"Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions"
http://www.nature.com/nature/journal/v4 ... 013-s1.pdf

Are the conditions really plausible as being "Prebiotic"?

No, that's not the way you start a thread.

If you wish to challenge the basis of this paper, then do so. Don't expect others to leap into defending a professional tenured scientist's peer reviewed paper with 37 citations. It stands as plausible until challenged by valid constructive criticism.

If you have a point to make then do so, otherwise this thread might as well be closed now.

Spearthrower wrote:No, that's not the way you start a thread.

I'll start it the way I like.
Please note that your appeal to authority is unwarranted. I would like to discuss the actual conditions and see where there is evidence that this is indeed 'plausible' in a prebiotic environment.
Any objections?

No mention of pre-existing biota is made in that set up so, yes.

Synthesis of 2-aminooxazole 11
Reaction of glycolaldehyde 10 and cyanamide 8 in aqueous solution in the absence of
phosphate
Glycolaldehyde 10 (60 mg, 1.0 mmol) was dissolved in H2O (1 mL) at pH = 7.0.
Cyanamide 8 (42 mg, 1.0 mmol) was added, and the solution was incubated at 60°C
for 3 h.

Rather concentrated solutions here.
Any evidence that Glycoaldehyde was present at concentrations as high as 60g/l, and Cyanamide at 42g/l?
Was the water on Earth at pH 7.0, and how do we know this?
How sure are we about the 60°C temperature?

rainbow wrote:

Spearthrower wrote:No, that's not the way you start a thread.

I'll start it the way I like.
Please note that your appeal to authority is unwarranted. I would like to discuss the actual conditions and see where there is evidence that this is indeed 'plausible' in a prebiotic environment.
Any objections?

Appealing to an authority is not always fallacious. In this case, the application of authority is most certainly warranted.

The paper was published in a respected journal.

There are 37 citations in a very brief period of time.

This indicates that professional chemists working on this topic accept the plausibility of the model.

That means that, should you choose to disagree, you need to provide substantive reasons why you challenge the plausibility of it.

You have opened yet another thread where you have provided zero input and asked other people to make commentary on something that is clearly stated as plausible.

You are most certainly obliged to state why you would even question that it is plausible otherwise this thread is redundant by definition.

I recommend merging it with the other, already opened, Abiogenesis thread.

rainbow wrote:

Synthesis of 2-aminooxazole 11
Reaction of glycolaldehyde 10 and cyanamide 8 in aqueous solution in the absence of
phosphate
Glycolaldehyde 10 (60 mg, 1.0 mmol) was dissolved in H2O (1 mL) at pH = 7.0.
Cyanamide 8 (42 mg, 1.0 mmol) was added, and the solution was incubated at 60°C
for 3 h.

Rather concentrated solutions here.
Any evidence that Glycoaldehyde was present at concentrations as high as 60g/l, and Cyanamide at 42g/l?
Was the water on Earth at pH 7.0, and how do we know this?
How sure are we about the 60°C temperature?

Any evidence that it wasn't? That's the standard way you go about challenging claims, not just asking open questions. Have you read the paper? Have you noted the 37 citations? Do the 37 citations suggest that other professionals working in this field consider it plausible?

Spearthrower wrote:

rainbow wrote:

Synthesis of 2-aminooxazole 11
Reaction of glycolaldehyde 10 and cyanamide 8 in aqueous solution in the absence of
phosphate
Glycolaldehyde 10 (60 mg, 1.0 mmol) was dissolved in H2O (1 mL) at pH = 7.0.
Cyanamide 8 (42 mg, 1.0 mmol) was added, and the solution was incubated at 60°C
for 3 h.

Rather concentrated solutions here.
Any evidence that Glycoaldehyde was present at concentrations as high as 60g/l, and Cyanamide at 42g/l?
Was the water on Earth at pH 7.0, and how do we know this?
How sure are we about the 60°C temperature?

Any evidence that it wasn't? That's the standard way you go about challenging claims, not just asking open questions. Have you read the paper? Have you noted the 37 citations? Do the 37 citations suggest that other professionals working in this field consider it plausible?

If you can't answer, just say:
"I don't know"
This gives the opportunity to someone that has the information to provide it.
Thanks.

rainbow wrote:

Spearthrower wrote:

rainbow wrote:

Synthesis of 2-aminooxazole 11
Reaction of glycolaldehyde 10 and cyanamide 8 in aqueous solution in the absence of
phosphate
Glycolaldehyde 10 (60 mg, 1.0 mmol) was dissolved in H2O (1 mL) at pH = 7.0.
Cyanamide 8 (42 mg, 1.0 mmol) was added, and the solution was incubated at 60°C
for 3 h.

