Scott Klarr Jr

A primer in abiogenesis - the origin of life often confused with evolution

In the natural sciences, abiogenesis, or origin of life, is the study of how life on Earth emerged from inanimate organic and inorganic molecules. Many people mix up abiogensis with evolution (ironically, its those same people who dont know squat about evolution that claim they know better than 150 years of scientists.) Here are three great videos that will explain to you what abiogensis is, how it could have happened, and why creationist arguments against it are wrong.

Video 1

Video 1

Video 3

The first video was produced by DonExodus2, the second cdk007, and the third potholer54. I transcribed the contents of the first two videos for text versions below.

First Video Transcription

This video is going to be discussing abiogensis. First id like to clear up a couple common misconceptions. First of which being spontaneous generation. Now, spontaneous generation is completely different from abiogenesis in both the timeframe and the mechanisms in which it occurs. Pasteur of course disproved spontaneous generation but he said absolutely nothing about abiogenesis. The only thing that Pasteur proved, is that when meat is not exposed to air, it wont get maggots. And how that can possibly relate to abiogensis is of course, anybodies guess.

Second of all is the probability thing. We all hear creationists comment on how improbable and impossible it is that abiogensis happened - its impossible. Well they also tend to have a fundamental misunderstanding of it in the sense of when they look at probability, they take the probability of "what are the odds that a man evolved from an ant." Well, of course that wouldn't happen, but heres a helpful analogy to help you kind of understand the flaws in the thinking. and exactly how evolution and abiogenesis would work.

Could a baby suddenly evolve into a, or give birth to, a man; no! that does not happen whatsoever. It takes, many years for a baby to turn into a man; each with small and highly probable steps turning into a big step. Small changed over time lead to large changes over a long period of time. When you understand exactly how that works, You'll understand the fundamental flaw in that probability calculation. You'll also understand how abiogenesis and evolution work.

Another common misconception is that if whats needed for life now, complex life, was needed from the beginning; thats not the case. For example we needs a heart and lungs to live, yet does that mean that all organisms do? No! in fact the majority of organisms on this planet do not have lungs or a heart and they live just fine. So you need to be careful commenting on that too. We might have hundreds of thousands of proteins necessary for us to live, does that mean the simplest of life formed needed it? absolutely not. In fact the simplest self-replicating systems did not have DNA or proteins; they simply used RNA, as I will discuss here in a minute. So without further a due, this is exactly how life could have formed on earth.

Were actually going to begin by discussing RNA and its function and the neat things about it before we actually go into the structure of actual replicating cells. So, bare with me there its a little bit backwards but I think that its necessary to give you information about RNA before I discuss why its needed to compartmentalize.

As a little preface I would highly recommend viewing my "understanding evolution 3" video which is on DNA; I touch slightly on RNA. Just to give you a little background as to give you an idea of how it actually works. RNA is very essentially similar to DNA but there are a couple profound differences that are important. It is a means of storing genetic material. however it is not present in the typical double helix form. RNA is typically single stranded so its lacking the paired strand. The advantage of this is that it allows RNA to form into complicated neat 3D structures. Another fundamental difference is that in DNA its ATCG whereas in RNA it is AUGC. So the T is being replaced with a U and thats another important thing to understand. Lastly the only other real difference is that RNA has an OH group, its basically an oxygen that DNA doesn't have on the phosphate triple background and thats really the only other fundamental difference. But the first genetic material was most likely RNA and it was extremely important and played an influential role in forming the primitive cell.

One of the fascinating things about RNA is that in addition to storing genetic information, it can also form or fold in a certain way and it can become what is called a ribosome which is an enzyme. This is actually what caused the winning of the 1989 Nobel prize in chemistry. Its very important. These ribosomes are actual enzymes. The tetrahymena enzyme is actually able to cleave RNA strands into two smaller pieces. So this double functionality is extremely important and believe it or not, the RNA world hypothesis, that is to say RNA was the initial genetic material, has been around since the 60's by three independently driven people, and none of them had even heard of ribosomes. It was several decades before ribozymes were even discovered. This is a strong piece of evidence. Even stronger is the fact that ribosomes in prokaryote cells which are responsible for the changing the DNA and RNA into actual proteins are ribozymes themselves. So this is very powerful evidence in the fact that RNA not only stores the genetic material, but it also catalyzes its own reproduction and it also is a very important enzyme in the cell too and will later on lead to protein synthesis.

This then begs the question, how could have RNA formed in the first place? Well clays such as montmorillonite are actually crucial and they have been experimentally shown to have a charge surface and to attract RNA nucleotides. What this does is catalyzes the polymerization reaction by clumping them together and putting them near each other so that the long-chain polymers will form. This has all been essentially demonstrated in the lab and has been shown to be completely feasible. The discovery of montmorillonite and this polymerization ability has actually been pretty impressive.

