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Mon Jun 25, 2018, 08:17 PM

Hot Cracks and Addressing Questions in the Origin of Life.

I spent part of my day yesterday reading about cracks in two ways, first in thinking about fracture toughness in silicon nitride, a cool material, which is not the subject of this post, and then about the effect of heat flowing through a crack to cause the polymerization of nucleotides into nucleic acids, which is the subject of this post.

I described my renewed interest in this topic here: Open source paper on "Defining Life."

Over the weekend, I found myself thinking about the anti-entropy that life is, and went poking around in the library.

Here's a cool paper I found on exactly that subject, the difficult case or the origin of nucleic acids, since many people postulate that life arose from an "RNA world:" Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length (Moritz Kreysing†‡, Lorenz Keil‡, Simon Lanzmich‡ and Dieter Braun, Nature Chemistry volume 7, pages 203–208 (2015))

Entropy is discussed in the introduction:

From a wide range of exploratory experiments much is known about the capabilities and limitations of chemical replication systems1–6. It has become increasingly clear that such replicators are delicate systems that require a suitable supportive microenvironment to host non-equilibrium conditions. These conditions permit the sustainment of molecular evolution and the synthesis of molecules against equilibrating forces1,7–9. To the same end, modern cells provide active compartments of reduced entropy that protect genetic information against its thermodynamically favoured decay8,10. This is facilitated by sophisticated membrane-trafficking machinery and a metabolism that feeds on chemical low-entropy sources or light energy (Fig. 1a).

It has been known since Spiegelman’s experiments in the late 1960s11 that, even if humans assist with the assembly of an extracellular evolution system, genetic information from long nucleic acids is quickly lost. This is because shorter nucleic acids are replicated with faster kinetics and outcompete longer sequences. If mutations in the replication process can change the sequence length, the result is an evolutionary race towards ever shorter sequences.

In the experiments described here we present a counterexample. We demonstrate that heat dissipation across an open rock pore, a common setting on the early Earth12 (Fig. 1b), provides a promising non-equilibrium habitat for the autonomous feeding, replication and positive length selection of genetic polymers...

...Here we extend the concept to the geologically realistic case of an open pore with a slow flow passing through it. We find continuous, localized replication of DNA together with an inherent nonlinear selection for long strands. With an added mutation process, the shown system bodes well for an autonomous Darwinian evolution based on chemical replicators with a built-in selection for increasing the sequence length. The complex interplay of thermal and fluid dynamic effects, which leads to a length-selective replication (Fig. 1c, (1)–(4)), is introduced in a stepwise manner.


The caption:

a, Modern cells feed on chemical energy, which enables them to host, maintain and replicate information-coding polymers, processes necessary for Darwinian evolution. b, The flux of thermal energy across geological cracks near a heat source (the white smoker28 is adapted from an image courtesy of Deborah S. Kelley). c, (1) A thermal gradient across a millimetre-sized crack induces the accumulation of molecules by thermophoresis and convection. (2) A global throughflow imports nutrients into the open pore. (3) Exponential replication is facilitated by the local convection, which shuttles the molecules repetitively between warm and cold, and thus induces the cyclic denaturation of nucleotides. (4) The combination of influx, thermophoresis and convection selectively traps long molecules and flushes out short ones. The inflow speed determines the cut-off size of the resulting length selection. Mechanisms (1) to (4) are described in detail in this article.


The authors take dilute short DNA fragments and drive the through a crack which has a temperature gradient on either end, the direction of flow being from hot to cold.

Here's a schematic picture from the paper:



A convective flow cycles the growing nucleic acid chain, and the overall flow determines the size of the DNA that exits from the system, and the heat provides the energy required for sequence replication:

Exponential replication by convective thermal cycling. Besides continuous feeding and length-selective trapping, the asymmetrically heated pore offers another important feature relevant to the origin of life: laminar convective temperature cycling of the accumulated nucleic acids20,21. This opens the door to Watson–Crick-type replication mechanisms, which are otherwise hindered by the considerable energy costs required to separate double-stranded oligonucleotides22. The thermal cycling can be predicted from a fluid dynamics model that includes thermophoresis and diffusion (Fig. 4a). It is sufficient to separate cyclically double-stranded DNA (dsDNA) to drive exponential base-by-base replication with duplication times on the order of minutes, as documented by SYBR Green I fluorescence (Fig. 4b and Supplementary Movie 4).


The famous PCR technique, albeit a process using a thermally stable enzyme as a catalyst, also relies on heat for replication - the authors do some PCR work in their experiments.

However in this case, the enzyme is omitted, and the reaction takes place via cycling through thermal gradients.

Another picture:



The caption:

a, The temperature gradient drives oligonucleotides horizontally from warm to cold by thermophoresis and simultaneously triggers the vertical thermal convection of water. Its combination results in a length-dependent accumulation at the bottom of an elongated pore within minutes (see Supplementary Movie 2). b, The accumulation of dilute double-stranded oligonucleotides (100–1,000mer) at the bottom is monitored within a 100 µm thin and 2 mm high capillary via SYBR Green I fluorescence. c, The accumulation is dynamic: the nucleotides cycle between the warm and cold sides, visualized in white for a single 500mer of DNA.