Rather concentrated solutions here.
Any evidence that Glycoaldehyde was present at concentrations as high as 60g/l, and Cyanamide at 42g/l?
Was the water on Earth at pH 7.0, and how do we know this?
How sure are we about the 60°C temperature?

Any evidence that it wasn't? That's the standard way you go about challenging claims, not just asking open questions. Have you read the paper? Have you noted the 37 citations? Do the 37 citations suggest that other professionals working in this field consider it plausible?

If you can't answer, just say:
"I don't know"
This gives the opportunity to someone that has the information to provide it.
Thanks.

Can you provide any evidence to contradict the plausibility of the peer-reviewed model?

If you can't - just say so then we can close this thread.

Thanks.

Preparative synthesis of 2-aminooxazole 11 using phosphate catalysis
To a solution of glycolaldehyde 10 (1.2 g, 20 mmol) in sodium hydrogen phosphate
buffer (1.0M, 10 mL, pH = 7.0) was added cyanamide 8 (840 mg, 20 mmol). The
solution was stirred at 60°C for 3 h, cooled to r.t., and extracted with EtOAc (5 × 20
mL). The combined EtOAc extracts were concentrated in vacuo to give 2-
aminooxazole 11 (1.2 g, 75%) as a white powder.

Now besides the problematic concentrations, pH and temperatures, has anybody got an idea how a vacuum pump got to be there in the PreBiotic Earth?

rainbow wrote:

Preparative synthesis of 2-aminooxazole 11 using phosphate catalysis
To a solution of glycolaldehyde 10 (1.2 g, 20 mmol) in sodium hydrogen phosphate
buffer (1.0M, 10 mL, pH = 7.0) was added cyanamide 8 (840 mg, 20 mmol). The
solution was stirred at 60°C for 3 h, cooled to r.t., and extracted with EtOAc (5 × 20
mL). The combined EtOAc extracts were concentrated in vacuo to give 2-
aminooxazole 11 (1.2 g, 75%) as a white powder.

Now besides the problematic concentrations, pH and temperatures, has anybody got an idea how a vacuum pump got to be there in the PreBiotic Earth?

Specious nonsense.

rainbow wrote:

Preparative synthesis of 2-aminooxazole 11 using phosphate catalysis
To a solution of glycolaldehyde 10 (1.2 g, 20 mmol) in sodium hydrogen phosphate
buffer (1.0M, 10 mL, pH = 7.0) was added cyanamide 8 (840 mg, 20 mmol). The
solution was stirred at 60°C for 3 h, cooled to r.t., and extracted with EtOAc (5 × 20
mL). The combined EtOAc extracts were concentrated in vacuo to give 2-
aminooxazole 11 (1.2 g, 75%) as a white powder.

Now besides the problematic concentrations, pH and temperatures, has anybody got an idea how a vacuum pump got to be there in the PreBiotic Earth?

The vacuum is a step in the preparation for analysis, not the actual reaction.

The reaction part is entirely about adding the solutions together and stirring them for 3hours. That's it. If you wish to claim these conditions aren't primitive earth plausible, please specify why. And if possible please back it up with peer-reviewed research.

Rumraket wrote:

rainbow wrote:

Preparative synthesis of 2-aminooxazole 11 using phosphate catalysis
To a solution of glycolaldehyde 10 (1.2 g, 20 mmol) in sodium hydrogen phosphate
buffer (1.0M, 10 mL, pH = 7.0) was added cyanamide 8 (840 mg, 20 mmol). The
solution was stirred at 60°C for 3 h, cooled to r.t., and extracted with EtOAc (5 × 20
mL). The combined EtOAc extracts were concentrated in vacuo to give 2-
aminooxazole 11 (1.2 g, 75%) as a white powder.

Now besides the problematic concentrations, pH and temperatures, has anybody got an idea how a vacuum pump got to be there in the PreBiotic Earth?

The vacuum is a step in the preparation for analysis, not the actual reaction.

And Rainbow has not even remotely shown that there is anything 'problematic' about the concentrations, pH or temperatures.

We await his evidence.

Rumraket wrote:

rainbow wrote:

Preparative synthesis of 2-aminooxazole 11 using phosphate catalysis
To a solution of glycolaldehyde 10 (1.2 g, 20 mmol) in sodium hydrogen phosphate
buffer (1.0M, 10 mL, pH = 7.0) was added cyanamide 8 (840 mg, 20 mmol). The
solution was stirred at 60°C for 3 h, cooled to r.t., and extracted with EtOAc (5 × 20
mL). The combined EtOAc extracts were concentrated in vacuo to give 2-
aminooxazole 11 (1.2 g, 75%) as a white powder.

