These molecules would continuously progress through these gradients continuously growing and changing. Growing cause at every different pH level there would be a different type of amino acid activated. Which would naturally react and combine with each other. This action of growing would also cause these molecules to change and acquire new shapes which would cause them to have new functions. This growth and changing of amino acid chains (polypeptides) would be occurring to trillions upon trillions of different polypeptides in the millions of square miles of ocean all around the world! Then multiply those millions of square miles by the trillions of molecular layers of depth into the oceans of the entire world! This is a three dimensional universe after all. These trillions upon trillions of molecules set the stage for the origin of Life in the ocean. 

Since the year of my birth 1970 the scientific community has been aware of carbonaceous meteorites carrying amino acids from space. Since then they have detected over 500 different types of amino acids, as well as plenty of water, in these meteors. It is commonly accepted that all the oceans water was delivered here during the Late Heavy Bombardment. Drop by drop the water was deposited here by billions upon billions of collisions of these water laden meteorites, asteroids, and comets who by default also carried over 500 different types of amino acids. Therefore those oceans back then must have been full of amino acids as well!

The main workhorse of Life’s chemistry, the main type of molecular workhorse, are the amino acids. All the catalytic functions, the starting material for all bio-molecules, and the stopping point for the digestion of proteins are the amino acids. Almost every important chemical reaction performed by life begins on and is carried out by amino acids. Amino acids form the proteins that are the catalyst who in turn, most of the time, work on transforming an amino acid. Which amino acid it transforms into which precursor molecule depends on the final bio-molecule that life is trying to create, i.e. RNA, DNA, etc.

Even when we take into consideration the one molecule most important to ALL Life ribonucleic acid (RNA), its creation begins with the transformation of an amino acid! Life cannot translate the DNA code into proteins without RNA. RNA is the template that ribosomes, which are also composed of amino acids in its proteins and RNA, need to make proteins. The RNA in the ribosomes is the main catalytic component of the ribosome. Which it  uses to cleave the amino acid from the transfer RNA and it also fuses the amino acid to the growing protein. All these functions that RNA carries out make it the most central and  fundamental bio-molecule necessary for life.

The way E. coli creates RNA is an important example of the viability of Emergent Chemical Evolution. First of all the protein used by E. coli to initiate the production of RNA is not one whole protein. The E. coli produces 12 polypeptides that unite and form a larger structure to start the production of RNA. When they unite they do so by encapsulating a specific amino acid. Which they then transform into another molecule that is the precursor to an RNA base. Once the molecule is transformed they disassociate and wait for another amino acid to fall into their trap. 

Then the precursor molecule is taken by another enzyme and is further altered to make an RNA base. The point is that the making of RNA is a multistage process, and being that one of the most simplest and most ancient bacteria does it this way, it looks like it has been done that way from the start.

Now why, after billions of years, has not the E. coli evolved a more efficient means of producing RNA. That does not involve so many pieces or steps.  A system with less components to do the same job. Just like I said before, once it has solved a problem life likes to continue using that same method and rarely changes to using another mechanism. Through evolution life makes that method either better or worse over time which leads to determining the survival or extinction of that species. This is clearly the case because 99.999% of all species since the beginning of life are now extinct! 

The reason for that poor survival rate for all species is due to the fact that if the environment that species lives in changes, evolution can't change its genes fast enough for that species to adapt. Then if that species does not find an equivalent environment then that species dies out.  That is another reason why E. coli is such an instructive and clear example for the validity of ECE because this species has managed to find itself consistently in an environment that is conducive to its survival i.e. the gut of animals. Despite surviving this way for at least half a billion years it has not changed or picked up (from its hosts) a better way to make RNA bases!

The more important question to ask at this point is not why it has not evolved a more sophisticated way of making RNA but how did its mechanism of making RNA evolve in the first place? Twelve smaller polypeptides uniting to initiate RNA. The most plausible explanation for this occurring is that Emergent Chemical Evolution is correct.

The genetic information to create these small polypeptides are located at different locations of the E. coli’s chromosome. Suggesting that the information was incorporated into its genome at different times during its evolution! Now how was that possible without the E. coli ancestors becoming extinct for not having the ability to make RNA? The most plausible solution is that the other smaller polypeptides were available in the environment before they became incorporated into the E. coli’s genome. Only a system like my theorized Chaos Engine could have produced enough polypeptides of the right type to make up for the lack of them during the time the E. coli ancestors did not have them in their genome. This is also the case for other simpler life forms that have the same mechanism for the production of RNA bases.

