rainbow wrote:

Rumraket wrote:

I don't think though that cyanamide, or her twin brother DICY are the Holy Grail you're looking for.

I can only speak for myself here, but I don't really see it's relevance at all since, in the majority of the papers I cited here, the formation of both primitive fatty acids, and ribose, is quite plausibly demonstrated at hydrothermal vents, entirely in cyanamide(and it's derivatives) absense.

I'm not sure what you're getting at. Is cyanamide, or DICY important to these reactions or not?
In any case, as I've said there are other compounds that can do the job.

Additionally the mechanics that achieve workable concentrations of these monomers is also demonstrated. It actually fits quite impressively together.

What sort of concentrations would you consider to be workable?

Rumraket wrote:So, I submitted this list of steps in contemporary origin of life research :

rainbow wrote:

Rumraket wrote:So, I submitted this list of steps in contemporary origin of life research :

Thanks, Rum.
Do you have any free links to these papers?

Rumraket wrote:

rainbow wrote:

Rumraket wrote:So, I submitted this list of steps in contemporary origin of life research :

Thanks, Rum.
Do you have any free links to these papers?

Yeah I have downloaded them all, I'll zip them and put them up in this post. brb.

Rumraket wrote:Uploaded, see above.

2009 Oct 14;131(40):14560-70.

Efficient and rapid template-directed nucleic acid copying using 2'-amino-2',3'-dideoxyribonucleoside-5'-phosphorimidazolide monomers.
Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW.

Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Harvard Medical School, Boston, Massachusetts 02114, USA.

The development of a sequence-general nucleic acid copying system is an essential step in the assembly of a synthetic protocell, an autonomously replicating spatially localized chemical system capable of spontaneous Darwinian evolution. Previously described nonenzymatic template-copying experiments have validated the concept of nonenzymatic replication, but have not yet achieved robust, sequence-general polynucleotide replication. The 5'-phosphorimidazolides of the 2'-amino-2',3'-dideoxyribonucleotides are attractive as potential monomers for such a system because they polymerize by forming 2'-->5' linkages, which are favored in nonenzymatic polymerization reactions using similarly activated ribonucleotides on RNA templates. Furthermore, the 5'-activated 2'-amino nucleotides do not cyclize. We recently described the rapid and efficient nonenzymatic copying of a DNA homopolymer template (dC(15)) encapsulated within fatty acid vesicles using 2'-amino-2',3'-dideoxyguanosine-5'-phosphorimidazolide as the activated monomer. However, to realize a true Darwinian system, the template-copying chemistry must be able to copy most sequences and their complements to allow for the transmission of information from generation to generation. Here, we describe the copying of a series of nucleic acid templates using 2'-amino-2',3'-dideoxynucleotide-5'-phosphorimidazolides. Polymerization reactions proceed rapidly to completion on short homopolymer RNA and LNA templates, which favor an A-type duplex geometry. We show that more efficiently copied sequences are generated by replacing the adenine nucleobase with diaminopurine, and uracil with C5-(1-propynyl)uracil. Finally, we explore the copying of longer, mixed-sequence RNA templates to assess the sequence-general copying ability of 2'-amino-2',3'-dideoxynucleoside-5'-phosphorimidazolides. Our results are a significant step forward in the realization of a self-replicating genetic polymer compatible with protocell template copying and suggest that N2'-->P5'-phosphoramidate DNA may have the potential to function as a self-replicating system.

Rumraket wrote:
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.

Such fluids show the presence of low concentrations
(nmol range) of C8-C16 linear fatty acids
(N.G. Holm and J.Oë . Bjarnason, unpublished
data).

rainbow wrote:

Rumraket wrote:
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.

From this paper:

Such fluids show the presence of low concentrations
(nmol range) of C8-C16 linear fatty acids
(N.G. Holm and J.Oë . Bjarnason, unpublished
data).

