible, and a number are undergoing active research. I will list them here and anyone is free to comment and tell me I misunderstood something:

As I understand the current model, scientists are trying to identify a number of abiotically plausible steps resulting in a protocell capable of undergoing Darwinian evolution. The protocell is basically a lipid bilayer vesicle(membrane of fatty acids) containing some form of simple genetic material. So, in order to demonstrate that this protocell can come about by natural means, scientists are working on showing how the individual constituents of the cell could naturally form and come together to form the final product.

As I understand it, the following steps have been demonstrated so far : (Steps in orange are subjects I haven't yet read much on and red are subjects which have not yet been satisfyingly demonstrated to occur under abiotic conditions).

1. Abiotic formation of fatty acids.
Initial indications of abiotic formation of hydrocarbons in the Rainbow ultramafic hydrothermal system, Mid-Atlantic Ridge, Nils G. Holma, , and Jean Luc Charloub.

2. Abiotic Fatty acid concentrating mechanics resulting in the formation of bilayer vesicles.
Extreme accumulation of nucleotides in simulated hydrothermal pore systems.
Philipp Baaske*, Franz M. Weinert*, Stefan Duhr*, Kono H. Lemke†, Michael J. Russell‡, and Dieter Braun*§

Formation of Protocell-like Vesicles in a Thermal Diffusion Column
Itay Budin,†,§ Raphael J. Bruckner,‡,§ and Jack W. Szostak*,§

Mineral Surface Directed Membrane Assembly
Martin M. Hanczyc & Sheref S. Mansy & Jack W. Szostak

3. Abiotic formation of Varying nucleotides * (Much depends on the type of nucleotides, I think the formation of Ribonucleotides have been pretty sufficiently demonstrated).

I'm not going to cite all the papers I have found on this, but propably most important is the classic contention that RNA cannot form because Ribose is not abiotically plausible. This has been demonstrated to be false:
Alkaline fluid circulation in ultramafic rocks and formation of nucleotide constituents: a hypothesis.
Nils G Holm*, Marion Dumont, Magnus Ivarsson and Cécile Konn.

4. Abiotic nucleotide concentrating mechanics resulting both in formation of oligomers and areas of high concentration of single nucleotides.
Extreme accumulation of nucleotides in simulated hydrothermal pore systems.
Philipp Baaske*, Franz M. Weinert*, Stefan Duhr*, Kono H. Lemke†, Michael J. Russell‡, and Dieter Braun*§

5. Ability of the bilayer vesicle to *ingest* nucleotides under abiotic conditions.
Semipermeable lipid bilayers exhibit diastereoselectivity favoring ribose.
M. G. Sacerdote* and J. W. Szostak†

Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division
Martin M. Hanczyc,* Shelly M. Fujikawa,* Jack W. Szostak†

6. Ability of bilayer vesicle to grow/split under abiotic conditions.
Coupled Growth and Division of Model Protocell Membranes. Ting F. Zhu†,‡ and Jack W. Szostak*,†

Now this is where it gets intersting and where to my knowledge most of the research is being done today:

7. Demonstrate ability of nucleotide-containing vesicle to develop increasingly complex nucleotide polymers.
8. Demonstrate ability of nucleotide-polymers to evolve into self-replicators. This has not yet been demonstrated.
9. Demonstrate ability of nucleotide-containing vesicle to reproduce with copies of genetic polymer. So haven't this.

From what I have gathered reading the most recent of the Szostak lab's papers, they are currently exploring alternative nucleotides (ignoring their abiotic plausibility) like DNA, TNA and LNA in order to better understand what is required to reach the goal of an abiotically plausible self-replicator.

Edited with some references. Cleaned up a little.

rainbow wrote:Ribose sugar isn't that easily formed under prebiotic conditions, and some of the bases are unstable. It remains unanswered as to how they could obtain any significant concentration in the vicinity of the lipids.

