Posted on 03/23/2002 3:08:55 PM PST by Heartlander
Abiogenesis: The First Frontier
There are a number of models and theories out there about how life might have arisen and originated. The goal of this article is educate the reader as to the facts and the myths associated with abiogenesis.
The best place to start off on abiogenesis would be the definition. Abiogenesis is the unguided arisal of life from non-living matter. Abiogenesis is basically an attempt to explain the origin of life while nullifying the possibility of a creator.
Conditions of the old Earth: There are a number of theories on what the conditions of the prebiotic (pre-life) earth may have been. There are three main scenarios.
Frozen Earth Model: The frozen Earth model is the ideal model for life on earth. In it, the oceans have frozen over completely and the world has taken on a climate like antarctica today. Now, deep beneath these ice caps are hydrothermal vents where nutrients and organic material are constantly being pumped out by the active volcanism below. Speckled throughout these ice sheets are pockets of water where nutrients become concentrated. The concentration builds up to the point that the reactions can't help but happen and the first early life forms come into being. The ice sheet scenario is most likely for the production of life because the cold temperatures keep those vital ingredients from decaying. The Frozen Earth Model has one serious flaw, however. There is no evidence for it. As a matter of fact, secular scientists have concluded that a prebiotic earth would have been brutally hot as the result of residual heat remaining from the Earth's molten accretionary formation. "Frozen Earthers", however, maintain that it may have been caused by cometary impacts that would have deposited the formaldehyde, cyanide, and ammonia necessary for life. One might note, however, that cometary impacts are believed to generate a great deal of heat so they would be very unlikely to cause any sort of freeze.
The Modern Earth Model: This was the model that Darwin envisioned. It is an environment that is much like we see today. Most secular scientists have agreed that this scenario is very unlikely. In it, however, life forms when rivers carry nutrient-rich sediment downstream from glaciers to accumulate in ponds. Another source may have been tidal pools. Still, this is pretty much the least accepted scenario.
The Hot Earth Model: This is the model most accepted by the scientific community as the environment for prebiotic earth and in which life may have arisen. The Earth is still hot from it's molten formation. Volcanoes rumble in the distance and deep thermal vents keep the ocean steamy and hot. There are large tidal lagoons where nutrients accumulate. Under the heat, the lagoons dry and precipitate their nutrients to form strong concentrations. With concentrations so strong, life can't help but form. The heat also supplies the energy needed to get the processes leading up to the creation of life started.
Most of what I'm going to talk about will apply strictly to hot earth scenarios since this is taken most serious by the scientific community.
Early Abiogenesis Experiments: Perhaps most influential to the study of Abiogenesis is the famous Stanley Miller experiment in which he ran large currents of electricity through a container of what he believed to represent the conditions of prebiotic earth. He turned on the machine one night and the next morning he discovered a rich broth of amino acids. This was an amazing discovery at the time. It was the first step toward abiogenesis and secular scientists were enthralled. Unfortunately for Stanley Miller, his assumptions for prebiotic Earth were wrong. He believed that it would have been composed of Hydrogen, Methane, and Ammonia. In reality, the earth would have been composed of predominantly Carbon Dioxide and Nitrogen. Attempts were made to replicate Miller's experiment with the new ingredients. Results were meager to say the least: the equivalent of a drop in a swimming pool. Scientists realized that this certainly was not enough so they devised the concept of tidal lagoons. (Note: Scientists often become flustered when we bring up the miller experiment and just say "let it go", but it's hard to do when sites and textbooks can still be found to proclaim the miller experiments as proof that life could arise spontaneously Life in the Universe)
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Tidal Lagoons? Ok, here's the deal with tidal lagoons. The ocean has all these nutrients and organic substances, but they are too dispersed to react with each other. The tidal lagoon fills up with the ocean water. When the tide recedes, a good portion of the water is still there. Now, the earth is very hot so the water in the lagoon rapidly begins to evaporate. As the water evaporates, the material it was holding in suspension drops out and the concentration in the lagoon grows. Next time the tide comes in, it drops some more nutrients and the process continues until the lagoon is full of organic material. Also contributing are hydrothermal vents feeding rivers into the lagoon which are pumping out more of these essential ingredients for life. It seems like a rather gentle process, right? That's the idea. The tide comes in and gently brings more material for life to form and gently meandering rivers add to the serenity. What a beautiful picture. Now let's take a quick glimpse of reality. The tidal lagoon idea NEEDS everything to be calm and gentle or else it will disrupt the material and carry it back to sea. What proclaimers of this hypothesis fail to recognize is what the early earth really would have been like. According to secular scientists, the moon was much closer to the earth than it is today. It caused the tides not to be gentle waves but raging tsunamis hundreds and even thousands of feet high that swept over the continents 2-3 times per day. Nothing like being pummeled by billions of gallons of water to break the serenity, huh? Already the chances of abiogenesis are being ruined and we've hardly begun!