Again with the environment being the way it was with a carbon dioxide laden atmosphere creating gradients in the ocean. Gravity was creating currents in the oceans that would grab the ocean's constituents and then pass them through the gradients. The heavy bombardment was responsible for the replenishing of our Earth with volatile compounds that were lost when the earth congealed and became a big molten ball of fire. When that happened all the volatile elements and compounds evaporated into space.

The volatile material were the lite gasses, water, and most, if not all, of the atmosphere were lost into space and collected and froze in the outer edges of the solar system. Attaching themselves to asteroids and comets. Then later when Jupiter formed and became bigger it knocked the majority of those asteroids off their orbits and sent them on a collision course with Earth. So for the next 200 million years asteroids and comets rained down upon the surface of the earth delivering- drop by drop and milligram by milligram- water, carbon dioxide, amino acids, and other volatile compounds.

This is not my speculation of how the volatile elements of Earth reappeared. This is one of the main Theories of modern astronomy. The evidence is very clear from the studies of meteorites that they contained that material and in the geologic record that there was a heavy bombardment for that amount of time. The murchison meteorite is the most famous of the chondrite meteors that was analyzed and was found to contain 70 different amino acids. As well as other carbon based compounds.

Imagine the number of impacts that would have had to occur by drop by drop as the oceans were brought to the Earth. The geological evidence points to the oceans being miles deep by the end of the heavy bombardment. With that amount of impacts it is inconceivable that the oceans were not saturated, chock full of amino acids. Which are by their nature soluble in water and would have been easily stored by the oceans. Someone once commented on one of my YouTube videos that one particular amino acid was not soluble in water. Now that amino acid is the least soluble amino acid of all the amino acids used by life, but it is still soluble. Now you may not get every amino acid to dissolve in water but 11 grams of the amino acid does dissolve in 1 liter. Albeit this is not one mole of the amino acid it still represents billions if not trillions of molecules of the amino acid. That is still plenty of that one amino acid being present in the oceans to react with other amino acids.

The mole of a substance is the number of molecules of said substance that will give you the weight in grams that equals the molecular weight of the substance. The number of molecules is 6.022 x 1023 which is called Avogadro’s number named after the Italian Scientist Amedeo Avogadro who discovered the relationship. Although 11 grams is significantly smaller than the molar weight of the amino acid it still represents a very large number of molecules being present in the water. We must remember that nature operates at the molecular level. We operate at the macro level where we need massive amounts of a substance to get it to react so we can see something happening. Whereas nature can take a molecule of a substance and can work with that one molecule and make something happen.

So we cannot limit the possibilities of how nature can do something based on our limited abilities. Nature does not need to get usable yields in order to get something to work. If it has one molecule it can make something happen with just that one molecule. Unlike us we need to get large quantities of something so we can use our macro appendages to be able to manipulate them. We do not have molecular tweezers; so compared to nature we are all thumbs!

Now at the origin of life, nature would have had plenty of molecules of amino acids of extraterrestrial origin in the water to get things started. With enough molecules of the more than 500 different types of amino acids that would have been delivered by the heavy bombardment, nature had all the components necessary to initiate the Chaos Engine. Those components are: gravity powered oceanic currents, carbon dioxide induced pH gradient in the ocean, and the extraterrestrial amino acids carried by the ocean currents.

To this point no extraordinary or exotic events have been used. All events described here, except one, are currently accepted tenets of astronomy and geology. The one event described here that is an assertion of the author is based on the author’s observations of the modern effects of increased carbon dioxide in today's atmosphere. The monumental effect of coral reef bleaching by just a minuscule increase of carbon dioxide in the atmosphere confirms that the author's assertions are correct. Demonstrating that the effect of atmospheric carbon dioxide is strongest near the surface of the oceans.

From these events that spontaneously formed from the physical environment of the prebiotic Earth emerges The Chaos Engine. What emerged is a mechanism, which the author calls The Chaos Engine, that was the key mechanism to not only create the proteins from the amino acids but also to power the origin of Life. The cycling of the proteins and the oceans constituents by the currents through the pH gradient continued continuously second after second day in and day out for literally billions of years! Once those cycles started there was nothing going to be able to stop them.

What is important to remember here is that amino acids are cations. They are ions that have  two charges on their molecules. A positive one on one side and a negative one on the opposite side. This property of amino acids is the reason they are able to bond to each other and make long chains called proteins. The negative side of an amino acid is attracted to the positive side of another amino acid and they bond to each other releasing a water molecule and forming a peptide bond. That peptide bond is a very strong bond where even if it folds upon itself and another peptide bond comes close together they will not react, keeping their integrity. Unlike other chemicals that would continuously react with other bonds that come near them. This property of amino acids is what makes them so useful to life and as is shown in this book to its initiation!