Another possibility is that RNA could have formed from salty ice-water. Its been shown in the university of California, that when you freeze a diluted solution of RNA nucleotides, as the ice crystals begin to form, the RNA gets pushed out and gets concentrated. This will also polymerize RNA. Both of these methods completely naturally lead to the formation of RNA.

Interestingly enough, experiments at a Harvard lab have completely shown that RNA can replicate without enzymes. So no ribozyme whatsoever is needed. What happens is chemically activated nucleotides will find their complementary place on an existing RNA strand and will replicate and make copies from there. Keep in mind the nature of self-replicating systems in the sense of: if something is self-replicating, its going to accumulate by the very nature of it. Theres no witchcraft or anything like that involved, thats simply how it works. This is just a wonderful backup explanation and to demonstrate that even if ribozymes or other things to replicate RNA aren't in existence which would be replicasis, RNA could still make copies of itself. That being said this is somewhat slow and error-prone so a ribozyme which would make copies of RNA called a replicase, would have probably evolved fairly early.

Another amusing fact surrounding this is that if you recall correctly, RNA is single stranded, however it can at times associate with complementary strands much in the way that DNA does. Well, if these were to separate, which what normally happens at sea temperature, one of them would spontaneously fold into a ribozyme and the other would serve as a template strand. So this is exactly how protein synthesis today works only replacing the ribozyme with a ribosome, which they are very similar to begin with. This is just another piece of evidence to stack on the pile.

The next question comes about "why does life need a membrane compartment?" and there are several answers for this. One of these is that the replicases will not only replicate each other but they will also replicate any RNA they come in contact with and over time if your not in a sequestered environment, the replicases will clearly become outnumbered and your gonna be left with just a bunch of RNA and very little things to replicate it. Creating a mini environment inside a larger one is extremely important its the fundamental backbone of biology today and it allows compartmentalization and all sorts of other things to occur.

So now I will be examining exactly how this compartmentalization could have come about to begin with. Fatty acids provide the essential backbone of the membrane compartments in the natural world. But the question arises, where do these fatty acids form? The likely answer to this would be in deep-sea hydro-thermal vents. Now, mineral surfaces can catalyze the formation of hydrocarbons from carbon monoxide and hydrogen. These over time will accumulate, aggregate, and be released as fatty acids. This has all been of course been demonstrated multiple times; its thermodynamically feasible and probable.

Ask yourself what happens when you place a drop of oil in water. It forms a drop or a circle. You don't have to do anything magic thats just what happens when you do it. Now when you place the fatty acids we just formed in water, you get what are called micelles. These first line up in a bi-layer but when the bi-layer, due to fluctuations in the water, when they reach around and connect at the end, you get formed whats called a vesicle which are extremely stable structures; they have been known to maintain the same size and shape for several months. Interestingly enough, montmorillonite clay, if you recall the same clay that will polymerize the RNA reaction to begin with, also catalyzes vesicle formation.

So now we have a basic protocell with two components. Its an RNA replicase and a fatty acid membrane. Now this is extremely basic, but nevertheless, its subject to growth, replication and evolution as well. As far as the protocell life-cycle is concerned, the two or more replicases will make copies of each other but its also prone to mutation. Most of the time when these mutation occur, these replicases will not be able to copy the RNA as effectively, however occasionally, a better replicase may be formed that might copy a bit quicker. Furthermore it could also have a mutation that would cause for example the synthesis of new fatty acids so it wouldn't rely on the environment to get them. All of these possible mutations, keep in mind this protocell is subject to evolution, would accumulate and these protocells with these advantageous mutations would be replicating at a rate higher than those without them. Its essentially all downhill from there.

Second Video Transcription

Since the dawn of humanity, civilizations have created myths to explain our origins. Grounded not in fact but in belief thousands of different creation myths all share one common thread... the supernatural.

No human mind could conceive of a means of life origination through purely natural processes. Life only appears to come from life, therefore a natural origin was out of the question.

Before we continue, lets get one thing straight. The origin of life, abiogensis, has NOTHING to do with the theory of evolution. Scientific theories are designed to explain a specific set of facts. You would not claim the theory of gravity is wrong because it doesn't explain germs (thats what the germ theory is for). Claiming evolution is wrong because it doesn't explain the origin of life, is like claiming an umbrella doesn't work because it doesn't predict the paths of hurricanes. Abiogensis explains the origin of life. Evolution explains how life changed once it already exists.

Creationists have made a number of arguments why they think abiogensis is wrong. Here are the top 4.