The Ingredients: So how did life actually get here? Well, many scientist believe it arose from a series of chemical reactions. I will now discuss the problems these reactions faced. First of all, under supposed prebiotic conditions, "building blocks" are more likely to break down then react positively with each other. One example is sugars, carbonyl compounds, and amino acids. These are all necessary for life, yet when sugars and carbonyl compounds come into contact with amino acids in an unordered environment, they form imines (which is what causes food to brown). To increase the likely-hood of abiogenesis, scientists have theorized that life may have depended on RNA rather than DNA. Let's look at RNA for a second.
RNA! An essential ingredient for RNA is ribose (hence the name ribonucleic acid). Stanley Miller ran experiments to find the half-life of ribose. At 0 celsius and neutral ph, ribose has a half-life of 44 years. This may seem like a long time, but chemically is not. Of course, this would only apply to a frozen earth model, which is so unrealistic it is hardly taken seriously. So we know that the ribose would have actually lived in a boiling hot environment. Ribose was found to have a half-life of 73 minutes at 100° C. This is incredibly fast considering that the ribose would only constitute a small portion of that potential life that needs to react to get it started. You see, now we find another flaw in the thinking of abiogenesists (also known as exobiologists). They believe that heat gave those "ingredients" the energy they needed to react. In reality, however, heat acts to break down substances. We're going to see this even more clearly in a moment. There are four more substances needed for life to form. These are: adenine, guanine, cytosine, and uracil. At 100° C cytosine has a half-life of 19 days, adenine and guanine are about a year, and uracil is about 12 years. These extremely young life-expectancies are a death sentence for any abiogenesis theory and get even worse when you consider the abundance of these material in prebiotic earth. Let's look at cytosine, for example. Cytosine has not been found in either gas discharge experiments nor meteors so it is believed that cytosine actually came from reactions of it's own. So now we look at cyanoacetylene and cyanoacetaldehyde which can be found in some spark discharge experiments. It has been shown that these two materials can react to form cytosine which in turn reacts with the ribose to form cytodine.
Those big words that start with cy! First of all, the highest yields produced in the above experiments only reached about 2% and that was with ideal conditions and purines. Now, what is so unrealistic about cytidine being formed? Both cyanoacetaldehyde and cyanoacetylene were produced in spark discharge experiments involving methane and nitrogen, an environment highly unlikely for prebiotic earth. Also, cyanoacetylene and cyanoacetaldehyde would be more likely to undergo side reactions, then the reactions that are necessary for life to form. For example, these materials can react with amino acids which destroys even more of the "ingredients for life." There are even worse problems for these materials. Cyanoacetylene rapidly hydrolizes in water to form cyanoacetaldehyde with a half-life of 11 days at ph 9 and 30° C (which is very cold considering the assumed conditions of prebiotic earth). Cyanoacetaldehyde also hydrolizes slower with a half-life of 31 years under these conditions. While the half-life of cyanoacetaldehyde may not seem too short, remember that the half-life will decrease as temperature increases and that it has nothing or very little to react with since the cyanoacetylene is completely or at least mostly gone. Add this to the fact that if the reaction ever did occur, the cytosine would only last about 73 minutes (perhaps a little longer) and you've got impossible odds for the formation of life. In case you are thinking that life still could have formed, you should know that cytosine decomposes even more rapidly in the presence of ultraviolet radiation which means that the reactions would have had to have been carried out in the dark. (And oddly enough I have found sites claiming UV radiation may have aided the formation of life.)
Past Experiments: In the past many experiments have been performed using different chemicals and compounds. They can often get a lot of media hype and no-one hears when they are shown to be wrong. This is going to trace some of these past experiments.
