Abiogenesis and Evolutionary Theory on Trial

Abiogenesis is not the same as Evolutionary Theory. However the latter heavily relies on the viability of the former to provide a naturalistic origin of life in a form that supposedly could then evolve from a small yet complex molecular level organism into the wide variety of increasingly complex life forms that we find today.

Thus, leaving aside the short comings of the Evolutionary Theory itself, that of life becoming more complex via mutations. If Abiogenesis can be shown to be untenable, it would cast serious doubt on the starting conditions of life on earth presupposed by Evolutionary Theory.


I intend to present the basic assumptions made by scientists regarding the viability of abiogenesis and then highlight the problems with these assumptions. I will provide sources where I can and leave the remaining details for further debate.

At a minimum the following components are essential to the theory proposed by advocates of a naturalistic origin of life.

1. An atmosphere full of reduced gas molecules and an energy source to convert these molecules into the biological precursors required for life.

2. An ocean full of the small biological molecules that result. (it should be noted that other locations such as clay, or volcanic rock have been put forth as possible cradles for the first living organism. Changing the location doesn't really change many of the problems that arise from their hypothesis.)

3. A mechanism to generate from this ocean of molecules the kinds of information-rich polymers necessary for a living cell.

4. A belief that if step 3 can be implemented, it will result almost inevitably in the formation of a living cell.


1. What evidence is there that the earth at one time consisted of reduced gas molecules with little or no oxygen present? Why is this necessary for abiogenesis in the first place?

The entire concept of a reducing atmosphere devoid of oxygen was proposed specifically to present an environment conducive to the chemical reactions necessary to create some of the amino acids that are the building blocks of complex proteins which enable life. If this environment did not exist, or if it could be shown that free oxygen was present in the time frame that abiogenesis is proposed to have occurred, many of these experiments should be thrown out. For they would not mimic the likely "real world" conditions of Earth during the required time frame. If oxygen or oxidizing compounds were present, the chemical reactions supposedly stimulated by energy from lightning(or similar energy source) to produce stable amino acids would not be possible.

So then was there oxygen or oxidizing agents present? And is there any evidence of an early atmosphere composed nearly entirely of methane, ammonia, hydrogen and water? Could such an atmosphere even remain devoid of oxygen for any appreciable amount of time?

Evidence that oxygen was present

1. Even the oldest rock layers in the geologic column show the presence of oxidized minerals and metals. These rock layers predate the era when abiogenesis is proposed to have happened. If there was an oxidizing environment during the formation of rocks in the oldest geological layers, then this is evidence that our planet has been oxidizing since its beginnings. There is no known mechanism where by that oxygen could have been removed from the atmosphere for a time period to have occurred devoid of oxygen and conducive to the chemical reactions required by abiogenesis. Amino acids that could be produced in a manner such as proposed by the Miller-Urey experiment would be nearly instantly destroyed by atmospheric oxygen in the form of O2 or ozone. In fact the presence of free oxygen would preclude virtually all scenarios that have been proposed for abiogenesis of life.

(E. Dimroth and M.M. Kimberley, "Precambrian Atmospheric Oxygen: Evidence in the Sedimentary Distributions of Carbon, Sulfur, Uranium and Iron", Can. J. Ear. Sci., Vol.13, pp. 1161-1185; I.B. Lambert, T.H. Donnelly, J.S.R. Dunlop, and D.I. Groves, "Stable Isotope Compositions of Early Archaean Sulphate Deposits of Probable Evaporitic and Volcanogenic Origins", Nature, Vol. 276, p. 808) and (Schidlowski, M. (1976). Archean atmosphere and evolution of the terrestrial oxygen budget. In The Early History of the Earth, ed. B. F. Windley. London; New York: John Wiley & Sons. Ohmoto, H. (1997). Evidence in pre - 2.2 Ga paleosols for the early evolution of atmospheric oxygen and terrestrial biota. Geology 24:1057-1184. Ohmoto et al. (2006) "Sulphur isotope evidence for an oxic Archaean atmosphere," Nature 442, 908-911. )


1a. Let us suppose for a moment that the above evidence of Oxygen present on the early earth is completely bunk and there really was a reducing atmosphere which then successfully produced amino acids in a manner similar to the Miller-Urey method. Without the presence of Oxygen, we would have no Ozone Layer(which itself is made up of oxygen). This would mean that the earth would have no protection against the UV (ultra-violet) rays from the sun. Intense bombardment of direct UV radiation would nearly instantly destroy any amino acids that happened to form in such an environment. The ability of Ozone to protect us from the suns radiation is not only critical to earths ability to support life in its present form, it would also be needed to protect any building blocks of life such as amino acids, or proteins at any time in earths history.

