Making life in a pot

In the last few posts, i wrote about the basics of submarine hydrothermal vents (SHS), here i will be posting about the simulators that we use in the lab to recreate this environment. This is useful as we can use many kinds of basic chemicals to test how they react when directed to massive heat and pressure similar to SHS. Today’s post will be about the most basic of simulator, we call it the autoclave; I will be also describing some of the experiments done in an autoclave system to date.; which literally a boiling pot.

Autoclave at Kensei Kobayashi lab at Yokohama National University, Japan
Autoclave at Kensei Kobayashi lab at previous university, Yokohama National University, Japan

When the hypothesis that life could have started at SHS was proposed; Miller and Bada was one of the first to come with real experimental simulations. They  argued that biomolecules decompose at high temperature and pressure, thus making SHS an unreliable spot for origins. They carried out the experiment at 250°C and 26 Mpa for about 6 hours, and adjusted the pH to neutral of amino acids, leucine, alanine, serine and aspartic acid. The experiment was conducted in an autoclave; a device conventionally used to sterilize equipment and supplies by subjecting them to high pressure and temperature (figure on the left and below, you can’t miss it!!). They showed that aspartic acid and serine decomposed rapidly, and the half life of leucine was about 15-20 min; and alanine appears to be much stable than the rest. Glycine, which was not part of the starting material, was produced during the course of the experiments. From this experiment, They went on to conclude that SHS is not ideal for origin of life, because amino acid being an monomer to proteins will be destroyed at high heat and pressure.

This finding, however received much criticism, some scientists mentioned that the duo did not control the redox conditions in their simulations, and started at a neutral pH; this is very much unlikely in a real situation hence, their results are not very realistic. Kohara and and his buddies showed that if a reducing condition (adding hydrogen) is introduced to an autoclave (similar to a real SHS), amino acid are better conserved up to 300°C. The stability of amino acids was dependent on the fugacity of hydrogen in the system compared to inert conditions shown by Miller and Bada. This is shown in Kohara and co workers’ work, that hydrolyzed samples exhibits higher recovery compared to the non-hydrolyzed ones.

Schemetic diagram of a simple autoclave
Schemetic diagram of a simple autoclave

Moving on, in 1992, RJC Hennet and friends managed to show that by using some basic chemicals found in the ocean (KCN with NH4CL and HCHO together with pyrite, pyrrhotite and magnetite to be precise) at 150°C, could form a variety of amino acids in an autoclave. Similarly, David Marshall also showed how amino acids and amines could be formed using aqueous NH4HCO3 solutions were reacted with gaseous C2H2, H2, and O2 at 200-275°C for 0.2-2 hours. These experiments seems to be supporting that bio-molecules especially amino acids (so far), could be formed in such conditions which could have existed on early earth.

Now on the cons of autoclave. Despite being robust and proven useful, the autoclaves severely lacks a cooling device. Conventionally, once the heating vessel is removed from the furnace of an autoclave, a fan is usually placed to cool it down for a few hours. This is not exactly how a real SHS will function, one could easily imagine that the hot fluids emitted by the vents will be rapidly cooled down by the near freezing water of the ocean. This limitation made researchers to come with a more dynamic system, which i will write about in the next post.

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Lost City hydrothermal field, an unique hydrothermal vent system

In 2000, a completely new kind of vent system was discovered at mid-Atlantic ocean that differ significantly from black-smokers and never seen before chemical enviroment. They are characterized by carbonate chimneys that rise up to 60 meters (picture below). The system, named Lost City hydrothermal field (LCHF) could also be a spot for origins. They are also located a few kilometers away from the spreading

Typical morphology of active chimney at Lost City showing multiple, delicate pinnacles of young carbonate material. (NOAA website)
Typical morphology of active chimney at Lost City showing multiple, delicate pinnacles of young carbonate material. (NOAA website)
Diagrammatic sketch showing geologic and tectonic relationships at Lost City. Hydrothermal structures are located on a faulted down-dropped block of variably altered and deformed crust composed predominantly of serpentinite; taken from Kelley, D. S, Karson, J. A, Früh-Green, G. L, Yoerger, D. R, Shank, T. M, Butterfield, D. (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science, 307(5714), 1428–1434
Diagrammatic sketch showing geologic and tectonic relationships at Lost City. Hydrothermal structures are located on a faulted down-dropped block of variably altered and deformed crust composed predominantly of serpentinite; taken from Kelley, D. S, Karson, J. A, Früh-Green, G. L, Yoerger, D. R, Shank, T. M, Butterfield, D. (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science, 307(5714), 1428–1434

zone. They fluids are heated up a ~ 200°C, but they are not in close contact with the magma chamber like a black-smoker. Instead they are fueled by chemical reactions between mantle rocks and seawater. The rocks contain large amounts of olivine (a Mg-Fe silicate) which reacts with seawater at temperatures ~200°C and forms serpentine minerals (hydrous Mg-silicates) and magnetite. This process, referred to as serpentinization makes the system highly alkaline (pH 9–11). An interesting fact is that, serpentinization have been producing geological H2 for as long as there has been water on the Earth. This new system, has yet to get an experimental focus for origin of life studies, although i do think they are researchers whom are looking in this idea. Do keep an eye on this.