Robertson and Miller? These two tried a somewhat different approach to the cytosine problem mentioned above. They took cyanoacetaldehyde and various concentrations of urea and heated them in a sealed container for about five hours at 100°C. They ended up with 30%-50% yields of cytosine. This was hailed by some as proof that cytosine could be produced in the quantities necessary for life. There are a few problems with this, however. First are the ones mentioned above about cytosine and cyanoactaldehyde. To avoid the cytosine problem, Robertson and Miller stopped the experiment after five hours. Of course, in reality, it would have continued and the cytosine would have hydrolyzed and disappeared. Another problem lies with the stability of urea. Urea exists in equilibrium with it's isomer, ammonium cyanate. Shapiro pointed out that cyanate rapidly undergoes hydrolysis so more and more urea would have to convert to ammonium cyanate in order for it to remain in equilibrium. This would ruin the concentrations required. To get around this problem, Robertson and Miller performed their experiment in a sealed container without water to prevent hydrolysis. On the other hand, this reaction is believed to have occurred in lagoons. In an open system, urea has a half-life of 5 hours at 90° C and neutral ph. Another problem is that urea can react with glycine, another essential ingredient, to form N-carbonyl and further reduce the number of amino acids.
Nagaoka? In Nagaoka, Japan, a team of five scientists has claimed to have proven that life arose from a hydrothermal vent. Let's take a look at how they did this. First they built a flow reactor. They inserted 500 ml of 0.1 M glycine solution into several chambers at the high pressure of 24MPa. The first chamber was heated to 200°-250°C. From there, the fluid was injected into a cooling chamber at 0°C and at a rate of 8-12 ml/min. The samples were then depressurized and analyzed. A .01 M solution of CuCl2 was added to some samples and were acidified to 2.5 ph with room temperature HCl. The most impressive results came from the samples that had HCl and CuCl2 added prior to the experiment. It turns out that the Cu2+ catalyzed (sped up) the formation of tetraglycine which yieleded the low amount of .1% and even less hexaglycine which yielded .001%. Diketopiperazine, an organic substance, was the highest yield which peaked at 1%. So what was wrong with this experiment? The glycine concentration (.1 M) is way too high! Glycine exhibits oxidative degradation in the presence of oxygen, but this doesn't matter much when you consider that prebiotic earth would have lacked oxygen. Realistically, however, glycine would be decomposed by UV radiation, be taken out of the system by absorption by clays, precipitate out, undergo complexation with metals, or undergo reactions with other organic molecules. Moreover, glycine was the only amino acid tested which is exceptional because it is the simplest and only achiral amino acid in use by living systems today. The fact that the samples were entered into a cooling chamber at 0°C shows that they were running tests for a frozen earth model. In reality, such cooling would not have occurred (at least not to such an extreme and not so rapidly). Hexaglycine was also the most complex enzyme formed, but most enzymes are composed of hundreds of amino acids, not six as hexaglycine is. This difference is emphasized when considering that hexaglycine was only produced at .001%.
Self-Replicating Molecules? A group led by Julius Rebek went out to prove that RNA life could reproduce. What he ended up doing is synthesizing a molecule by the name of amino adenosine triacid ester (aate). The name gets even funner as you go along. You see, it is composed of two molecules: pentafluorophenyl ester and amino adenosine. When the aate is dissolved into a chloroform solution with it's other two components, the aate essentially acts to "guide" these two molecular components together to form new aate molecules. So, at first glance, Julius seems to have made a great discovery. In fact, it is a great discovery and it is of this author's opinion that that's pretty cool. It is irrelevant to abiogenesis, however. There are several problems with this in regards to life. My favorite are: there wouldn't be any chloroform for pre-biotic earth (or if there was, only the most inconsequential amounts). There was no water involved with the experiment which would act to break down the molecular components rather than join them together. Finally, the molecules did too good of a job. There was no chance of darwinian evolution occurring because the reaction was too perfect. Life couldn't have arisen from that.