Thus this idea of amino acids forming out of a oxygen free atmosphere is essentially untenable. It is a lose/lose situation for proponents of a naturalistic origin for life. With oxygen, the amino acids instantly begin to suffer from oxidized degradation. Without Oxygen the amino acids are destroyed by UV Radiation. There is much evidence that Oxygen has always been present in our atmosphere.

1b. Another interesting tidbit is that recently since the Apollo 16 flight we have observed UV induced photodissociation of water in the upper atmosphere and it is theorized that this could be a major source of free atmospheric oxygen. If the reduced gas atmosphere ever did exist without Oxygen, it would not remain that way for very long. Once again, without Ozone to block the UV radiation, oxygen would have been produced at a very high rate due to this photodissociation of the water molecules in the atmosphere. This has lead many people to concede that such an atmosphere as required for abiogenesis to happen is highly unlikely and that it is far more likely that the atmosphere of the early earth was closer to the form in which we find it today.

I will continue my critique of the viability of Abiogenesis in my next post.

Soul

Originally posted by SoulReaper
However the latter heavily relies on the viability of the former to provide a naturalistic origin of life in a form that supposedly could then evolve from a small yet complex molecular level organism into the wide variety of increasingly complex life forms that we find today.

No it doesn't. Unicorns could have farted life into existence for all it matters, it would not change the theory of evolution one bit.

Thus, leaving aside the short comings of the Evolutionary Theory itself, that of life becoming more complex via mutations.

What shortcomings? The imaginery ones you pull from creationist websites?

If Abiogenesis can be shown to be untenable, it would cast serious doubt on the starting conditions of life on earth presupposed by Evolutionary Theory.

No it wouldn't.


From here on it's apparant that the entire premise of your argument is flawed. Do not pass go, do not collect $200.

You do realize this reducing atmosphere neednt be the entire earth right? What if theres a cave and something in the cave caught on fire, then a rock falls on the opening into the cave? The fire would burn all the oxygen away within minutes.

We dont even need abiogenesis. How about panspermia?

Originally posted by SoulReaper
cast serious doubt
problems with these assumptions.
the problems that arise
A belief
What evidence is there
Why is this necessary
The entire concept
is there any evidence
Could such
There is no known mechanism
Thus this idea
is highly unlikely

Dont have time to dive into the scientific arguments presented here, but I will just offer a general note on the Creationist arguments.
FUD
Everywhere I look, from online to the ICR Creation Museum, the argument FOR creationism is always presented as a lets throw doubt and uncertainty on science argument.

As if proof of "god did it" lies in the success of confusing people about science.

Some recent advances related to abiogenesis:

Spontaneous formation of most or all RNA bases

Spontaneous formation of autocatalytic RNA molecules, which are postulated to be first living things on Earth by the RNA world hypothesis

links
the.. Abstract ? and..

as back.. from the future
www.apple.com...

or .. de-vice versa

anyway ,it all comes together
as we all know now 1 and 1 is
3,,,,...

Just one observation. Earliest branching prokaryotes (most basal) are without exception extremophiles. They thrive in anoxic and hot environments. This is quite good indicator that first cellular life had similar likings. Since some of our parts (e.g. ribosomes and tRNAs) are thought to predate cellular life, it's safe to bet that also they evolved in the same environment. In fact, high temperatures are very favorable for RNA catalyzed reactions. This makes the ancient sea floor and a proximity to a hydrothermal vent a good location for the ancient RNA world. There's a really good chapter about such scenario in Campbell Biology, however, I'm far too lazy to look it up.


ps. I'm obviously not claiming any of the above as a fact.

Let us grant the existence of a reduced gas atmosphere to the naturalists for a moment, even though the geologic, chemical evidence suggests otherwise.

