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Author
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Topic: Answering: The advantages of theft over toil
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Jerry D. Bauer
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Member # 756
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posted 21. May 2004 22:35
Evan. Sorry about that, I haven’t posted in here for a while.
I feel that UPBs are very relevant. And really they are little more than common sense.
There has do be some figure where the odds are so staggeringly against something happening that it will, in effect, never happen.
As a chemistry major, I was taught there is an UPB in which no chemical reaction can occur even in 50 billion years. Considering those things that must be considered in order for a reaction to occur which you re-list in this post, heat, cold, proximity of atoms, speed of moving atoms, etc. There is a UPB of 10^-67 where chemical reactions cannot and will not occur, even though there may be 1 chance that they can.
You know well by now that Idists are obsessed with flipping coins. Doesn’t take that much to entertain us. ![[Wink]](wink.gif)
So let’s consider this again. You are flipping the amount of coins that the UPB is 10^-150 that all of these coins will turn up heads. Well, isn’t there still a 1:10^150 chance that all of them will turn up heads? On paper, yes. But in reality, no way.
Because the stark reality of you doing this is impossible. If you could somehow supernaturally flip a coin once a second, there still are only 4.6 x 10^17 seconds in the universe since the big bang.
Stickability does not alter probability mathematics because the overall calculation must be performed before any events begin.
If we were studying statistical entropy or simple coin tossing we still will always have the overall amount of reactants whether they are proteins, skirknobs or coins. And I believe this figure will be the one which must always be used to calculate probability.
My point is, that in the coin analogy I showed the exact same probability in 100 coins tossed together at the same time as for those 100 coins in which stickability occurred with me flipping every one of them independently of the others. Either way the odds are 1:(.5)^100. When we calculate the statistical entropy of both systems, that figure would also be the same S = log2(100).
Further in your post you point out that I fail to account for natural forces that must be considered if we are to calculate probability.
May I remind you that the first tenet of the EF is to consider if natural law could have played a role in the existence of a system?
I dutifully (being a rather devoted Idist) excluded natural law before I did any calculations.
Remember that we were calculating protein probabilities. While there ARE natural reasons that amino acids react together, I know of none that would cause proteins to assemble together.
Many amino acids are polar and opposite charges will attract them to each other. But can the same be said of proteins?
No, because proteins formed with the proper chirality in nature are assembled by preprogrammed intelligence--ribosomes, mDNA and the such
I think that your Yahtze analogy is the same system proposed by Charlie-d in that you are using intelligence to get to a goal. Give yourself enough throws and you will achieve your goal of all 5 dice being the same 100% of the time because you are intelligently deciding which dice to throw, or not throw. And your probability math will be the same every time it is your turn to roll the dice. 6 numbers, 5 dice and three throws.
I don’t agree that things formed by chance almost immediately fall apart by chance. Mountains are formed by the chance forces of the natural process and many of these are very old. I don’t know if you’re an Idist or a detractor as I haven’t conversed much with you. But you are asserting that intelligence ‘caused’ that first organism because had it formed by chance, it would have just immediately fell apart.
Finally, I fear that if you are to refute or add to the math I presented you will have to do so mathematically. And if you are to show that I failed to account for the laws of chemistry and physics, you are going to have to get specific, state what those laws are, and how they operate in nature.
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Jerry D. Bauer
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posted 21. May 2004 22:59
Well, I have no way to know WHAT those papers show or do not show since I can’t find them to read. Would you please post links to your references? Or email them to me when you cannot? I will do the same for you.
But I’m afraid your analogy of layers of gravel, sand and clay are different phenomena than protein assembly accomplished by the intelligence of ribosomes and mRNA.
Quartz and Calcite are not intelligent. I agree. I was referring to the system you designed which DOES necessitate intelligence. The system that would keep all heads and reject all tails until all of the coins are heads.
We Idists use the word design a bit differently than the dictionary definition of the word. We realize there exists such a thing as the natural design you are referring to--deposits, mountains and sand dunes created via uniformatarianism or catastophism and another type which must arise by intelligence, such as a car, skyscraper or a bob cat. This is where mathematical analysis come into the picture.