Self-Replicating Peptides? Ok, I want to start this off by saying this: That was an unintentional plagiarization of one of my source articles (the part in italics). In order to avoid that, I would have to change the style I was using. I didn't want to do this. If you've read the article, just lettin' you know. If you haven't, try to find where that came from... Ok, now to get to the info part. As mentioned above, amino acids can be produced in nature (just barely). This led some people to think that perhaps proteins came first and then the rest. This hypothesis got a big boost when David Lee reported that he had formed a 32-unit peptide that could reproduce itself in 1996 (a peptide is a no. of amino acids bonded together with a carboxyl group [an organic acid]). The media got wind of this and created a goodly sized hype. The peptide is derived from a part of a yeast enzyme and the following steps were taken to observe this event:
The peptide (GCN4 [Guanine Cytosine Nitrogen4]) was dissolved in a diluted solution of fifteen and seventeen unit fragments of the peptide, itself (which is 32-units long [15+17=?]). The peptide acted to catalyze the reaction between the 15 and 17-unit fragments. These joined together to form the GCN4. I'm wondering if you caught on to the problem yet. Let's take a look. First of all, the 100% left-handed peptide was assumed to just magically appear. No attempt was made to figure out how the original one got there. Second, where did all these magical little fragments come from that were dissolved in the solution? These were just assumed to always be there also. Now, I've got a confession to make. I was holding out on you. Another component of the reaction was a thiobenzyl ester derivative of the peptide to activate the reaction. Why? Because these reactions don't occur spontaneously (on their own) in water. What we see in this instance and in the others we've looked at is intelligent interference. The chemists were directing these reactions and occurrences to take place because they do not occur naturally or readily under natural conditions. Yet they use these influenced reactions, which they directed, to claim that life could arise without direction.
More problems for abiogenesis: Are things looking grim for this doomed hypothesis? Not as grim as they're gonna look...
Complexity of Life? So let's look at a few of the processes and components of life for a moment. A cell (or any living creature for that matter) must produce very specified reactions to the right order, degree, and place in order to survive. The original cell or life proto-type would have to be the most versatile creature the Earth has ever seen in order to survive those conditions of prebiotic life. Theoretically, they should be found all over the place on earth, but are yet to be found. In order to perform those reactions that are necessary for life, enzymes are needed to catalyze the reactions. These are proteins. Proteins are polymers of amino acids. Nucleic acids (in our case, RNA), the units that transfer information within the cell, are polymers of nucleotides. These nucleotides are, in turn, composed of a sugar (ribose), a nitrogenous base, and a phosphate group. Note: Components of polymers are frequently referred to as monomers. The RNA in the original life form would have needed to be capable of reproducing all of these things. Now, in order for life to actually occur via RNA, the following conditions must exist: A source of purely or predominantly right-handed ribose molecules must exist (I will explain what this means later)and remain stable and separate from all other sugars. Meanwhile, a large quantity of bases must exist in the same area along with high concentrations of phosphates that have not precipitated out (as would most likely occur). Ribose then goes to combine with those bases and phosphates to produce b-D-Ribonucleotides. These then must produce the RNA polymers of the appropriate form capable of self-replication and retaining all the functions necessary to it's survival.
Chirality? Does this word scare you? It won't in a moment. Chirality deals with the condition of a molecule. See, molecules can be compared to your hands. They are the exact same things...except opposite. Confused? Chiral molecules are often referred to as "left" or "right-handed" (hence the hand comparison...+ chiral means hand). So if these molecules are exactly the same, how can they be opposite? The two forms of the chiral molecule are called enantiomers or optical isomers. The defining characteristic is the direction they rotate plane-polarized light. Left or right. Not everything is chiral (achiral), but all amino acids and many sugars exhibit these types of properties. Almost all biological polymers must be homochiral (same chirality). All amino acids in proteins are left-handed while all sugars in DNA and RNA are right-handed. Now, when amino acids are created, they always occur in racemic proportions. Racemic means a 50/50 ratio of left-handed to right-handed. What is even more interesting is that the two enantiomers must be in equilibrium with each other to exist and equilibrium only occurs in a racemic mixture. Remember what was stated above? In order for life to arise, all of the left-handed molecules would have to gather on one side of the lagoon and all the right on the other. The problem is, this can't happen because they will be out of equilibrium with each other and the homochiral mixtures will begin to convert into their optical isomers trying to recreate a racemic environment. So how do we get the two opposites to break up? Introduce a new substance. Because the isomers are essentially the same, they will bond to it the same. Now the two chiral particles are no longer dependant on each other. So now we know that the two can separate, but that still leaves the question of how. What mechanism would cause these particles, identical in nature, to separate? There is no known mechanism for doing this. What irks scientists even more are the odds. The probability of a protein being homochiral (all left handed in our case) is 2-N where N equals the number of amino acids in the protein. A short protein uses about 100 amino acids so the odds of this forming is 2-100 or 10-30. Now, you should know that this is just the odds of any homochiral protein forming at all. Many homochiral amino combinations produce inactive proteins (useless) so the odds drop rather dramatically when this is taken into consideration. Then you consider the number of different kinds of homochiral polypeptides required for life and you have outrageous odds.