2. Even if such an environment existed, what have they really proven with experiments such as Miller-Urey? Are such process' responsible for the mass amounts of small biological molecules needed to populate the ocean or other locations in order for the next step in the chemical evolution process to be successful?

What evidence is there that the process used in the Miller Urey experiment created the correct building blocks of Life? Is there evidence in the sediments of the earth that such a chemical process occurred on the large scale needed for abiogenesis to be viable?

We shall consider some of these questions.

So it has been proven that the Miller-Urey experiment produced a number of amino acids that are critical to the polymerization of the more complex proteins found in the living cell. Does this prove Chemical Evolution to be possible? Many people would say yes. However we must consider every product that was yielded by their experiment, not just the ones pertaining to life. After all, if this really did occur according to natural causes, there was nobody there to pick out the proper amino acids and concentrate them apart from the other products in the hopes that they would correctly polymerise into proteins. Why is this important?

2a. There is a vital problem with the products of every experiment that has been done in the attempt to show how nature could produce the building blocks of Life. This pervasive problem involves the nature of enantiomers or stereoisomers.

What are they? In short, carbon containing compounds (such as those found in carbon based life forms) depending on how many other molecules are present will form as enantiomers into one of two possible stereoisomers which are mirror images of each other but are not identical. The common example is that of the manner in which your right and left hands are mirror images of each other, yet oriented opposite of each other. These enantiomers are chemically identical to each other and as such will react similarly in chemical reactions however they are decidedly different and are referred to as either Left-handed (laevoroary or l) or Right-handed (dextorotary or r). If you still struggle to grasp the concept you can check out the wiki links below.

en.wikipedia.org...
en.wikipedia.org...

The problem this presents for evolutionist or naturalists is that all biological life systems on Earth utilize proteins that have been produced exclusively from Left handed amino acids. Thus far not a single exception to this rule has been found. This is remarkable because outside living biological systems, every natural chemical reaction produces both Right and Left handed amino acids. This remains true for the products of every experiment that has been done, including Miller-Urey.

2b. Miller-Urey produced a variety of simple compounds which included a number of amino acids as well as a quantity of tar. The amino acids which were produced were a racemic mix, containing both right and left handed enantiomers. These amino acids would be useless as building blocks of life for both l and r amino acids would chemically bond in any polymerization activity that resulted. If any protein incorporates even a single dextrorotrary amino acid into its chain, it becomes useless in biological cell systems.

Amazingly enough within biological cells , nucleotides, the building blocks of DNA and RNA, are all found to be in the destro or right-handed form. While all experiments done to synthesize nucleotides from natural process' in the lab have yielded a similarly useless racemic product of nucleotides. An example of this is the work done by Jaun Oro.

An additional strike against the Miller-Urey version of abiogenesis is the large quantities of tar or organic sludge that was produced along with the amino acids. If the process they demonstrated truly accounted for mass numbers of amino acids on the early earth. There should be evidence of even larger quantities of the organic sludge that is produced as a by product. However no evidence has been found for the existence of this sludge anywhere in the geologic column. It should have been produced in large quantities and fallen out into the sedimentation during the entire time they claim the process of abiogenesis was occurring.

2c. Even if we grant that all the correct amino acids and nucleotides were produced in sufficient quantities there is still the problem of how the amino acids would polymerize to create proteins. It is rather amusing that any chemist worth his salt would actually locate the polymerization of proteins from amino acids in the ocean when in fact this is one of the least likely places it would occur. I will explore this in my next post.

Soul

The modern evolutionary synthesis makes no assumptions regarding the origin of life. It explains the biodiversity of life. As such it doesn't need to delve into the origins of life as it depends on life to already be existent. As for abiogenesis no scientist will claim it as 100% fact. That's why it's still a hypothesis. Evidence certainly points to it being the correct hypothesis in regards to the origin of life but there's not enough to elevate it to the level of theory.

So now we have granted the unlikely reduced gas atmosphere as well as given them the benefit of the doubt that All the necessary building blocks of life on a molecular level can be produced via natural chemical process. Disregarding how likely or unlikely it is that all the correct building blocks can be produced in this manner. We shall proceed as if they have.

So now we have what many naturalists claim as near certain fact, that there is a ocean full of the small molecules necessary for building the proper proteins, information holding systems, cellular membranes and the like that make up a biological living cell.

