Sunday, July 15, 2007

Origin Of Life Aquarium #2

For some background on my work, I own a scientifically valuable dinosaur tracksite in Holyoke.

I also write simple experiments that demonstrate the "self-assembly" of life as a way to counter misinformation being spread over the internet and to improve the way science is being taught in schools and to the public. This is now my most popular experiment:

What I'm now attempting to do is advance the following simple experiment that modeled the Earth's ocean where Jello was used as a source of proteins and an airstone for water motion to show what the beaches of the ocean may have at one time looked like.;f=3;t=001054#000000

The next version of the OOL aquarium will be a sealed environment inside of a 10 or better yet 70 gallon aquarium where amino acids should form then polymerize to become proteins. Possibly forming protocells.

A comprehensive model should contain the following:

(1) Atmosphere that is as close an approximation as possible to what is currently hypothesized to have existed.

(2) Weather System that precipitates fresh water into lakes and streams that will flow into an increasing saline ocean from erosion of basalt that was baked in a kiln (to return carbonates to monoxides). In addition to Clouds it should include Vog and Laze. Vog is a cloud system made up of sulfate aerosols. Laze is a highly acidic HCl (hydrochloric acid) steam that is produced when molten lava reacts with sea water.

(3) Volcano system to supply trace gases where basalt and other minerals are periodically heated to temperature of molten lava. This would run off a low-voltage high-current transformer. Maximum temperature of 2300F is possible using Kanthal resistance wire. This will be the source of reactants for producing Vog and Laze. Miniature kiln will be located inside the tank, in such a way that it is fail-safe.

(4) Ocean with tides.

(5) Underground water table.

(6) Two land areas on either side of the tank. One a dry desert region and the other wet and rainy.

(7) Expansion bag to maintain atmospheric pressure. Good choice might be a vinyl beach ball or inflatable tube. Mylar balloons might also work but easily rupture.

(8) Ionization. Electrostatic, UV light, or both.

Teachers who are inspired by this can omit certain features they do not need. For example, if they only want to demonstrate cloud formation and circulation then there is no need to seal the environment. A match or candle can be used in place of the volcano to provide nuclei for cloud formation.

It can be used by teachers to demonstrate many scientific principals such as. Global weather patterns and climate. How clouds form. Hydrologic cycle. Evolution of Earth's atmosphere. Chemical emergence (self-assembly) and origin-of-life. Humidity. Dew point. Chemistry of volcanoes. Some geology. Convection currents. Internal combustion and combustion products.

SAFETY NOTE: Including all of the following together has the potential of building up explosive gases including hydrogen cyanide. Do not attempt it without the ability to monitor. I will be using a Mass Spectrometer.


I found that an excellent source of volatile organic compounds and gasses one would expect where organic molecules are being heated to combustion temperature on a still partially molten planet is exhaust from a dirty internal combustion motor. This also helps make the point that what is sealed inside the tank is in fact a toxic atmosphere that would not support life as most understand it. Some will say nothing can survive this. But are they correct?

Unless a better method can be found I expect to use a 4 cycle rotor-tiller motor with old gas to establish the CO2 based organic component of the atmosphere.

Ammonia may need to be added in a separate step. Either already dissolved in water (probably not store-bought since it contains surfactants and clarifier) or directly added as a gas.

The following is a brief but very informative discussion of prebiotic chemistry.

This paper from 1966, CHEMICAL EVENTS ON THE PRIMITIVE EARTH, by Philip H. Abelson, is a classic worth including in our reading list.


Basalt, also called trap rock, provides a wide range of useful compounds. It's quarried locally for use in building roads. Basalt gravel will be used to form the bulk of the material used as land areas.

Hydroxylapatite would provide a supply of phosphorus. The natural occurring mineral is also found in teeth and bones.

Pyrite has interesting properties.


During a storm colliding particles of rain, ice, or snow negatively charge the lower storm clouds as the upper region becomes positively charged. The ground below the cloud becomes positively charged.

This could be simulated with a static generator that has a positive lead into the model ocean, and a negative lead to one or more electrodes that runs above it. Heavy duty graphite spark plug wires could be silicone glued into the opposite corners of tank with thick bead of silicone surrounding it for added insulation. Graphite roving pulled from graphite cloth would make corrosion resistant electrodes.