The proteins we were discussing are excellent examples of the latter type of design.
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Evan
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posted 21. May 2004 23:21
Jerry, I believe that you are missing some of my points.
1) You write,
quote:
My point is, that in the coin analogy I showed the exact same probability in 100 coins tossed together at the same time as for those 100 coins in which stickability occurred with me flipping every one of them independently of the others.
There is nothing “stickable” about your example, analogous to the rules of my Yahtze example. Obviously I am using this “bonding” rule to be analogous to the rules, embedded in physics and chemistry, by which molecules build up naturally from simpler elements.
The fact that amino acids do stay assembled in a protein shows that there are chemical forces which cause them to do so, and therefore there are chemical forces which were must be considered as possible forces at play in early interactions. Saying that these were “assembled by preprogrammed intelligence--ribosomes, mDNA and the such” entirely begs the question, because the question is the ways in which ribosomes,mDNA, etc. might have been formed themselves.
Also, there is nothing analogous to steps - multiple throws in Yahtze, in your example. As I took pains to point out, when there are steps at the junctures of which laws can operate, then you get probability trees, not simple multiplicative probabilities. The fact that you get part way to a Yahtze at one step and then build on that on the next step is exactly opposite the independence of the coin flips that you point out.
You also object that in my Yahtze example
quote:
you are using intelligence to get to a goal. Give yourself enough throws and you will achieve your goal of all 5 dice being the same 100% of the time because you are intelligently deciding which dice to throw, or not throw.
But as I explained, the “intelligence” of the player can be replaced by simple mechanical rules that are analogous to the laws of chemistry. It may very well be that the laws of nature were designed in order to make interesting chemical interactions possible through natural processes - as charlie says, that is a metaphysical position that goes beyond what is being discussed here.
But that is not the question here - the question here is whether the pure chance hypothesis has any relevance to the real world of biology. My claim is that due to the existence of very complex possibilities for interaction in chemistry, the pure chance hypothesis is not meaningful.
You also write,
quote:
May I remind you that the first tenet of the EF is to consider if natural law could have played a role in the existence of a system?
I dutifully (being a rather devoted Idist) excluded natural law before I did any calculations.
An interesting observation. If this is your understanding of the EF, then of course you are left with nothing but chance to consider. You seem to be saying that a “devoted IDist” is one who excludes natural law from the start, not because it is ruled out but because that is consonant with the inference of design you wish to reach.
That is not how the EF is intended to work, The EF eliminates design by showing, positively, that the event in question is not one that has been formed by natural law - that is, it proposes to examine all possible natural pathways and show that the probability of each is so low that each is eliminated. It is quite circular reasoning (and I’m beginning to understand this a little better) to eliminate natural law as a cause by excluding it right from the start, and therefore prove design by assuming that chance is the only alternative.
You write,
quote:
While there ARE natural reasons that amino acids react together, I know of none that would cause proteins to assemble together.
The question is not whether you know of such laws - the question is whether people studying these matters know of situations (whole complexes of environments and laws spread over periods of times) by which natural causes might be at play. The fact that we don’t know exactly how this happened is not sufficient cause to claim that no laws were at play at all, and that only chance was involved.
And last you write,
quote:
Finally, I fear that if you are to refute or add to the math I presented you will have to do so mathematically. And if you are to show that I failed to account for the laws of chemistry and physics, you are going to have to get specific, state what those laws are, and how they operate in nature.
Hmmm. I am not “refuting your math” by showing that you have done your calculations wrong, I am “refuting your math” by showing that it does not correctly model the real world. To do so, I do not have to know exactly which chemical reactions acted when, where, and how. Just because we do not know exactly what natural laws were are work 3.5 billion years, over a period of many millions years, is not a justification for therefore declaring that no natural laws at all were involved and that therefore the pure chance hypothesis is valid.
[ 21. May 2004, 23:33: Message edited by: Evan ]
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charlie d.
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posted 22. May 2004 08:46
I don't understand while random assortment has to apply to aminoacids, but not to sedimentation of gravel, sand and clay.