It is, indeed, possible that the formose reaction is responsible for the prebiotic formation of ribose in natural environments and that this occurs in close vicinity to purine synthesis and phosphorylation processes. Shapiro a couple of decades ago concluded: 'The evidence that is currently available does not support the availability of ribose on the prebiotic Earth... This situation could change if some alternative pathway for ribose synthesis were discovered; one that produced it in better yield and was not as vulnerable to interferences from nitrogen-containing substances' [26]. The discovery of the stabilization of pentoses – ribose, in particular – by borate has now changed our view of the formose reaction from a seemingly random and nonselective reaction into a very precise pre-RNA process.

Shrunk wrote:

rainbow wrote:

locutus7 wrote:This is one bizarre thread. Rather than proffering a disjointed critique of Cali's paper, why doesn't Rainbow offer HIS explanation of the beginnings of life?

What perhaps you should realise that the person opening a thread decides on the format of that thread.
This gives a three options:
1) Accept the way I've set it up.
2) Ignore the thread.
3) Open a new thread with the format you prefer.

OK?

Umm, no. Beyond starting the thread, the one who opens it has no more authority over how the thread proceeds from there than any other member. If people want to bring up topics that you don't like or ask questions you'd rather ignore, that's just the way it goes. You're not obliged to acknowledge or answer them, of course.

Rumraket wrote:It's kind of annoying having two threads more or less discussing the same thing.

rainbow wrote:

Rumraket wrote:It's kind of annoying having two threads more or less discussing the same thing.

Agreed, but I'd like to discuss your points under the Chemistry Section, rather than Debunking. I've opened a thread there if you care to move the discussion over.

OgreMkV wrote:Oh good grief rainbow.

rainbow wrote:

OgreMkV wrote:Oh good grief rainbow.

Yes or No.
Did you read the full paper?

If you did, I've got some questions I'd like to ask that are relevant to the discussion.

OgreMkV wrote:Assume whatever you like. I'm done with you.

With the advent of this discovery in appropriate laboratory research, protocell formation is but a short step away, and indeed, the latest research is now actively concentrating upon the minimum components required in order for a viable, self-replicating protocell to exist.

Prebiotic lipid formation is also a part of the repertoire of the literature in the field, and some papers now extant document the first experiments aimed at producing viable self-replicating protocells

Whilst scientists naturally accept that 'joining the dots' between these individual steps is entirely proper, particularly on a body the size of a planet over a 100 million year period, the absence of experiments actively coupling these stages is a matter remaining to be addressed, though such experiments will be ambitious in scope indeed if they are to produce complete working protocells at the end of a long production line starting with a Miller-Urey synthesis.

starting with a Miller-Urey synthesis

rainbow wrote:

Whilst scientists naturally accept that 'joining the dots' between these individual steps is entirely proper, particularly on a body the size of a planet over a 100 million year period, the absence of experiments actively coupling these stages is a matter remaining to be addressed, though such experiments will be ambitious in scope indeed if they are to produce complete working protocells at the end of a long production line starting with a Miller-Urey synthesis.

There is nothing to support the argument that the origin of life would've required an Earth-sized planet, or a 100 million years. Molecules are very small and the Original Replicator could've formed in the tiniest of puddles, or even in a moist crack within a particle of clay on a dried out lake, or a micron-sized pore in a volcanic vent.

Newmark wrote:

rainbow wrote:

Whilst scientists naturally accept that 'joining the dots' between these individual steps is entirely proper, particularly on a body the size of a planet over a 100 million year period, the absence of experiments actively coupling these stages is a matter remaining to be addressed, though such experiments will be ambitious in scope indeed if they are to produce complete working protocells at the end of a long production line starting with a Miller-Urey synthesis.

There is nothing to support the argument that the origin of life would've required an Earth-sized planet, or a 100 million years. Molecules are very small and the Original Replicator could've formed in the tiniest of puddles, or even in a moist crack within a particle of clay on a dried out lake, or a micron-sized pore in a volcanic vent.

Are you saying that some random chemical reactions has the same chance of happening in a short time in "the tiniest of puddles, or even in a moist crack within a particle of clay on a dried out lake, or a micron-sized pore in a volcanic vent", as it has of happening on "a body the size of a planet over a 100 million year period"? If not, would you care to explain your point a bit more?