These concentrations are very low. They would need to be concentrated somehow in order for them to form protocell membranes. There was a discussion on the minimum concentrations required on the RD forum. I'll see if I can find the references.

We compare the assumptions on pore geometry with the geological
record. As seen from the representative cross-section in
Fig. 1a, an aspect ratio between 25 and 50 can be estimated for
single elongated pore spaces in the mounds at the Lost City vent
site (20–100
m across and 1 mm long). Although, at Lost
City, pore shapes may be governed by filamentous bacterial
growth, chemical garden-like growth with even higher aspect
ratios is likely to occur in comparable hydrothermal systems with
moderate temperatures. For example, the 500-mm-long hydrothermal
pyrite spires from the 352-million-year-old Tynagh
zinc-lead sulfide deposit, Ireland, have central cavities that are
100
m in diameter (aspect ratio r  5,000:1) (ref. 29 and Fig.
3b). Similar structures have been realized in laboratory simulations
(30). Thus, the projected extreme accumulation should be
easily reached in natural settings. In any case, the accumulation
is exponentiated when low aspect ratio clefts are interconnected.
Note that pore concatenation is an especially interesting feature
from a geological point of view. During hydrothermal dissolution
pores enlarge, become more interconnected (i.e., the value of the
aspect ratio increases), and can substantially promote the accumulation
of molecules. Based on these results, and given the
large number of clefts in any one of multitudinous submarine
hydrothermal mounds on the early earth (29), the opportunities
would have been manifold for a critical accumulation of organic
monomers and polymers synthesized in the same milieu.

In conclusion, we propose a type of mechanism, driven solely
by a temperature gradient, which strongly accumulates even
small protobiological molecules in semiclosed hydrothermal
pore systems. This setting provides a compelling, dissipative
microenvironment to promote the first steps in the molecular
evolution of life.

Thermal diffusion columns (or Clusius-Dickel separations) were
used for industrial purifications during the middle of the 20th
century.9 Using experimentally measured thermal diffusion coefficients,
Baaske et al. performed simulations suggesting that
nucleotides and nucleic acid oligomers could be locally concentrated
in the prebiotic vent context outlined above. Here we experimentally
demonstrate that a microcapillary thermal diffusion column can
concentrate dilute solutions of nucleotides, oligonucleotides, and
fatty acids. Upon concentration, the self-assembly of large vesicles
containing encapsulated DNA occurs in regions where the cac of
the fatty acid is exceeded. Our findings suggest a novel means by
which simple physical processes could have led to the spontaneous
formation of cell-like structures from a dilute prebiotic reservoir.

Conclusions
The interactions of simple, single-chain amphiphiles with many different surfaces results in
the organization of membranes and the formation of vesicles. This effect could have played
a key role in the organization and formation of the first cell-like structures on the early
earth. Since mineral particles have been implicated in very early chemistries and
polymerization reactions (Bernal, 1951; Wächtershäuser, 1988; Ferris and Hill et al.,
1996; Sowerby and Cohn et al., 2001; Sowerby and Petersen et al., 2002; Monnard, 2005),
it is intriguing that minerals might have also been involved in the formation of yet another
essential component of life—the cellular membrane. Mineral-mediated vesicle formation
occurs with many disparate types of minerals and is therefore a more general property than
clay-catalyzed RNA polymerization.
Orig Life Evol Biosph
The formation of vesicles in the presence of minerals occurs proximal to the mineral
surface and is not due to the release of some soluble factor or change in the micelle to
vesicle transition concentration. In addition, the rate of vesicle formation is influenced not
only by the available surface area of the mineral, but also by the curvature of the surface.
Mineral surfaces that are intrinsically negatively charged may directly stimulate membrane
formation, while in other cases an adsorbed layer of amphiphiles may coat the mineral
particle and serve as the catalyst for subsequent vesicle formation. If such mechanisms
operated on the prebiotic Earth, diverse types of mineral particulates with a variety of
catalytic properties may have been efficiently encapsulated within membrane vesicles.