The important thing about the twenty amino acids that are used by life, and what a lot of origin of life researchers consider a hindrance, is that the activation of certain amino acids are very, very different. There are certain amino acids that are only activated at the pH of 3 or 4 and the same amino acid’s other side would require a much different pH of a more basic 8 or 9. So those researchers were like how is that going to be accomplished if these compounds were going to be found in water. Then again they never looked at how that water was going to be affected by the atmosphere and the carbon dioxide creating pH gradients.

Well if we look at one of the most popular origin of life hypothesis today is that compounds would have found themselves in small puddles and gone through drying and wetting cycles. What happens when it drys and no water comes back? Or it drys and gets buried by other material and it does not come back? First of all the period of wet dry cycles would have been very short. Most of the evidence points to the Earth being almost immediately covered in miles of water.Well if we look at one of the most popular origin of life hypothesis today is that compounds would have found themselves in small puddles and gone through drying and wetting cycles. What happens when it drys and no water comes back? Or it drys and gets buried by other material and it does not come back? First of all the period of wet dry cycles would have been very short. Most of the evidence points to the Earth being almost immediately covered in miles of water.

The Earth was in that state for a large portion of the first 2 billion years before life completely changed the chemistry of the atmosphere by introducing oxygen. Which completely changed the entire surface of the Earth. Starting with the oceans because before that point all the oxygen produced by life was absorbed by the oceans and reacted with the dissolved iron contained in it. Which the iron dissolved in the oceans is going to play an important part in the origin of life later.

Getting back to the drying and wetting cycles as a means of creating RNA molecules. There would have been a very short time for those RNA molecules to form with the correct sequence of bases. There would also have to have  been quite a number of them with the correct bases to have the right catalytic ability in order to replicate themselves. If they did not before the oceans formed that would have been the end and no other shot at life would have been possible. This scenario also creates another problem: after water covers the Earth’s entire surface, how are the other nucleic bases going to be formed in order for these RNA molecules to replicate? The purpose for the wet and dry cycles was for the prebiotic inorganic chemicals to have a means of reacting without a catalyst to form RNA.

This scenario, once the oceans are formed, would also give these RNA molecules the additional duty of producing their own nucleic acids in order for them to replicate. Though this scenario would make it easier for RNA to form from inorganic chemicals before the coming of the oceans. It does nothing to answer how the nucleic acid bases would appear once the oceans are formed. A whole new mechanism would have to spontaneously appear in order to do what the wet and dry cycles were supposed to make easy.

Also depending on the temperature of the surface and the prevailing winds, I do not know how the integrity of the molecules would have been preserved until they were covered with water again using that scenario. For these reasons and many more I find the hypothesis of the dry and wet cycles untenable. We are back at square one in my opinion once the oceans are formed.

So getting back to my Chaos Engine and how it will solve all the problems the drying and wetting cycles hypothesis had and how it will also address the amino acid conundrum the origin of life researchers have. These researchers could not see how these different pH levels could be achieved and if they were could only see a jumbled mess being formed by the amino acid chains.

So the activation of one amino acid which each side would have to be activated at a different pH level in order for it to bond to another amino acid is solved by the pH gradients in the oceans. That same amino acid could be taken closer to the surface, where it is more acidic, and one of its sides would be activated. Then at that point whatever susceptible amino acid was nearby, whose complementary side would have been activated at that pH, would cause them to bond. The case would always be that at whatever pH level there were the amino acids that would be activated there would interact. As the amino acids kept being passed through the different pH levels by the current the amino acids would form longer and longer chains(polypeptides). This cycling of the amino acids would be happening all of the time to trillions upon trillions of amino acid chains(polypeptides) at every cubic millimeter of the 196.9 million square miles that is the entire surface of the ocean covered Earth! The ocean would continue to churn and cycle all those polypeptides through those pH gradients continuously making longer and longer polypeptides.

Again looking at modern cells, what controls the specific metabolic reactions of the cell? They are coordinated by the pH of the surrounding cytoplasm, the medium of the cell or specific organelle which has similar composition as the oceans, would hold strings of amino acids(polypeptides) but functioning as enzymes would only react at a specific pH with its substrates. How would you mimic or control that before life began? Again the gradient created by the ocean would be a great substitute for that process to occur naturally in the prebiotic oceans.