In the next post i will be reviewing some of the hydrothermal vent simulators i have used in the past for origin of life based experiments.

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From Russia with love: another meteorite explosion

A meteorite like object lit up the skies at the wee hours at Murmansk, Russia (check the video footage out). There is a possibility that the object is part of the Lyrid meteor shower which happens annually when it’s nearing its peak. I find this amazing as this is the second time this is happening in Russia (northern hamisphere??). In February 2013, a surprise asteroid about 20 metres and 5,000 kilograms came across the sky over Chelyabinsk, Russia. The blast from its explosion was worth millions of euros worth of damages and injured over 1,000 people. Nobody saw it coming. I am aware that almost every day the Earth gets hit with hundreds of tons of material from space, most of them ranges from the size of a grain of sand to something of an object the size of a sim card. This kind of meteorite strikes (for the second time) kinda scares me a little, its like a sign that every now and then a meteorite or asteroid can hit us and exterminate life as we know it. Gosh, I am thinking about the extincted dinosaurs now, or worst, aliens rising from them.

Basic characteristic of submarine hydrothermal systems (SHS)

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The figure above shows the schematics of a typical submarine hydothermal system (SHS). The magma at the hottest zone is about 1200°C. Seawater from the sea penetrates into the crust of the spreading axis (down flows) and towards the “reaction zone” which is about ~400°C. Seawater-rock interaction happens here, the water is then released through and is cooled down rapidly by cold seawater. A quenching effect takes place here. The abundance of minerals and/or metals are also part of the system. Some of the chemical composition of a typical black- smoker type of SHS is shown here. The diagram above represent what we typically call a black-smoker, A black smoker is a type of hydrothermal vent typically found in the abyssal and hadal zones.

A black smoker from NOAA

Common pictures on SHS are generally black smokers. They appear as black chimney-like structures that emits a cloud of black material containing high levels of sulfur-bearing minerals, or sulfides. Black smokers are formed in fields, hundreds of meters wide when superheated water from below earth’s crust comes through the ocean floor. This water is rich in dissolved minerals from the crust, most notably sulfides. When it comes in contact with cold ocean water, many minerals precipitate, forming a black chimney-like structure around each vent. Effluents from black smokers are acidic (pH 2-3) and are rich with transition metals. All the fluids gives out nutrients to all the unusual organisms at the area. Google it!!!

On the other hand, a diffuse flow is an area where hydrothermal fluids flow out instead of a chimney. The fluids from here are much cooler and slower compared compared to a typical SHS. Minerals are usually left behind in this fluids. White smoke appears to come out of the sea floor, hence the term white-smokers were coined. Unlike the black smokers, the fluids coming out of here lacks minerals which comes from their black counterparts. These two type of smokers are typical in a SHS environment. It is speculated that SHS could have existed throughout earth’s ocean, this subsequently fueled the idea that life could have started here, together with the heat loving bacteria. So far, the experiments of SHS are done with simulators at laboratories mainly in Japan and the U.S only. Research using simulators usually utilizes basic chemicals exposed to heat and pressure similar to the vent system (so far the black smokers). Another area of interest is to see the survivability of common bio-molecules such as amino acids in SHS simulators. This is important as data from these kind of experiment usually presents the thermal and pressure limits of the chemicals used in life’s processes. We know now that amino acids (not all) can survive in SHS simulators, which gives a good account to SHS being a good spot to origins. On the other hand, genetic materials (DNA and RNA) are instantly destroyed when exposed to the simulators. This proves to be a difficult scientific problem to solve so far.

In the next post i will be posting briefly about the LOST CITY type of hydrothermal systems, an entirely unique system and will follow with the various kind of SHS simulators i have used before.

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Hydrothermal vents vs. Miller-Urey experiment

SHS: Submarine Hydrothermal Vents

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MIller-Urey experiment (Click on the image for more details)

Previously, i showed how the link between hydrothermal vents and origin of life is fueled by the discovery of hyperthermophiles. In todays post. i will be showing the limitation of the Miller-Urey model and will discuss a little about how SHS can be a good site for origins (and their limitations too). 