3. How could Information-rich bio-polymers have emerged from this proposed system?
If the Ocean was found to be not suitable for this process, what of other terrestrial locations?
What of extra-terrestrial locations?
What factors contribute to the viability of these sorts of chemical reactions happening?

We shall consider these matters.

3a. Let us first consider the viability of polymerization within the primal ocean. In light of our understanding of chemistry it is frankly incredible that any educated scientist would ever propose the abiogenesis of proteins from amino acids in a large body of water.

The reaction necessary to polymerize proteins from amino acids is called a condensation reaction. This means that two reacting amino acids are joined together into one product molecule called a dipeptide, with the additional production of a free water molecule as a by product. This would then be repeated to attach another amino acid to the chain with the by product of another H2O molecule and so on and so forth to produce a protein.

For a further understanding of condensation reactions read the following.
en.wikipedia.org...

The bottom line here is that in organic chemistry there is something called Le Chatelier's Principle, which in essence tells us that a reversible process (which the joining of amino acids into Dipeptides would qualify) will always progress the reaction in the direction that will maintain equilibrium between the concentration of the products and reactants. Water being a product of this reaction and the ocean being a rather large body of water (i think we can agree on this point) will necessarily push the reaction toward hydrolysis. Put simply, if you dump a bunch of amino acids in the ocean, it is the furthest thing from reality to expect that they will tend toward polymerization into proteins. In fact the opposite will happen, proteins would tend to break down in the ocean, not come together.

Experiments have been done on an aqueous solution with extremely high concentrations of amino acids. Even testing done with a 1 molar solution of amino acids (this is 100 million times the concentration inferred for our abiogenesis ocean.) have been evaluated and to obtain a concentration at equilibrium of a singular protein with 100 peptide bonds(101 amino acids) would require an unfathomable volume of water. They estimated that you would need an ocean with a volume equal in size to 10^229 of the known universe. This is the definition of impossible.

Thus we must look outside the ocean if we are to have any hope for polymerization. What else have the naturalists proposed.

3a Lava rock test tubes.
Sidney Fox conducted an experiment where he tried to melt pure crystalline amino acids in an effort to promote peptide bonds by driving off water from his mixture. He was only able to melt to a liquid two of the 20 amino acids in his original sample (aspartic and glutamic acid). The other 18 amino acids would degrade into a tarry product long before they melted. He then dissovled the other amino acids in the molton aspartic and glutamic acids and the resulting amber liquid contained polymers of amino acids which resembled proteins.

This product he called proteinoids and when it was poured into water it resulted in the formation of spherules of protein like material. He of course likened the spherules to the structure of a living organic cell. He then proposed that a lava rock could be substituted for his test tube and claimed that this process took place on the early earth. Isn't this amazing evidence of the viability of chemical evolution?? Is it??

Consider the following problems with his method.

1.) These proteinoids are not proteins. They contain not only peptide bonds but also many non peptide bonds and other unnatural cross-linkages.
2.) The peptide bonds that are present are beta bonds and not the alpha bonds which are the only type found in biological organisms.
3.) He began his experiment with purified amino acids which would never be found as a material present in nature and yet he claims this represents a plausible process that could occur in nature. If you were to repeat this experiment with a condensed aqueous solution you would have a tar as the only product.

More coming
Soul

Originally posted by SoulReaper
We shall consider these matters.

3a. Let us first consider the viability of polymerization within the primal ocean. In light of our understanding of chemistry it is frankly incredible that any educated scientist would ever propose the abiogenesis of proteins from amino acids in a large body of water.

I agree. However, RNA world hypothesis is the most accepted framework for abiogenesis. That's why the above is somewhat off the mark. Anyway, your posts seem well written. I haven't had the time to read them all through, but I will eventually get there and comment back more. Also, I don't think left-handedness of amino acids is a problem. It's probably due to some fundamental working mechanism of the ribosome (as is the triplet nature of the genetic code).

TextDont have time to dive into the scientific arguments presented here, but I will just offer a general note on the Creationist arguments. FUD Everywhere I look, from online to the ICR Creation Museum, the argument FOR creationism is always presented as a lets throw doubt and uncertainty on science argument.

reply to post by alfa1


That's really really funny , because if you can not offer a viable scientific theory as how it began then it becomes a matter of faith and a pseudo religion . I have said this for a long time Atheism is a religion , evolution is your dogma and the scientists purporting this are your priests .