You are just arbitrarily excluding from consideration the possibility of all kinds of known natural laws that can result in homochiral assembly of oligopeptides, while accepting the laws of sedimentation.
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Jerry D. Bauer
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posted 22. May 2004 16:30
Evan, I’ll get to your post later today. Charlie-d’s is short and sweet.
*****I don't understand while random assortment has to apply to aminoacids, but not to sedimentation of gravel, sand and clay.*****
In the long run, its not the assortment of amino acids we need consider, but protein assembly. The latter is not random, its accomplished by intelligently preprogrammed DNA. Are you aware that a human dermal cell contains more information than all 30 volumes of the Encyclopedia Britannica? This is not analogous to forming mountains by random natural forces because that mountain can take many shapes, but considering protein assembly in the initial protist, you get one chance to get it right.
*****You are just arbitrarily excluding from consideration the possibility of all kinds of known natural laws that can result in homochiral assembly of oligopeptides, while accepting the laws of sedimentation.*****
I’m excluding those because I’m not aware of those laws. I asked you both to tell me what they are so we can discuss them. I can’t discuss them if I am ignorant of them, can I?
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charlie d.
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posted 22. May 2004 20:02
quote:
I’m excluding those because I’m not aware of those laws. I asked you both to tell me what they are so we can discuss them. I can’t discuss them if I am ignorant of them, can I?
There you go. That's exactly where the problem is.
Before writing what you seem confident is the definitive refutation of abiogenesis scenarios, it would really help if you familiarized yourself with what those scenarios actually are, which is really only a simple Pubmed search and a visit to the nearest university library away.
As for those papers, should you actually attempt to get them, you'd find out that 2 of them are in fact freely available. Regardless, they are just the tip of an iceberg of peer-reviewed articles which any serious critic of abiogenesis should at least try to have an understanding of.
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Rex Kerr
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posted 22. May 2004 21:05
To properly apply the filter, you need to consider all relevant laws and chance hypotheses. If you avoid considering some laws because you are unaware of them, then you cannot properly apply the filter. (I am not saying that you are necessarily trying to apply the filter, just pointing out that it's impossible to follow the procedure when one is ignorant of relevant laws. Since the original thread was a criticism of an article by E&W where one of their points was that people would conclude design by ignoring relevant laws, this seemed a relevant comment.)
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Jerry D. Bauer
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posted 22. May 2004 23:39
But in one of my coin toss examples something like 47 heads became stuck, or stabilized into the system just as two or three of your dice did. Is there something about the Yahtze analogy I’m not understanding?
I’m aware you are using this analogy to show certain rules in chemistry and physics, but rather than analogous scientific rules can’t we just get to the ones you are referring to? Quite frankly, you seem a little vague on them and I would like to know what they are so we can cut to the meat of the matter.
The fact that amino acids bond together and often stay bonded are due to electrical charges. But we are not discussing the amino acids themselves, but the protein polymers they form. I think you’re going to have to show me what laws of science would cause these to suddenly jump together (or even form over time together) in order that a organism can form.
I also am curious as to how you believe ribosomes for protein assembly might have ever formed in this first organism when before this organism there was no reason for proteins to assemble. I suppose the same question might be asked of mRNA.
What are these probability trees you refer to? Please use one of them to demonstrate how they are relevant.
Evan:
*****But as I explained, the “intelligence” of the player can be replaced by simple mechanical rules that are analogous to the laws of chemistry. It may very well be that the laws of nature were designed in order to make interesting chemical interactions possible through natural processes - as charlie says, that is a metaphysical position that goes beyond what is being discussed here.*****
This is just too vague to be intelligently addressed, Evan. WHAT simple mechanical rules. I’m afraid you are going to have to list them if we are to further the discussion on this.
And I’m not left with ’only chance” unless the EF concludes this. If there is law to consider, I will consider this and the EF will detect it. If the odds fall below the UPB the filter will detect chance, if the odds soar above the UPB, the EF detects design.
This is nothing new in science. Dembski just took an old concept, explained it well, defined it better and it works.
I’m afraid I would have no earthly idea of what you mean by the EF eliminates design, it only eliminates it if the math shows that design must be eliminated. And if in our particular incident natural law prohibits us from going forward, what is this natural law?