Miller and Urey both designed their experiment assuming that the primitive atmosphere was reducing. This was a valid assumption at that time, and organic compounds are formed better in a reducing conditions. However, this reducing atmosphere scenario has changed, most scientist nowadays would envision a more redox neutral atmosphere. This is because there are no evidences of a reducing atmosphere documented in the rocks[1,2,3]. However, there is a small chance that a reduced atmosphere could happen for a short  period of time in the presence of a meteorites impact or vapors from an erupting volcano[4]. Also it is worth noting, because there is lack of ozone layers during those periods, UV rays could have destroyed the biomolecules in the atmosphere as soon as they are formed. All this leads that the prebiotic atmosphere is limited in the sense of origins; moreover this biomolecules needs to be protected by the UV rays [5]; hence a SHSs’ reducing powers and its UV cloaking ability makes them an ideal spot for origins. The reducing conditions in hydrothermal vents (before the discovery of Lost City Hydrothermal field) is fueled by it reduced minerals which could act as a template for various catalytic activity [6,7,8,9,10] including polymerization.

SHS is also the only place that primitive life forms could have been protected during an event of meteorite shower and/or partial vaporization of the ocean[5]. Although, SHS could well be a spot for origins, critics often cite that residence times in axial hydrothermal environments range from years to decades, ( in other word, the time spent by fluid in the hydrothermal vents is long) while those in lower temperature off-axis diffuse flow systems may be on the order of thousands of years. These residence times are impossible to model experimentally, the effects of long residence times in SHSs are not generally considered in SHS experiments. This is one of the major limitation for experiments on SHS simulation.

1. Lambert, I.B, Donnelly, T.H, Dunlop, J.S.R and Groves, D.I (1978) Stable Isotope Compositions of Early Archaean Sulphate Deposits of Probable Evaporitic and Volcanogenic Origins: Nature, v.276,p.808.

2. Dimroth, E and Kimberley, M.M (1976) Precambrian Atmospheric Oxygen: Evidence in the Sedimentary Distributions of Carbon, Sulfur, Uranium and Iron: Canadian Journal Earth Science, v.13,1976, pp.1161-l185.

3. Zeschke, G (1960) Transportation of Uraninite in the Indus River, Pakistan: Geological Society of South Africa v.63, p.87. 

4. Johnson, A. P, Cleaves, H. J, Dworkin, J. P, Glavin, D. P, Lazcano, A and Bada, J. L. (2008). The Miller volcanic spark discharge experiment. Science, 322(5900), 404–404. 

5. Sleep, N. H, Zahnle, K. J, Kasting, L F and Morowitz, H.J (1989) Annihilation of ecosystems by large asteroid impacts on the early Earth, Nature 342, 139-142. 

6. Wachtershauser, G (1988) Before enzymes and templates: Theory of surface metabolism, Microbiology Review. 52, 452-484.

7. Wachtershauser, G (1988) Pyrite formation, the first energy source for life: A hypothesis, Systematic and Applied Microbiology 10, 207-210.

8. Wachtershauser, G (1990) The case for the chemoautotrophic origin of life in an iron- sulfur world, Origins of Life and Evolution of the Biosphere 20, 173-176

9. Russell, M. J, Hall, A. J and Turner, D (1989) In vitro growth of iron sulphide chimneys: Possible culture chambers for origin-of-life experiments, Terra Nova 1, 238-241 

10. Kadko, D and Butterfield, D.A (1998) The relationship of hydrothermal fluid composition and crustal residence time to the maturity of vent fields on the Juan de Fuca Ridge. Geochimica et Cosmochimica Acta 62:1521– 1533

11. Turekian, K.K, Cochran, J.K (1986) Flow-rates and reaction-rates in the Galapagos Rise spreading center hydrothermal system as inferred from Ra-228/Ra-226 in vesicomyid clam shells. Proceedings of the National Academy of Sciences of the United States of America, 83:6241–6244

12. Johnson, H.P, Pruis, M.J (2003) Fluxes of fluid and heat from the oceanic crustal reservoir. Earth and Planetary Science Letters 216:565–574 

Origin of life and heat loving bacteria

SHS=Submarine hydrothermal system

In the last post, i discussed briefly about SHS, here i will be posting some details on why SHS is suitable for life to start. I will be going one by one to help sell the idea on why SHS is good for origins and will show their shortcoming as well