But wait! There is even more to this complicated story! Remember that we know chiral particles can be separated if they bond to something. One mechanism that may act to create higher concentration of one relative to the other is light. As you may know, light can be circularly polarized. Now recall that chirality of substances are dependant upon the reflection of polarized light. Thus, particles of different chirality absorb different amounts of light. Now photolysis comes into play. Photolysis is the process through which substances are broken down by light. Since differing chiralities have different responses to the light, they also maintain different degrees of photolysis. This means that some particles will decay slower than others, thus found in greater abundance. So, have scientists found the mechanism for homochiral polypeptide formation? Nope! Why? Tests were run to...well...test that hypothesis. The greatest effect created 20% homochirality in the mixture and this was after 99% of the original material had already been destroyed by the light. In fact, if you ever got so much as a 35.5% (meaning 35.5% more of one than the other) pure mixture, you would have destroyed 99.99% of the original material. While photolysis is a good concept, it fails to produce the results necessary for life. Remember that all proteins are made from left-handed amino acids and all sugars involved with life are right-handed. Also, the effects of photolysis depends on the frequency of light and since the sun produces many frequencies of light, any advantage one chirality might hold over another in nullified (the experiments above did not involve sunlight).
Other Chirality "Things": One of these "things" is b-decay. b-decay is a form of radioactive decay that has slight chirality. Some scientists, desperately trying to prove abiogenesis feasible, attempted to explain the homochirality by blaming the decay. To the dismay of such scientists, b-decay is so minor that it might as well not even be mentioned.
Quartz Powders: Quartz can also exist in left and right-handed states. Attempts were made to see if the quartz would absorb one isomer more than the other, but the results yielded failure.
Clay: Certain clays have been claimed to exhibit slight preferences in one chirality over another. The results of tests used to confirm this have been questioned due to the techniques used and the potential presence of biomolecules (produced by living creatures) in the clay, which would affect isomer absorption.
Homochiral Crystallization: Louis Pasteur, a great scientist, found that some racemic mixtures can crystallize into homochiral parts (such as sodium ammonium tartrate). This is very interesting, but relatively irrelevant because the crystals, in an aqueous environment, would redissolve into a racemic solution. The only case where this would be valid is in the evaporation lagoons, but that has already been shown to be unfeasible. Copy-cats: Some theorists thought that a homochiral polymer could arise from chance and cause other homochiral polymers to form. Scientists CREATED a homochiral poly-C (cytosine). This substance guided the formation of small chains of activated (homochiral) Guanine nucleotides to form. The problem is that if the solution wasn't homochiral (guanine solution), then it would be mostly homochiral, but with molecules of the wrong chirality acting as terminators (end points) for the nucleotide.
Magnetism: A team of German scientists announced that large magnetic fields could produce 98% homochirality from achiral material. There are several reasons why this evidence is no longer cited. First, the field was about 10,000 x's greater than the earth. Second, no-one could duplicate it. Third, it was shown that Guido Zadel had added a homochiral additive to create the results they reported.
Chemical Equations and Math: Now, let's do some equations (thanks to Jon Sarfati).
Now, the general form for polypeptide formation is: Amino acid 1 + amino acid 2 à dipeptide + water. We're going to assume the two amino acids in order to perform the equation.
H2NCHRCOOH +H2NCHR¢COOH à H2NCHRCONHCHR¢COOH + H2O (1) Next we use the equation: K = exp (-DG/RT). R = universal gas constant (8.314j/Kmol).
T = temp in kelvin. DG (change in free energy) = 20-33 kJ/mol.
Then figure that K = [H2NCHRCONHCHR¢COOH][H2O]/[H2NCHRCOOH][H2NCHR¢COOH]
And what you finally end up with is .007 at 298 K.
Please read on - it gets better!
Well, that didn't take long. You can
let me off here, driver. If abiogenisis
is correct, there is no need to add the
extra layer of having a creator. It
is not an attempt to repudiate creators,
tooth faeries, Santa Claus, or Tinkerbell.
If abiogenisis can be demonstrated, the
need to postulate primal chimera does not arise.
Orhanic material is life. Life plus nutrients begat life? Pretty circular, no?
I agree completely. Science does not take a stand one way or the other on a creator. Science is creating the best model to fit the data discovered to date. As that data is revised and new discoveries are made, the models themselves must also be revised to incorporate the new data.
That sounds real good and doubtless many scientists do just as you say, but the field of evolution and abiogenesis specificially excludes the possibility of a creator so the data is never revised in that direction regardless of the evidence.
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