1. Spontaneous generation of complex organisms is impossible. Spontaneous generation was actually scientifically tested and proven false in 1668 by Francesco Redi; in 1765 by Lazzaro Spallanzani; in 1859 by Louis Pasteur; and has been claimed by scientists since. Way to be current!
2. The probability of a single cell forming by chance is 1 in 10^50,000. Disregarding the fact that these numbers are made up, all it shows is that early life could not have been as complex as modern cells.
3. Taken from Ben Stein. "Life was created by lightning striking a mud puddle.. and thats just silly." Actually, there is only one book that claims life was formed from dirt -- the holy bible!
4. The 1953 Miller-Urey experiment did not create life. This is like claiming its impossible to fly to the moon simply because the Wright brothers didn't.

The early earth had order of magnitude more: Time, Space, Complex chemistry and environmental conditions. So what can science tell us about the origin of life? This video is a summary of work by Dr. Szostak, Professor at Harvard Medical school.

We know from experiments and observations made in the fields of Astronomy, Chemistry, Geology and meteorology that the early pre-biotic earth was filled with organic molecules, the building blocks of life. Organic molecules are actually quite common in space. We also know from the creationist arguments discussed earlier, that early life must have been extremely simple, meaning no complex protein machinery.

Modern cells separate themselves from the environment with a lipid bylayer. The problem with modern phospholipids is they are too good at what they do. They form a nearly impenetrable barrier. Modern cells must use proteins to move molecules across their surface. But life dint have to start with modern chemicals. The pri-biotic environment contained many simple fatty acids. Under a range of Ph they spontaneously form stable vesicles and they are permeable to small organic molecules meaning no complex proteins are required to get stuff in.

When a vesicle encounters free fatty acids in solution, it will incorporate them. Eating and growth are driven purely by thermodynamics. When a vesicle grows it adopts a tubular branched shape (surface area grows faster than volume) which is easily divided by mechanical forces (waves, currents, rocks, etc). During mechanical division, none of the contents of the vesicle are lost.

So far, with naturally occurring simple fatty acids, we have a vesicle that can spontaneously grow and divide. So what about the genetic material? Again, modern nucleotides are too stable and require complex protein machinery to replicate. The pre-biotic environment contained hundreds of types of different nucleotides (not just DNA and RNA). All it took was for just one to self polymerize.

Recent experiments have shown that some of these are capable of spontaneous polymerization, such as phosphoramidate DNA. Monomers will base pair with a single stranded template and self litigate. They can also polymerize in solution, and spontaneously form new templates, or extend existing templates. No special sequences are required, it's just chemistry.

So far we have lipid vesicles that can grow and divide, and nucleotide polymers that can self replicate, all on their own. But how does it become life? Heres how:

Our fatty acid vesicles are permeable to nucleotide monomers, but not polymers. Once spontaneous polymerization occurs within the vesicle, the polymer is trapped. Floating through the ocean, the polymer containing vesicles will encounter convection currents such as those setup by hydrothermal vents (fatty acid vesicles are stable under near boiling conditions)

The high temperatures will separate the polymer strands and increase the membrane's permeability to monomers. Once the temperature cools spontaneous polymerization can occur. And the cycle repeats. Heres where it gets cool.

The polymer, due to surrounding ions, will increase the osmotic pressure within the vesicle, stretching its membrane. A vesicle with more polymer, through simple thermodynamics, will "Steal" lipids from a vesicle with less polymer. This is the origin of competition. They eat each other.

A vesicle that contains a polymer that can replicate faster, will grow and divide faster, eventually dominating the population. Lets review:

• Monomers diffuse into a fatty acid vesicle
• Monomers spontaneously polymerize and copy any template.
• Heat separates strands, increases membrane permeability to monomers
• Polymer backbones attract ions increasing osmotic pressure
• Pressure on the membrane drives its growth at the expense of nearby vesicles containing less polymer
• Vesicles grow into tubular structures
• Mechanical forces cause vesicles to divide
• Daughter vesicles inherit polymers from the parent vesicle
• Polymer sequences that replicate faster will dominate the population

Early genomes were completely random and therefore contained no information. It was their ability to spontaneously replicate, irrespective of sequence, that drove growth and division of the fatty acid vesicles. Any mutation that increases the rate of polymer replication would be selected for. Mutation + natural selection = increased information.

Early beneficial mutations would include:

• change sequence to contain only the most common nucleotides
• Don't form secondary structures that block replication
• Form sequences that are stable yet separate easily.
• Form secondary structures that show some enzymatic activity.
• Just like RNA, early nucleotides could both store information and function as enzymes.

Early polymer enzymes would:

• Enhance replication
• Use high energy molecules in the environment (near thermal vents) to recharge monomers.
• Synthesize lipids from other molecules in the environment.
• Modify the lipids so they dont leave the membrane.

Thats it! A simple 2-component system that spontaneously forms in the pro-biotic environment can eat, grow, contain information, replicate and evolve. simply through thermodynamic, mechanical, and electrical forces.

No ridiculous improbability.. No supernatural forces.. No lightning striking a mud puddle.. Just chemistry... Think about it.