Critique on Calilasseia's "The Emergence Of Life On Earth"

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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#81  Postby locutus7 » Mar 09, 2010 7:31 pm

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?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#82  Postby rainbow » Mar 12, 2010 11:24 am

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?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#83  Postby rainbow » Mar 12, 2010 11:29 am

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

Well I've been through this thread, and I can't find it.
Can't you just answer directly:
Have you read the full paper?
Yes or No?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#84  Postby aspire1670 » Mar 12, 2010 11:32 am

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 doesn't do explanations he does resentments and dodges. He's still smarting from the spanking Cali and others gave him on the old RDF and hoping his assertion that the OP decides the format dodge will save him.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#85  Postby Shrunk » Mar 12, 2010 11:37 am

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.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#86  Postby Rumraket » Mar 12, 2010 12:09 pm

It's kind of annoying having two threads more or less discussing the same thing.
Some premature or outdated information have already seen light in this one so i'm going to quote my post from the "Abiogenesis" thread :

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.

Take note of the ribose formation paper's final conclusion :
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.
Last edited by Rumraket on Mar 12, 2010 12:38 pm, edited 1 time in total.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#87  Postby Rumraket » Mar 12, 2010 12:17 pm

Aditionally, as I have also shown in the other thread, the dimer of cyanamide, dicyandiamide, which performs the dehydration-function of cyanamide, is readily avaiable both from UV radiation of HCN and electron-beaming(spark-discharge experiment) of CH4, NH3 and N2O, also making this substance abiotically plausibe.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#88  Postby 95Theses » Mar 12, 2010 12:29 pm

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.


I was wondering if he was under the impression that this was some sort of fancy new blog where he gets to moderate the comments.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#89  Postby rainbow » Mar 12, 2010 2:03 pm

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.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#90  Postby Rumraket » Mar 12, 2010 2:33 pm

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.


Sure.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#91  Postby OgreMkV » Mar 12, 2010 2:38 pm

Oh good grief rainbow.

Your attempts to segregate information that doesn't agree with you doesn't bode well for our discussion. We can't even get you to accept the standard definitions from chemistry.

abiogensis, no matter how many threads you create, is a highly interdisciplinary process. You can't take ribose in one thread, and RNA in another thread, and lipids in another thread. All these things have to work together.

By seperating things out like you are trying to prevents people from an actual discussion. Did you read the thread I posted about what a real scienitific discussion looks like?

If have specific doubts about the ability of cyanamide to be a part of the generation of ribose sugars and lipid vesicles, then bring it up. Oh wait, I forgot, you don't have the papers that discuss this, so you're making up shit.

"I can't imagine this happening, so it didn't."

Whatever... start reading.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#92  Postby rainbow » Mar 12, 2010 2:49 pm

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.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#93  Postby rainbow » Mar 14, 2010 12:45 pm

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.


In view of the evasion of this question, we'll just have to assume the answer is 'No'.
OK.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#94  Postby OgreMkV » Mar 14, 2010 1:38 pm

Assume whatever you like. I'm done with you.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#95  Postby rainbow » Mar 14, 2010 1:52 pm

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

Fair enough.

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.

Quite a non-sequitur.
Nevertheless it fails to explain what is meant by a 'short step away' - 1 year?, 10 years?, 100years?
We should not forget that after Miller-Urey it was proclaimed that the synthesis of life was just a short step away.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#96  Postby hackenslash » Mar 14, 2010 1:55 pm

So what? It was also proclaimed in the 19th century that all the secrets of the universe had been unlocked, and that all that was left to do was tie up a few loose ends. We're a lot wiser now. A short step away in this context is literal steps, and makes no claim regarding how long it will take.

Meanwhile, still no movement with regard to the thread title. No critique, just a load of waffling.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#97  Postby rainbow » Mar 14, 2010 2:02 pm

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

This is a repeat of what was discussed above, but we are no nearer in discovering if the lipids are phospholipids, and whether they will form under early earth conditions - or whether this refers to the relatively easy to form fatty acid lipids.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#98  Postby rainbow » Mar 16, 2010 7:41 am

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.
starting with a Miller-Urey synthesis

Doesn't follow at all. We have more convincing evidence that building blocks for RNA and protocells could form in volcanic vents. Miller-Urey doesn't have to be involved. Maybe even the organics came from space in the form of chondrites.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#99  Postby Newmark » Mar 16, 2010 7:56 am

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?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#100  Postby rainbow » Mar 16, 2010 8:18 am

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?

No. It doesn't matter how long you have, or how big the planet might be, if you don't have conditions conducive to the origin of life. If you do have conditions conducive to the origin of life, they can be there on a micro-scale - and the reactions can take place in a very short period, perhaps hours or days.
We actually don't know how big and how long.
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