Category: Start Here

Kensei Kobayashi’s flow-reactor, the SCWFR, part 2

Posted on by Kuhan Chandru
The SCWFR at Kensei Kobayashi's lab at Yokohama National University
The SCWFR at Kensei Kobayashi’s lab at Yokohama National University

Kensei Kobayashi’s group with the help of Takeo Kanaeko (a brilliant man) came up with another design where they named it Super Critical Water Flow Reactor (SCWFR) utilizing an infrared (IR) gold image furnace (Figure above). This enables the fluid in this system to heat up to 400 °C (or any desired temperature) within seconds (without pre-heating). This one specification is important as most autoclave and other flow reactors utilized an electrical heater which takes time to heat up to the desired temperature. This is undesirable as this “pre-heating” is also making the initial chemicals to react (or altered) to lower and rising temperature, which is not very realistic to a real vent. In other case, this is one of the slightly more realistic simulators i have worked to date.

Kobayashi’s ex-student, Nazrul Islam performed the survivability experiment using several amino acids (aspartic acid, threonine, serine, sarcosine, glutamic acid, α-aminobutyric acid, β- alanine, γ-aminobutyric acid, 5-aminovaleric acid and 6- aminohexanoic acid), 10 mM each) by heating them up at four different temperatures (250, 300, 350 and 400°C ) at 25 MPa for 2 min (that’s pretty fast). They showed that amino acids tend to show better recovery when it is hydrolyzed, suggesting some kind of aggregation and/or condensation is happening within the system. Additionally they also showed oligomerization of glycine (100mM) with the same temperature. At 400°C, no oligomerization was found. However, at 200-350°C, diketopiperazine, diglycine, triglycine and tetraglycine were formed. It was suggested that the glycine reactions in a supercritical fluid (300°C to 400°C) are quite different from those in the liquid phase (at 200–350°C). There were many other peaks of unknown compounds in all of the chromatograms of the unhydrolyzed products. Most of those peaks disappeared after acid hydrolysis. This particular findings however remains a mystery.

Another of Kensei’s sudent, Hironari Kurihara, used the SCWFR to test the stability of complex compounds produced from simulated primitive atmosphere (similar to Miller and Urey’s work). He then tested these compounds to assess the stability of some known amino acids. The complex-combined amino acids (from the primitive atmosphere simulation) preserved more amino acids (including amino acid precursors that give amino acids after acid hydrolysis) than free amino acids after heating in simulated SHS environments. In other words, these complex chemicals which could come from atmosphere (or space) could be better preserved if they are come into contact with the hot hydrothermal system which could have existed during the prebiotic-earth setting. This also hints that “clean or perfect” chemicals like amino acids used in many kinds of experiments are not necessarily showing the right picture when comes to chemical evolution on early earth. More on this in the future.

Many critics of hydrothermal vent simulators often argues that, simulators mentioned on this post and previous ones have a rather short flow-rate and short flow-length (showing low residence time, meaning how long the sample stays in the system). Critics usually cite studies that refer to residence time of fluids in axial hydrothermal environments range from years to decades, while those in lower temperature off-axis diffuse flow systems may be on the order of thousands of years. The problem with these studies about residential axial time of fluids is that, they’re are based on models and calculation only, no work has been done so far in regards to real time sampling or measuring the length of vent system (although, there are work in measuring the velocity of fluid emitting from a vent which looks promising for future measuring). Despite this limitation, i believe the future of simulators will be done using computer simulators, where experimental data from physical simulators (like the ones mentioned in this blog) could be used as parameters. The biggest advantage in this, is that, we do experiments on a larger scale which is could make the origin of life more complicated, interesting and not so straightforward, which I believe is a good problem to have in the future.

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Making life in a pot

Posted on by Kuhan Chandru

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

Posted on by Kuhan Chandru

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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Basic characteristic of submarine hydrothermal systems (SHS)

Posted on by Kuhan Chandru

Image

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

Posted on by Kuhan Chandru

SHS: Submarine Hydrothermal Vents

Image
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

Posted on by Kuhan Chandru

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.

Geological time scale part 2

Posted on by Kuhan Chandru

Before starting the second part, i  would like to apologize for the delay. I was not super busy or anything, just being plain lazy without any excuses.

Moving on, When did life actually started? No one can actually tell. However scientists believe that life could have started or originated on multiple occasion and scenarios, only to be denied by major impacts. Despite this, it is speculated that life must have started around 3.8 billion years ago, when the LHB seized.

As mentioned in the previous post, the Archean period indicates, that earth has more water and minerals to make life plausible but, before that the atmosphere and the ocean has to form and cool off from HLB impacts. Only after this events, life could kick-start. Prebiotic chemistry happened during this time where the formation of lipids and peptides aggregates were formed. The idea of a “prebiotic soup” also must have happened here too. Many models were designed to imitate this period as well.