It has been reported that a graphite electrode is a source of elemental carbon that will react with ammonia water to form amino acids.

Elemental carbon can also be provided in the form of soot either directly to tank where it will tend to float on the surface of water or to graphite roving that forms the upper electrode to provide a small amount of carbon particles to the atmosphere as would have in nature been provided by a volcanic discharge. A supply of soot can be impregnated by teasing the roving apart, coating over a burning candle, reforming back into a single roving by pulling back together.


A metal halide lamp on a timer is placed on one side of the aquarium that heats both the desert region and model ocean. For a 70 gallon tank 400 watts will be used. The other side is left cold, preferably with a box on top where cold outdoor winter air can be pumped through. An old air conditioner can also be used to lower temperature with best results from placing the condenser coil on top of the tank opposite the light. An ice pack is also good for establishing circulation, with or without a light to warm the water.

The land mass directly under the light will be a zone of rising air currents therefore will receive little if any rain. The cold side will be where clouds form and with the downdrafts it will normally be wet and if cold enough it will snow.

I already bench tested the weather system using a 10 gallon tank with warm water and an ice pack on one side using smoke to induce nucleation. It worked very well. Dirt adhering to the inner glass made it easier to see inside after a film of water formed. Condensation on clean glass was a problem, so there should be no need to provide a way of keeping the inner glass clean. I have a line laser to make clouds highly visible for taking pictures to display on the internet.


The ocean should become more saline and at some point precipitate CaCO3 as the CaO of the baked basalt takes up CO2. This is thought to have happened. Due to the volume of basalt gravel being large in comparison to the volume of water processes inside the tank should be on a greatly accelerated time span.

What has yet to be worked out is what else should be included in the gravel mixture to provide sodium and where the chlorine ions now in the ocean came from. There is information on the composition of sea water here:

And one that speculates on the source of sodium and chlorine here:

Since sodium is highly reactive, it may be that it was quickly washed into the ocean. If there is no better explanation then sodium and chlorine can be added in a separate step.


It would be advantageous to start off with a completely sterile tank. It's easy enough to seal the top tight by removing the plastic rim around the tank then silicone glue the cover glass on to it then pressure test for leaks where hoses and wires run through.

The gravel will have been heated to white hot in a kiln and can be thrown directly into the water while still glowing. This will destroy all bacteria that live inside.
The ammonia that is added might destroy more of the bacteria, especially since the contact time is measured in weeks or months.

Since the easiest way to fill the tank with motor exhaust is to have two hoses running to outside air, these two lines could be used for sterilization purposes.

If anaerobic bacteria should survive the environment then it will produce relatively easy to detect oxygen. This is not a bad thing where that is what the model is designed demonstrate. But I would like to start off by demonstrating chemical emergence, look for prebiotic "life". It would therefore be best to include an easy way to destroy all bacteria and spores if the starting atmosphere alone is not enough.


I would also like to form amphiphiles since they are necessary to form cell membranes. Small amounts of clay can be added to the gravel to encourage their formation, and intake of cell forming compounds especially catalytic proteins into vesicles. I'm definitely a believer in the protein-first model and Muslims believe that clay played a role in the origin of life so including naturally occurring minerals and compounds that will test this hypothesis are necessary. Here's a paper on this and please don't mind where it's now being posted due to that probably being my fault considering I sent them a link to it.

Many of my readers are highly religious people from many faiths. Hopefully you don't mind it sometimes being necessary for me to plan what they would like to see science do, into my work.

Auto exhaust will add the hydrocarbons needed to form the amphiphile "tails" while local basalt should contain phosphorous (but cannot find an analysis online). That leaves glycerol, which I'm not sure about:

With there apparently being thousands of reactions that could possibly turn basalt and volcanic gasses into amphiphiles I'm happy to let the experiment run and look for formation by the tell-tale bubbles and cloudiness of the water. But any input on what I would want to include to encourage formation besides the sulfur gasses and other things mentioned would be very helpful.

Update: This link to papers by Robert Hazen was provided by "daividtufte" at the Kansas Citizens For Science forum, where we can also discuss this experiment. Although Dr Hazen's work deals with hydrothermal vent temperatures and pressures unobtainable in this simple aquarium model, it is still important to know about.