Fluids of Mid-Atlantic Ridge hydrothermal systems in basaltic settings have been collected and subsampled by the same procedure as used for the Rainbow £uids. The basaltic systems sampled were Menez Gwen, Lucky Strike, TAG, and
Snake Pit (Fig. 1). The concentration methodology using HLB Sorbents has also been successfully applied for the concentration of 1^2 l of fluids at 240³C and 290³C from terrestrial hydrothermal systems in basaltic settings on Iceland.
Such £uids show the presence of low concentrations (nmol range) of C8^C16 linear fatty acids (N.G. Holm and J.Oë . Bjarnason, unpublished data).

Compared to the Rainbow fluids much lower concentrations of organic compounds were detected in fluids collected from Mid-Atlantic Ridge hydrothermal systems in basaltic settings (Menez Gwen, Lucky Strike, TAG, and Snake Pit).

Thus, the projected extreme accumulation should be
easily reached in natural settings.

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

Thermal diffusion columns (or Clusius-Dickel separations) were
used for industrial purifications during the middle of the 20th
century.9 Using experimentally measured thermal diffusion coefficients,
Baaske et al. performed simulations suggesting that
nucleotides and nucleic acid oligomers could be locally concentrated
in the prebiotic vent context outlined above. Here we experimentally
demonstrate that a microcapillary thermal diffusion column can
concentrate dilute solutions of nucleotides, oligonucleotides, and
fatty acids. Upon concentration, the self-assembly of large vesicles
containing encapsulated DNA occurs in regions where the cac of
the fatty acid is exceeded. Our findings suggest a novel means by
which simple physical processes could have led to the spontaneous
formation of cell-like structures from a dilute prebiotic reservoir.

In order to investigate concentration-dependent vesicle self-assembly,
we first showed that fatty acids can become highly concentrated
within thermal diffusion columns. Linear capillaries were loaded
with 60 μM 3H-labeled oleate at pH 11 to prevent vesicle assembly.
The capillaries were incubated at ΔT ) 30 K for 24 h and then
fractionated, after which the oleate concentrations were determined
by liquid scintillation. Fractions (0.75 cm or 300 nL) from the bottom
of the capillary showed a 5-fold accumulation over those taken from
the top (Figure S2). The concentration of fatty acids in a thermal
diffusion column leads to the possibility of vesicle formation from a
dilute solution. However, the convective flow running along the
concentration gradient poses a problem, in that newly formed vesicles
would be carried up the capillary, where they would dissolve as a
result of the low local fatty acid concentration.

Rainbow wrote:Please bear in mind that the starting concentrations used (60 μM 3H-labeled oleate) are 60 000 times higher than those expected in thermal vents. Even starting from these relatively high concentrations, they were only able to achieve a '5-fold accumulation'.

Heat-driven molecular accumulation in hydrothermal pores. (a) Section through aragonite (CaCO3) from the submarine hydrothermal vent field at Lost City (kindly provided by D. Kelley; ref. 20). (b) Simulation of a part of the pore system. If subjected to a horizontal thermal gradient of 30 K, a 1,200-fold accumulation of single nucleotides is expected (logarithmic concentration color scale). A concatenation of three of these pore sections leads to a 10^9-fold accumulation. (c) The mechanism of accumulation is driven by heat in a twofold way. Thermal convection shuttles the molecules vertically up and down and thermophoresis pushes the molecules horizontally to the right. The result is a strong molecular accumulation from the top to the bottom (linear concentration color scale).