The protocell or LUCA (last universal common ancestor); could have emerged right after the prebiotic chemistry has taken place with metabolic diversification (which is about 3.8 -2.5 billion years ago). However, these are all scientific hypothesis, there are no fossilized records what so ever. Overall the origin of life idea is based on several hypothesis to build the prebiotic world and it’s chemistry. This grey area is where many chemical astrobiologist (like me) are focusing on. The idea however, is heavily supported by present knowledge of chemistry and geology with the power of models.

The earliest Stromatolites which is considered as the earliest micro fossils we have, is hypothesized (with heavy dispute) to have occurred right after this . The cyanobacteria rose with the power of photosynthesis giving an influx of oxygen to earth’s atmosphere, the very reason we have oxygen now. However, it should be noted that oxygen is toxic, meaning that other life forms utilizing non- oxygen metabolism during that time, must have went extinct without evidence. The Proterozoic eon starts here. The Cambrian explosion also starts here with the increasing of oxygen, leading to life forms which were well fossilized such as Opabinia and Marrella. Watch the video above to see how these creatures look like.

There are plenty of scientific evidence here. I will not be elaborating further on what happened after this. Many studies have been done, it is an establish science. We pretty much know what happened after the Cambrian explosion, but not what happened before that.

That’s all for now. The next post is about the possible sites of life’s origin.

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Geological time scale (part 1)

Posted on by Kuhan Chandru

I first knew about the geological time scale during my college years, back then the only geological time i knew was “Jurassic” due to a certain Hollywood movie. Learning it was fun but memorizing it for exams was horrible. The lecturers will first show the scale like the one here (very very boring btw), and they will explain one by one what happened with pictures of dinosaurs, plants, ancient humans and etc. It was remarkable, but how did geologists came to this scale always puzzled me, it still does, as we have loopholes in it too. The scale is basically a convention agreed by geologists based on research which were agreeable from time to time.

Here i will briefly explain some key events and how they got there. Most importantly i will put emphasis on how and when life started, the rest is evolution which you can read/view elsewhere. I will be also breaking this topic to a few parts for easy understanding.

Lets start,

After the big bang, the HADEAN period named after Hades begin. The sun was already formed and the rise of giant planets (Jupiter and Saturn) could have happened during this time. This is based on “numerical models“. After the formation of Mars, earth was finally formed in it’s hottest state (hot as hell). It is also postulated that the moon was also formed right after this, and her origins came from earth. Check out the video below on how this could have happened

From here on, our primitive atmosphere begin to arise, which is absolutely hypothetical in case you were wondering. After this particular sequence of events, the building of the habitable earth begins. The first proto ocean were already in play after the cool down effects on earth . There are some speculation that life could have started here; but right after this, the late heavy bombardment (LHB) of comets and meteorite came showering on earth, the planet was destroyed, water evaporated completely and it was a mess. This phenomena is also observable on the moon .If you have wondered why the moon has craters, its because of LHB (despite not having tectonic plates etc).

Now, The ARCHEAN period begins, which is generally the post HLB. Earth during this time has a lot of minerals and more water because of the LHB. In other words, she has received more materials to allow life to flower.

The rest of story is to be continued in the near future, stay tuned

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What makes life work

Posted on by Kuhan Chandru

Life as we know it displays a high degree of organization. All living things look different only on the outside but inside, all of them have the same molecules and systems. The fundamental chemicals of life consist of fats (lipid), proteins (amino acid), DNA/RNA (sugar) and water. This is universal. Basically, Lipid plays a role of the membrane, protein as the building blocks and DNA/RNA as the genetic materials. Amino acids are the monomers of proteins. Interestingly life only utilizes 20 amino acid to form proteins (we call them proteinous amino acids). When amino acid joins each other they become a poly-peptide by forming a peptide bond. Proteins are a combination of large polypeptide. Now when it comes to genetic materials, we have our DNA and RNA which are made up by nucleic acids. Both of them consist of a ribose sugar, a phosphate group and bases. The bases are important since it is used in transcription and translation. Both these processes are fundamental in the building of life. I suggest you take a look at the video below. Every hormones and enzymes which came into existence in your body are through this way. its mechanism is simply amazing (and this happens from the simplest of cells to the biggest whale in the world!!).

When you put all the ingredients together you get life. NO. all this molecules will simply flow aimlessly unless you put them in a cell. This increases the concentration and separates the molecules from the outside world. But then again this is still an impossible feat in synthetic biology. However this does not stop scientist from trying to get this to work. The video below is simply an example on how to make “life” from raw materials and make them “function”.

Generally, origin of life studies are categorized in either being a ‘bottom-up’ strategy or a ‘top-down’ strategy. A bottom up strategy involves using basic chemical mentioned above and putting them to certain feasible environmental stress and see what they do (like the video above). On the other hand the top-down methods, looks at modern biology and uses information from there to extrapolate towards the simplest living entities. Hopefully by using both approaches we can find a mutual meeting point.  But this is going to take time, lots of time.