I will stick with my faith on God and His son Jesus , it is a much more viable explanation especially if you understand the letter God wrote to you through His Prophets and that would be the KJV Bible.

If we have ruled out miraculous lava rock test tubes and the ocean as polymerization locations. What else has been proposed?

Clay?
Ocean vents overcoming hydrolysis?
Extra-terrestrials?
How about Auto catalytic RNA molecules that allow us to bypass the protein polymerization step altogether?

Let us consider these options as well.

3b Clay has been proposed as a structure which could direct the polymerization of amino acids into more complex biologic molecules such as proteins. While the nature of the complex aluminum silicate array found in clay can cause basic amino groups to organize into polymers of several dozen amino acids. There is not much hope here of any meaningful advancement of useful information or of polymers useful to life. If you would like to read further about the naturalist claims regarding the ability of Clay to further their hypothesis you could read (A. Katchalsky, "Prebiotic synthesis of biopolymers on inorganic templates", Naturwissenschaft, Vol. 60, pp 215-220 or A.G. Cairns-Smith, Genetic Takeover and the Mineral Origins of Life)

Non the less this concept still faces insurmountable odds to become a plausible hypothesis. These include

1) They still have not solved how these amino acids were created in the first place with out being destroyed by either oxygen present or extreme UV radiation.

2) Though they have shown ordered amino acids joined by peptide bonds resulting from this method. The product contains no meaningful information. The Biological Cell cannot survive without meaningful information to direct its process.

3) Even if amino acids did survive to make it into the clay, the natural origin of those acids would still promote a racemic mix of right and left handed amino acids which would make any proteins resulting from them useless to biological life.

4) Pure activated amino acids attached to adenine are used in the tests being done. If free amino acids are used, no polymerization results. Adenylated amino acids are not very likely to be found concentrated together into one particular location of a clay surface so as to allow polymers to be produced.

3c) How about thermal oceanic vents on the sea floor?

A Japanese researcher, Koichiro Matsuno demonstrated a concept where by the heat from thermal ocean vents could cause two amino acids to collide together, form a peptide bond.. then be swept away from the vent to cool off before the heat destroyed the newly created bond. Only to then be swept up in to the thermal vent again to join with another amino acid and so on and so forth. The idea being that the energy present at the thermal vent allowed amino acids to overcome the normal forces of hydrolysis that prevent polymerization.

His research was published here (E. Imai, H. Honda, K. Hatori, A. Brack, and K. Matsuno, "Elongation of oligopeptides in a simulated submarine hydrothermal system", Science, vol. 283, pp. 831-833)

Naturalists have latched onto this concept with great excitement, yet with little or no skepticism of whether on not this is a logical and plausible idea. There are a number of problems with his findings. As follows

1) Matsuno fed glycine into his flow system to obtain peptides but his theory does not cover where the glycine came from to begin with. It is just assumed to already be present in the concentrations around thermal vents as needed.

2) The concentration of glycine that he used was a solution of 0.1M which is far higher then any feasible estimate of concentration found in the early oceans. In fact it has been theorized that it could not have been any higher then a 10^-7M which is six orders of magnitude lower.

3) Further even with his unrealistic concentration he yielded at best a hexapeptide with six amino acids. To get this result he used a catalyst of Cu++ ion as CuCl2 which boost the chances of a peptide bond. There is certainly no evidence that this catalyst was present around deep ocean vents. So with factors that don't resemble reality at all he managed molecules with six peptide bonds, while even the simplest Biological proteins have upwards of 100 peptide bonds.

4) Matsuno used the simplest amino acid and the only one which is achiral centre, which means that it has no enantiomer properties. However if he were to add more complex amino acids to his flow system he would undoubtedly end up with a racemic mix of right and left handed enantiomers in the construction of his polymers. Which again has been shown to be incompatible with the construction of biological organisms.


3d) Extraterrestrial Origins
With the difficulties of abiogenesis here on earth, some naturalists have looked to space as the savior of their hypothesis. While I see no need to get into the details unless somebody insists. There are many problems with this grand hypothesis which we could discuss.