Now besides the problematic concentrations, pH and temperatures, has anybody got an idea how a vacuum pump got to be there in the PreBiotic Earth?

The vacuum is a step in the preparation for analysis, not the actual reaction.

Then how did they get the pure 2-aminooxazole required for the next step?

General procedure for preparative synthesis of 2,2'-anhydrocytidine nucleosides and
nucleotides
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution. The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

A somewhat disurbing fact is that the DOW Chemical Company, had not yet begun production of their ion exchange resins, Dowex - 3 500 million years ago.
...as far as I know.

rainbow wrote:

General procedure for preparative synthesis of 2,2'-anhydrocytidine nucleosides and
nucleotides
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution. The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

A somewhat disurbing fact is that the DOW Chemical Company, had not yet begun production of their ion exchange resins, Dowex - 3 500 million years ago.
...as far as I know.

This level of ignorance is staggering for a supposed chemist. Let me break it down for you:
The reaction consists of :
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution.

The preparation of the sample for analysis consists of:
The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

Spearthrower wrote:
And Rainbow has not even remotely shown that there is anything 'problematic' about the concentrations, pH or temperatures.

We await his evidence.

Further down in the SAME paper:

Endo-2′,3′-cyanoethylidene-α-D-ribocytidine 41
D-Ribose aminooxazoline 21 (350 mg, 2.0 mmol), and sodium dihydrogen phosphate
(312 mg, 2.0 mmol) were dissolved in H2O (20 mL) at pH = 7.5, and freshly prepared
aqueous cyanoacetylene solution (0.98M, 20 mL) was added. The solution was stirred
at r.t. for 16 h, then the pH was increased to 8.5 with NaOHaq. (1.0M), and stirring
continued at r.t. for 2 d with readjustment to pH > 7.5 as necessary.

...so now the pH has changed, and the temperature, as has the concentration of cyanoacetylene.
This could be problematic, one set of conditions for one reaction, another for the later reactions.
I wonder too how the 1.0M NaOH got there.
How was the pH adjusted to > 7.5 'as necessary'?

rainbow wrote:

General procedure for preparative synthesis of 2,2'-anhydrocytidine nucleosides and
nucleotides
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution. The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

A somewhat disurbing fact is that the DOW Chemical Company, had not yet begun production of their ion exchange resins, Dowex - 3 500 million years ago.
...as far as I know.

Goodness me, it's like a merry-go-round where we keep coming back to the same stalking horse repackaged.

The resins produced by DOW are artificial zeolites which most certainly do occur naturally. The idea being that they are generally contaminated, and therefore not useful for control purposes.

International Zeolite Association, Database of Zeolite Structures, http://www.iza-structure.org/databases

Zeolites naturally form where volcanic rocks and ash layers meet alkaline groundwater.

Are you going to object to the natural presence of these 3 500 million years ago?

Rumraket wrote:

rainbow wrote:

General procedure for preparative synthesis of 2,2'-anhydrocytidine nucleosides and
nucleotides
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution. The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

A somewhat disurbing fact is that the DOW Chemical Company, had not yet begun production of their ion exchange resins, Dowex - 3 500 million years ago.
...as far as I know.

This level of ignorance is staggering for a supposed chemist. Let me break it down for you:
The reaction consists of :
An aqueous solution of the aminooxazoline (0.049M), sodium dihydrogen phosphate
(0.049M 1 eq.), and cyanoacetylene 7 (0.49M, 10 eq.) at pH = 6.5 was stirred at r.t. for
16 h resulting in a pale yellow solution.

The preparation of the sample for analysis consists of:
The solution was lyophilised, and the residue
purified by ion-exchange chromatography (Dowex® 50W 4 × 400 H+-form cationexchange
resin (50 g), eluting with HClaq. in the following stepwise concentration
gradient: 0.5M (2 × 50 mL), 1.0M (2 × 50 mL), 1.5M (2 × 50 mL), 2.0M (2 × 50 mL),
2.5M (2 × 50 mL), 3.0M (2 × 50 mL), 4.0M (2 × 50 mL)).

You still need the pure product for the next step. How was it purified, then?

In any case, why don't you write the people who published the paper with your critique instead of random forum dwellers? Surely, if you have doubts about the veracity of the experiment they should be much more qualified to answer your it.