Whereas certain reactions would occur only at certain pH due to the different amino acids sequence of the individual polypeptides. One polypeptide could have a sequence that would take a conformation that makes it rigid and become active only at one specific pH and no other. Another polypeptide would in contrast have a sequence of amino acids that would only allow it to take a conformation and become rigid in order to react in a completely different pH level. This type of control is the only way modern cells can function. Although the membrane of the cell separates the cell's contents from the rest of the world it does not separate the individual reactions inside a cell from each other. The enzymes and their substrates within a cell are bumping and rubbing against each other all the time there is no separation between them. Thanks to the lock and key principle substrates and enzymes don't act on other substrates that only work with another enzyme.

The way they are controlled so that the right sequence of events unfolds is that certain enzymes are activated only when a particular pH level of the cytoplasm is reached. Then the first step in that metabolic reaction occurs before the pH changes again so that the next enzyme activates for the next step in the metabolic sequence to occur. So there is no reason this could not also occur in an open environment, that is conducive for these reactions to occur, such as that found in the prebiotic ocean. Again the pH of the prebiotic oceans would be variable but in a very orderly manner. As the currents pass through the pH gradients they would do so in a repeating pattern.

Certain metabolic reactions would not occur at all pH levels. So within these cycles we would get a type of synchronicity where certain reactions would only occur at certain pH levels. Then the cycle would continue and then you would only get certain components that would mimic the enzymes we have today. The thing is that you have different life forms doing the same metabolic activities in a different manner. What is called a homolog protein. Proteins that cause the same reaction in E. coli are different from the proteins that do it in humans.

Now in E. coli they are made of smaller polypeptides that unite and take the shape of an enzyme. Which then causes that metabolic reaction to occur. In humans we have a much more advanced enzyme where it is a large one single chain of polypeptides, protein. This mega polypeptide takes a certain conformation, shape, at a particular pH it becomes rigid and engulfed the substrate and causes that chemical reaction to occur.

Now the difference between the large enzyme in humans and the small puzzled together enzymes in E. coli is of course they are made of different amounts of polypeptides. The human is made of a single large polypeptide and the E.coli is made of many small polypeptides that unite to form a larger enzyme to do the same reaction. A lot of times we have seen that the overall shape of the enzyme of the united twelve pieces compared to the larger one piece human protein is almost exactly the same. Maybe one more bulge here or one bulge less there but basically they are the same. But when we look at the active site of the enzyme you find the same amino acids in the same position in both active regions. Meaning that the only thing that should stay the same between homolog proteins are the amino acids within the active site and all the other amino acids are there for just structural reasons to maintain and to create the lock and key activation and selectivity of those enzymes.

That being said, let's go back to the proteins that create RNA. You have proteins that are replicators of RNA and in the different kingdoms there are different examples of proteins that copy the RNA sequence. There are twenty different types of these proteins in the different kingdoms of  life. In each kingdom of life there are multiple versions of these proteins. Some of these twenty different varieties of proteins come in multiple pieces and all have very different amino acid sequences. Some are more modular than others but what is the same is the reaction that they perform.

This means that the enzymes do not need to have the exact same sequence of amino acids in order to perform that work. So what these twenty examples of very different proteins doing the same job show us is that one exact sequence is not needed to perform life’s most important reactions. Which also means the probability of an enzyme that does the same work as modern enzymes is not the probability of calculating that exact sequence of amino acids appearing in any one lifeform today. We know that there are at least twenty different sequences that are probable. According to my theory and according to some of the calculations I have done based on my theory there are hundreds of millions of different sequences probable of having the same active site.

With the increase in the number of sequences able to make useful proteins, makes it more probable that the Chaos Engine would find useful sequences sooner than later! With the cyclic nature of the Chaos Engine making trillions of sequences all at once greatly increases the chances of it making multiple useful proteins. Again the chaos engine is created by the ocean current’s repetitive cycles that can have multiple outcomes of sequences of amino acids that are totally random. But what’s important, again, the reason why these multiple sequences can do the same metabolic reactions is because of the amino acids’ properties. Amino acids form repeating structures; they either form an alpha helix or a beta sheet.

Why are these structures important? The reactive sites of enzymes are always composed of these structures in combination with each other. You have reactive sites composed of alpha helices with beta sheets. Other  reactive sites are composed of beta sheets with another beta sheet. As well as alpha helices with other alpha helices forming the catalytic region of an enzyme. These structures can form regardless of the sequence of the amino acids. So they could be completely variable and still form the same structures. That could easily combine and create reactive crevices in proteins by the billions, even trillions. These repeating structures formed by any random sequence of amino acids give the chaos engine the ability to easily create any metabolically beneficial protein(enzyme) that could then initiate Life!