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Origin of life – a brief history

Posted on by Kuhan Chandru

The study of astrobiology involves 3 things, finding the origin of life, finding aliens and also the future of life. The latter is fully theoretical and often described as the one for the future. When it comes to finding aliens (FA), we are looking for more simpler life forms (bacteria etc), the complex ones are mostly being investigated by the UFO junkies. I will touch on FA in the future. My focus today will be on origin of life (OL).

Viewpoints from all over the world has shaped the philosophy and early sciences in regards to the OL. In 1778, Buffon, a french naturalist was one of the first to postulate the origin of life theory, he claimed that during the early stages, with colder temperature (probably referring to the ice age), organic molecules could produce spontaneous generations, thus producing each species as we know them now. 80 years on, Charles Darwin wrote a letter to Joseph Hooker, a botanist describing a primordial condition on earth:

 It is often said that all the conditions for the first production of a living organism are now present, which could have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sort of ammonia and phosphoric salts,—light, heat, electricity, present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.

Darwin was referring to the OL. He did not define or even hinted about how the origin of life might have been in his famous book. Since his work in “origin of species” involved the history of life, he must have thought that there must have been a starting point. However, OL questions were considered buried once Louis Pasteur concluded that life came from preexisting life-forms. He stood by his words that there is a difference between non-life and life, hence life would not have occurred by inert molecules. In 1917, a young Russian, Aleksandr Oparin begin thinking; How did life first started. He wrote his thoughts in his book The origin of life; published in 1924. During the same time JBS Haldane, a British born geneticist independently publish an essay indicating the similar ideas to those of Oparin’s. Hence, the Oparin-Haldane hypothesis was introduced. Oparin suggested that organic chemicals could have went through a series of reactions which would then lead to more complex aggregates. The aggregates then form a colloidal mixture in watery environment. He calls them ‘coacervates’. Coacervates would be able to perform simple metabolic functions and with evolution become the first life form. Haldane posed a similar idea where the primordial sea would serve as a chemical reservoir powered by the sun. He also added that the group of chemicals was enclosed in a lipid membrane system, thus developing to become the first living cells. He coined the term ‘prebiotic soup’, and this became the expression of the Oparin-Haldane view of the origin of life.

In the early 1950s, Harold Urey, already a nobel price winner for his discovery of heavy water simulated a chemical model of primitive atmosphere. This was done with his then graduate student, Stanley Miller. They put up a mixture of simple gas to an electrical discharge, any products from this will accumulate in the flask below the apparatus. They left the experiment to run for a week. The products of the experiment contained organic chemicals including several amino acid (monomer of proteins). This results were indeed ground breaking and became an instant sensation among fellow scientist. The detection of amino acid shows that natural laws allows them to be synthesized under prebiotic condition. Till date many modified version of this Miller-Urey experiment has been conducted which further enhance our knowledge of creating amino acids from simple gas or molecules. Miller-Urey experiment started the bandwagon, on what kind of life’s chemicals can be created prebioticaly. John Oro showed that the highly reactive hydrogen cyanide under alkaline conditions will polymerize to become adenine, a nucleobase essential to DNA. Lastly in 1978, Dave Deamer and co-workers managed to produce vesicle from fatty acids under certain prebiotic condition. The vesicle here mimics a simple membraneous vesicles. He then used fatty acid extracted from Murchison meteorite (carbonaceous chondrites) to produce vesicle with prebiotic conditions. This indicates that fatty acid formed in space had/has the capacity to form vesicles which can encapsulate DNA or proteins to possibly form the Proto-cell.

The discoveries mentioned above are landmark discoveries which gave scientist the hope that we can get closer to the origin. The experiments (and many more) indicates that under prebiotic condition we can produce life’s chemicals. When it was discovered that Europa could have an ocean below its ice crust; and Mars used to have seas, scientist became excited because if Primitive Earth can yield life’s chemicals towards living beings, then the same could have/had happened in Mars and Europa respectively.

What i have mentioned above is simply a brief history of OL, many experiments have been conducted ever since. Its worth to mention that there are many limitation and unsolved riddles when comes to this study. For example, although we can produce amino acid prebioticaly, there isn’t a prebiotic way where we can polymerize the amino acids to proteins. Also on close examination, life is very selective; only left handed amino acids are utilized to perform life’s activities. But in prebiotic experiments (e.g Miller-Urey), a racemic mixture is always produced, in other words 50% right handed and 50% left handed amino acids. There are many hypothesis that can explain on why these phenomena known as homochirality happens, but there are no explanations on HOW this must have happened 3.5 billion years ago. If we look further into the formation of genetic materials, it is known that DNA denature under prebiotic temperatures (200 C to 400 C). So how did the DNA molecules formed when the earth was hot as hell?. This is only the the tip of the iceberg. Till then this is the story we have.

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