I will address the matter of autocatalytic RNA molecules next

Soul

Originally posted by Azadok2day

TextDont have time to dive into the scientific arguments presented here, but I will just offer a general note on the Creationist arguments. FUD Everywhere I look, from online to the ICR Creation Museum, the argument FOR creationism is always presented as a lets throw doubt and uncertainty on science argument.

reply to post by alfa1

 

That's really really funny , because if you can not offer a viable scientific theory as how it began then it becomes a matter of faith and a pseudo religion . I have said this for a long time Atheism is a religion , evolution is your dogma and the scientists purporting this are your priests .

I will stick with my faith on God and His son Jesus , it is a much more viable explanation especially if you understand the letter God wrote to you through His Prophets and that would be the KJV Bible.

Amazing you prove his point with your response using good old "god of the gaps".
Then pull out the even older chestnut of atheism is a religion.

Comedy gold.

You win.

The entire field of study known as abiogenesis is a fraud because we haven't figured it all out yet.

Good thing scientists don't continue researching the unknown, because they might eventually figure out more things.

Scientists should probably just rely on a single textbook written a few thousand years ago, because that would probably answer more of our questions about how we got here.

reply to post by SoulReaper

Free oxygen is highly unstable, which is why oxygen was largely present on Earth in the form of oxides, as noted in your source.

There is no known mechanism where by that oxygen could have been removed from the atmosphere for a time period to have occurred devoid of oxygen and conducive to the chemical reactions required by abiogenesis.

It was removed from the atmosphere by oxidation – obviously. Some of it would form ozone under the influence of ultraviolet light.

Ozone is formed from dioxygen by the action of ultraviolet light and also atmospheric electrical discharges Source

Intense bombardment of direct UV radiation would nearly instantly destroy any amino acids that happened to form in such an environment.

Other gazes besides ozone block UV radiation, and many of these would have been present in the early Terrestrial atmosphere. Murky water is also a good UV blocker.

UV induced photodissociation of water in the upper atmosphere... is theorized (to) be a major source of free atmospheric oxygen.

Taken verbatim from this creationist web page without attribution. The page quotes J.C. Walker's Evolution of the Atmosphere, published 1977. But on p.174 of that book, the author tells us that

Since... hydrogen is produced by the photodissociation of water vapour, we find that the oxygen left behind when hydrogen escapes is removed from the atmosphere by photochemical escape. Jeans escape of hydrogen and photochemical escape of oxygen are balanced so that no change in the oxidation state of the atmosphere results from the two processes.

So the assumption being made is wrong.

Are such processes (as those occurring in the Miller-Urey experiment) responsible for the mass amounts of small biological molecules needed to populate the ocean or other locations in order for the next step in the chemical evolution process to be successful?

Probably, though not necessarily. At this point we do not really know.

There was nobody there to pick out the proper amino acids and concentrate them apart from the other products in the hopes that they would correctly polymerise into proteins.

Here is the heart of your argument. All the rest is easily dismissed. No, we haven't figured out yet how (or whether) amino acids spontaneously polymerise into proteins. The RNA World hypothesis forms one possible answer, based on the concept of simpler replicating organic molecules and natural selection among them to produce RNA, which then mediated the formation of proteins.

All biological life systems on Earth utilize proteins that have been produced exclusively from Left handed amino acids. Thus far not a single exception to this rule has been found. This is remarkable because outside living biological systems, every natural chemical reaction produces both Right and Left handed amino acids.

Since all life evolved from a common ancestor, this is precisely what we ought to expect.

*

No doubt there are difficulties with all hypotheses of abiogenesis, and as long as there are, creationists will try to pick holes in them. What they cannot do is provide a scientifically plausible account to support their own beliefs.

Science will, eventually, build a solid, falsifiable theory that explains the origin of life. For the time being, we can say that the above objections do not come close to exploding the ideas we already have about abiogenesis. They are eminently answerable.

Finally – as has been already pointed out to you a few times, but creationists always seem to need things repeated to them – the theory of evolution is not dependent on an abiotic origin of life.

reply to post by SoulReaper


Maybe this video will be usefull to you or not.

It shows step by step the process which MAY have lead to our current hour. This process seems VERY logical to me and science community. Strange how logic wins over desparate religious ferver....