Another figure shows the effect of flow rate on strand length:




a, A steady upwards feeding flow is triggered by opening the asymmetrically heated pore. A ladder of dsDNA (20–200 bp, 20 bp steps) was injected into the trap. Subsequent flushing of the capillary with pure buffer at a single velocity (vs = 6 µm s–1) revealed the filter's thresholding characteristics—lengths ≤80 bp flow through the pore whereas longer strands are trapped. b, An asymmetric flow pattern is generated by the superposition of the upwards flow and the convection. Thermophoresis pushes the long strands into the downwards flow and traps them. Short strands are subjected to the overall upwards flow and leave the pore. The trapping is a function of the feeding flow speed. c, The velocity of the external flow vs tunes the fractionation of nucleic acids. As in the experiment before, a DNA ladder was initially introduced at a low flow velocity, which was then sequentially increased. The released DNA was measured using gel electrophoresis. d, The fraction of trapped DNA obtained from the electrophoresis gel constitutes a selection landscape of this thermal habitat in favour of long oligonucleotides. The velocity-dependent trapped fraction is described by a fluid dynamics model (see Methods). Error bars reflect the signal-to-noise ratio of the gel images (see Supplementary Fig. 11 for details).



Finally "size selection habitats" are shown:



The caption:

Figure 4 | Selection of a replicating DNA population that occupies the thermal habitat. a, Strands are subjected to temperature oscillations by the combination of thermophoresis, convection, feeding flow and diffusion. Simulations of stochastic molecule traces show that strands of 75 bp cycle inside the system for 18 minutes on average. In comparison, 36mers, owing to their enhanced diffusion, show faster temperature cycles, but are flushed out of the system after five minutes. b, Taq DNA polymerase-assisted replication of 80mer dsDNA by convective temperature cycling. Quantitative SYBR Green I fluorescence measurements show an exponential replication with a doubling time of 102 seconds (see Supplementary Movie 4). c, An open pore (see Fig. 1c) was seeded with a binary population of nucleic acids. Quantitative gel electrophoresis revealed sustainable replication for only the long strand. Short strands became diluted and then extinct despite their faster replication. d, Relative concentrations of the two competing species inside the thermal habitat. The selection pressure of the thermal gradient altered the composition of the binary population with time (yellow diamonds) in good agreement with an analytical replication model. The absolute fitness values were 1.03 and 0.87 for long and short strands, respectively. Without the thermal gradient, the short oligonucleotides won over the long strands (blue circles), analogous to the Spiegelman experiment. Error bars reflect the signal-to-noise ratio of the gel images (see Supplementary Fig. 11 for details).


The authors write:

On the hot early Earth, the pore system we describe was probably widespread because of porous, partially metallic volcanic rock, both near the surface and at submarine sites. As metals have a more than 100-fold larger thermal conductivity than water23, metallic inhomogeneities near the pores can focus the thermal gradient from centimetres down to a micrometre-sized cleft (Supplementary Fig. 1). The kinetics of replication and selection were realized in the most simple geometrical setting of a single pore section with dimensions of 0.07 mm× 3.5 mm. Metallic inclusions do allow thermal gradients to be focused up to 100-fold to reach the thermal gradients of realistic geological settings (Supplementary Fig. 1)...


...and in their conclusion state:

...Our experiments reveal how temperature gradients, the most simple out-of-equilibrium setting, can give rise to local environments that stabilize molecular replication against the entropic tendencies of dilution, degradation and negative length selection. A thermal gradient drives replication of oligonucleotides with an inherent directional selection of long over short sequence lengths. Interestingly, when replication and trapping inside the pore reach their steady state, the newly replicated molecules leave the trap with the feeding flow. This ensures an efficient transfer of the genetic polymers to neighbouring pore systems. Heat dissipation across porous rock was probably in close proximity to other non-equilibrium settings of pH, ultraviolet radiation and electrical potential gradients, all of which are able to drive upstream synthesis reactions that produce molecular building blocks. An exciting prospect of the presented experiments is the possible addition of mutation processes to achieve a sustained Darwinian evolution of the molecular population inside the thermal gradients of the early Earth. Accordingly, the onset of molecular evolution could have been facilitated by the natural thermal selection of rare, long nucleic acids in this geologically ubiquitous non-equilibrium environment.


In another paper, not cited here that I encountered this weekend, John D. Sutherland, who has done very exciting work demonstrating a potential path for sugar containing phosphorylated sugars to arise out of simple molecules, used a Churchillian phrase to discuss where we are with explaining the generation of life from prebiotic very simple molecules, saying that the science of the prebiotic generation of life has reached "the end of the beginning."

Fascinating stuff, I think.

I hope you're having a pleasant week thus far.


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Reply Hot Cracks and Addressing Questions in the Origin of Life. (Original post)
NNadir Jun 2018 OP
WheelWalker Jun 2018 #1
Bernardo de La Paz Jun 2018 #2
NNadir Jun 2018 #3

Response to NNadir (Original post)

Mon Jun 25, 2018, 08:22 PM

1. "Fascinating" is the word that came to my mind as well

I would appreciate your continuing to post your interests. Thank you very much.

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Response to WheelWalker (Reply #1)

Mon Jun 25, 2018, 08:38 PM

2. Indeed




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Response to WheelWalker (Reply #1)

Tue Jun 26, 2018, 01:26 PM

3. I plan to do so on this subject. I've seen that a lot of really cool stuff has happened...

...since I last surveyed this field, which was 7 or 8 years ago.

Thanks for your kind words, stay tuned.

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