Some of the accepted hypothesis on hyperthermophilles phylogenetic tree. The positions are based on 16S/18S rRNA phylogenic positions29. The root for trees A and B are placed in the bacterial branch30, hence making LUCA a hyperthermophile. In C, the root is placed under the eukaryotic branch making the hyperthermophile a last common prokaryotic ancestor (LCPA)31. D is unrooted, making the LCPA a mesophile.  Adapted from DeLong, E.F, Wu, K.Y, Prezelin, B.B and Jovine, R.V.M (1994) Abundance of Archaea in Antarctic Marine Picoplankton. Nature 371, 695–697
Some of the accepted hypothesis on hyperthermophilles phylogenetic tree. The positions are based on 16S/18S rRNA phylogenic positions29. The root for trees A and B are placed in the bacterial branch30, hence making LUCA a hyperthermophile. In C, the root is placed under the eukaryotic branch making the hyperthermophile a last common prokaryotic ancestor (LCPA)31. D is unrooted, making the LCPA a mesophile.
Adapted from DeLong, E.F, Wu, K.Y, Prezelin, B.B and Jovine, R.V.M (1994) Abundance of Archaea in Antarctic Marine Picoplankton. Nature 371, 695–697

One of the biggest reason associated with origins and SHS, is related to hyperthermophiles. They are microorganism that strive at extreme heat. These organism cultivated from the vents areas could strive at 110 ℃ of heat, which could flourish at temperature up to 110℃. Several authors1,2,3, have proposed that these microbes could have close relation to LUCA. This hypothesis derives from the construction of archaeal and bacterial phylogenetic trees based on 16S rRNA sequence comparisons4. Hyperthermophiles are clustered at the base of these trees and many of their branches are short, suggesting that they have conserved ancestral phenotypic characters3. However, there are also contradicting studies, which indicate that these microbes posses  “missing” enzymes, that uses other energy co-factors, instead of conventional ATP molecule. In other words, this finding shows that these enzymes have adapted to function at high temperature thus indicating that these microbes are more recent than suggested5.

A limitation to this finding is that it assumes that ATP have existed long in time; this argument can be refuted if one also imagine that ATP is also a recent and high adapted energy co-factor in life. This hyperthermophiles, was the first hint which made SHS suitable for origins; however the theory is not limited to this reasons only.

  1. Baross, J.A, and Hoffman, S.E (1985) Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life. Origins of Life and biosphere 15, 327–345.
  2. Pace, N.R (1991) Origin of life–Facing up to the physical setting. Cell 65, 531–533.
  3. Forterre, P (1996) A hot topic: the origin of hyperthermophiles. Cell, 85(6), 789–792.
  4. Stetter, K.O (1994) In Early Life on Earth, S. Bengston, ed. (New York: Columbia University Press), pp. 143–151
  5. Siebers, B and Hensel, R (1993) Glucose catabolism of the hyperthermophilic archaeum Thermoproteus tenax Microbiology Letters. 111, 1–8.
  6. Forterre, P, Confalonieri, F, Charbonnier, F and Duguet, M (1995) Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive. Origins of Life and biosphere. 25, 235–249.

Submarine Hydrothermal system (SHS) and the link to origin of life

http://www.whoi.edu/cms/images/lstokey/2005/1/v41n2-tivey1en_5063.jpg

Plate tectonic is the theory which unified on how the earth worked. The theory has always been there (since 1879)1,2 and was only accepted in the 1950‘s. The theory also predicted the existence of hydrothermal vents; a deep-sea hot springs is formed when cold seawater seeps into magma-emitting cracks on the oceanic surface, heats up, and rises. Although scientists had been actively searching for vents since the early 1960s, it wasn’t until the 1977; when the Galápagos Hydrothermal Expedition led by Richard Von Herzen and Robert Ballard of the Woods Hole Oceanographic Institution, that confirmed their existence using the famous submersible, Alvin ,3,4.

The relationship between SHS and origin of life on the other hand, first came out through Jack Corliss, John Baross and Sarah Hoffman5. They claimed that the conditions surrounding the vent area provided all the conditions for life’s creation on earth. Over time this idea has sprouted and have been elaborated with many in-situ integration with simulation data. I will elaborate more on this in the next post.

  1. Darwin, G.H (1879) On the procession of viscous spheroid, and on the remote History of the Earth.Philosophical Transactions of the Royal Society of London Vol. 170, 447-538
  2. McKenzie, D. P (1969) Speculations on the consequences and causes of plate motions. Geophysical Journal International, 18(1), 1–32.
  3. Corliss, J. B. J, Baross, J.A and Hoffman, S.E (1981) An hypothesis concerning the relationship between submarine hot springs and the origin of life on Earth.  Oceanologica Acta 4, 59-69.
  4. Corliss, J.B, Lyle, M, Dymond. J and Crane, K (1978) The chemistry of hydrothermal mounds near the Galapagos Rift. Earth and Planetary Science Letters, Volume 40, Issue 1,12–24.
  5. Corliss, J.B, Baross, J.A. and Hoffman, S.E (1981) An hypothesis concerning the relationship between submarine hot springs and the origin of life on Earth, Oceanologica Acta 4, 59–69