Predicted effects of the molecule size and pore length on the accumulation level. The simulation results are based on the experimentally measured Soret coefficients and diffusion coefficients for DNA and RNA (see Table 1). (a) The accumulation increases exponentially with the size of the molecule. Whereas single nucleotides are accumulated 7-fold in a short cleft of aspect ratio 10:1, double-stranded DNA comprising 1,000 base pairs accumulates 10^15-fold. The equilibration takes 9 min for single nucleotides and 14 min for single stranded RNA comprising 22 bases. For DNA polynucleotides of 100 and 1,000 bp it takes 18 or 33 min, respectively. (b) Elongation of the cleft exponentially increases the accumulation. For example, the accumulation of single nucleotides is raised to a 10^10-fold level in a pore with an aspect ratio of 125:1. A linear concentration scale is used in both plots, scaled to the respective maximal concentration. The time to reach steady state is 9 min for r = 10, 4 h for r = 50 and 23 h for r = 125.

Pertinent to our argument is the fact that accumulation grows exponentially both with the size of the molecule and the length of a concatenated pore system. In concatenated pores accumulation of molecules increases exponentially, a result of the considerable concentration independence of thermophoresis below molar concentrations (23–25). Thus, although single nucleotides accumulate merely 7-fold in the short pore of Fig. 2 a, concatenating 12 of these pores using a wide variety of orientation angles exponentiate the accumulation to an extreme 712 = 10^10-fold level. Elongation of the pore has exactly the same effect. As shown in Fig. 2 b, a pore system with a total aspect ratio of r = 125:1 accumulates single nucleotides 10^10-fold. Notably, the length of this pore system is only 18 mm, below the typical lengths of pore systems in hydrothermal settings.

Our approach has the advantage of offering an active concentration mechanism in an already existing, robust enclosure. Because thermophoretic drift is common for molecules, the accumulation scheme applies similarly to nucleic acids, amino acids, and lipids.

Rumraket wrote:

Rainbow wrote:Please bear in mind that the starting concentrations used (60 μM 3H-labeled oleate) are 60 000 times higher than those expected in thermal vents. Even starting from these relatively high concentrations, they were only able to achieve a '5-fold accumulation'.

This is only related to the Linear capillaries, which, according to the "Extreme accumulation of nucleotides in simulated hydrothermal pore systems." - paper, differ markedly from concave or shaped capillaries.

Before you object to the fact that the above citation deals specifically with nucleotides, the paper goes on later to state:

Our approach has the advantage of offering an active concentration mechanism in an already existing, robust enclosure. Because thermophoretic drift is common for molecules, the accumulation scheme applies similarly to nucleic acids, amino acids, and lipids.

Fair enough, but it is a mathematical simulation, and not an actual experiment. The lab experiments done by Szostak show lower accumulations, is my point. If laboratories could achieve these, then the simulation would be validated. This isn't the case (yet).

No objection. This does introduce another problem, and a very big one. If the concentration effect is non-selective, then it will result in accumulation of all the other molecules in the hydrothermal system.
If we go back to paper 1, then we shall see that hydrocarbons are produced in greater quantities than are fatty acids. If these are accumulated as well then they would interfere with micelle formation.

Rumraket wrote:

No objection. This does introduce another problem, and a very big one. If the concentration effect is non-selective, then it will result in accumulation of all the other molecules in the hydrothermal system.
If we go back to paper 1, then we shall see that hydrocarbons are produced in greater quantities than are fatty acids. If these are accumulated as well then they would interfere with micelle formation.

This seems more like an assertion than an experimentally derived fact. I'm not rejecting it out of hand, i'm just saying it remains to be seen.

rainbow wrote:

Rumraket wrote:

No objection. This does introduce another problem, and a very big one. If the concentration effect is non-selective, then it will result in accumulation of all the other molecules in the hydrothermal system.
If we go back to paper 1, then we shall see that hydrocarbons are produced in greater quantities than are fatty acids. If these are accumulated as well then they would interfere with micelle formation.

This seems more like an assertion than an experimentally derived fact. I'm not rejecting it out of hand, i'm just saying it remains to be seen.

It is a rather well known reaction, and one that you probably use every day!
The fatty acids are the basis of common soaps, they are in fact the sodium or potassium salts of these acids. If you were to get a mineral oil (long chain hydrocarbon) on your hands, you'd most likely use soap to remove it.