Even though the papers describe a promising OOL pathway this does not mean that modeling a hydrothermal vent is necessary for the success of this experiment. These compounds could be directly added. It is also worth mentioning that it might be better to be able to form fatty acid based amphiphiles, as opposed to the types formed in their reactor. Either might work equally well. It is also possible that protein and/or RNA came first with the amphiphiles being catalyzed later. I have to mention this since I used to get excited about every new OOL discovery that came along then felt that I had to include it but in time learned that it's best to stick to the approach that has worked well in the past, namely aquarium experiments that focus on amino acid - protein formation in an ocean environment.

There is also the possibility that the most interesting reactions will take place in the model's atmosphere. This paper "Atmospheric Aerosols as Prebiotic Chemical Reactors by Christopher M. Dobson, G. Barney Ellison, Adrian F. Tuck, Veronica Vaida" is also important to consider.

It would be nice to include vesicle forming amphiphiles, or at least make the model realistic enough that some may form without going to the extreme of modeling a hydrothermal vent which would be dangerous to attempt.


Although I am a strong advocate for the lesser known protein-first model Dr. Gerald Joyce who was key in popularizing the RNA World Model still complemented my home/classroom scale work, so I cannot disregard the RNA-first model out of respect for his work, and the good science that backs it up:

Cellular structures such as the vital to life as we know it ribosomes are a protein/RNA complex. It is therefore possible that both models are equally important to the origin of life.

In this experiment I will look for the formation of protein/RNA complexes. I feel that the protein skimming from the bubbler will concentrate these on the model beaches inside the OOL aquarium as easily as it did pure protein. The only problem I will have here is not having the setup to detect small amounts of RNA and ribose but since it will take time before a sample might be ready for analysis, I'll only mention that I might later need to check for it if proteins that should be observable from outside the tank appear to be concentrating. Once the tank is unsealed the contents will become bacteria food and require fast work to prevent its loss. This is another reason why I feel it is important to try to achieve 100% sterility inside the aquarium.


To periodically monitor the gasses I have a HP5988A research grade Mass Spectrometer and spare parts including sources, filaments, detectors and electronics. Here is a picture of the setup. And must mention that the stainless steel vacuum chamber is so shiny it reflected the light in such a way it looks all burned up, but it's not.

I tested it to make sure she's ready to go, worked fine. The O2 and CO2 peaks of air were easy to get a reading on. The original data system with NIST library had to be scrapped. I wrote a custom control system that interfaces to a PC and have been downloading the spectra I need from the NIST website. I also have their demo library program that seems to work well, automatically identifies common compounds from files the program I wrote creates.

Although not at this time connected, I own a Varian 3700 Gas Chromatograph (shown in above photo) running helium originally designed for 1/4 inch columns that can be adapted to use a .25 mm capillary. I have about 20 meters of used J&W Scientific #1225631 DB-5.625.

Since there is a chance that the capillary is contaminated and adapting to a capillary type is time consuming while buying a retrofit more than I can afford, it might be best to use a 1/4 inch packed column. The larger volume works well for gasses, allows for a much larger sample, resulting in higher sensitivity. There is a discussion of both types in this free online book:

Even though packed columns are not very common anymore, they are still available. I also have 400 grams of Chromosorb P (Non-Acid Washed) mesh size 30/60 to pack my own but that would of course increase the complexity of this experiment due to it having to be coated. On the other hand it would be inexpensive and allow repacking if necessary. It would of course be best to buy what I need but unfortunately I'm on too very low a budget, local colleges and universities cannot offer any help, so all of this is out of pocket and I'm already in danger of losing the house and tracksite.


Having some experience in what to look for that was gained from the previous experiments, this higher level experiment could lead to an exciting new discovery. Possibly even the isolation of a once abundant very simple protein/RNA based organism that would no longer stand a chance against the highly evolved DNA based organisms that now exist.

Keeping it simple by using motor exhaust as the source of a complex mixture of organics might at first sound silly but has many advantages over the studying of one reaction at a time, while making it possible for others to try their luck even if what forms inside my tank is nothing to get excited about. The relative ease of this experiment will hopefully inspire the science minded who never thought that scientific discovery was something they could participate in.

If you have an idea that could be included or would be able to offer advice then please email me at