Finally, you conclude that just because I don’t know what natural law would have taken place to ’cause’ this event I must surmise one. I don’t agree. You are going to have to state these laws and define them, I’m afraid.
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Jerry D. Bauer
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posted 22. May 2004 23:50
***To properly apply the filter, you need to consider all relevant laws and chance hypotheses. If you avoid considering some laws because you are unaware of them, then you cannot properly apply the filter.*****
Fine. But you guys are going to have to point out what laws and chance hypothesis I should be considering, aren’t you? Can you see that all three of you are positing that I fail to apply laws where there is no law? If the debaters on your side know of a law that would cause proteins to jump together, pray tell the others what this law is.
Please list them so we can discuss them.
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Rex Kerr
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posted 23. May 2004 04:26
But I probably don't know the relevant laws either. The filter doesn't say, "ask people for relevant laws and if they don't know them, there aren't any". It asks for an awful lot--it asks for you to know that there aren't any relevant laws, which means you must understand the physics and chemistry of the situation extremely well (or at least well enough so you can put bounds on what can happen, followed by a demonstration that nothing within those bounds will work).
The difference between Evan's example and Jerry's coin flips is that in Evan's example, you get to roll multiple times. In Jerry's example, you only get to try once. Reality is more like Evan's example: things happen over and over again, with some of what has happened being preserved.
Let's suppose you're trying to get a certain set of 500 coin flips in a row. The probability of doing this in one try is 2^-500. But--and this is the point of Dawkins' "METHINKS IT IS LIKE A WEASEL" example--if the "correct" coins stick and the rest fall out, and we flip the ones that fall out, we can improve these terribly low odds.
The first time, about 250 coins will be in the right orientation in their spot and will stick, and 250 will fall out. The next time, about 125 of 250 will be right, and then about 62, and then about 31, and then about 16, 8, 4, 2, 1, and then we have one coin left which we can flip a few times until it sticks. So after about 16 flips, we have got the exact sequence with a very high probability (about 99%).
Now, if you flip all the coins 16 times, you have a probability of approximately 16 x 2^-500 = 2^-496 of getting the exact sequence.
What a difference keeping partial results can make!
So, back to chemistry. Do conditions on the surface of the earth produce racemic mixtures of proteins? Were early reactions protein-dominated, RNA-dominated, peptide nucleic acid-dominated, or dominated by some other species? Can proteins work if they're mixtures of L and D amino acids? Can they self-catalyze? How effective is a short polymer of whatever was there at self-catalyzing? (That part is equivalent to coins sticking, since if you can get a short bit that self-catalyzes, you can add to it rather than starting randomly from scratch again.) And so on and so on.
My answers to these questions are: don't know, don't know, probably yes, probably no but short RNAs can self catalyze, don't know.
But as the sticking coin-flip example shows, you need to know these things to calculate the probability, or you can get an error in your calculation as large as the UPB. So the filter says: you must know, you must know, you must know, you must know, you must know.
Therefore, I can't apply the EF to abiogenesis. I don't think there are any really compelling theories of abiogenesis out there--there are some intriguing ones, but they're more at the level of "interesting ideas" than "thoroughly supported historical facts". So scientifically, about all I can say about abiogenesis is that I know that I don't know enough to draw a conclusion about what happened, and I am pretty sure that not enough is known for anyone to legitimately draw a conclusion.
Added in edit:
As a result of this lack of knowledge, people who boldly proclaim an RNA world don't have that much more to stand on than IDists who boldly claim that the origin of life must have had intelligent intervention. The difference there is that the RNA world people can do additional experiments to advance our understanding of early chemical conditions, which may support the RNA world hypothesis, or may show that it's wrong and point at what's right. But the IDists, upon claiming design, have a much less clear path to follow.
Nobody should be drawing a solid conclusion, but the RNA world people even if wrong will make progress towards the right answer (even if the answer is design!--since they will be learning more about the relevant laws necessary to apply the filter). I'm not convinced that the ID answer will lead to progress towards the right answer. So as a practical matter, I prefer the traditional materialistic abiogenesis answer since we really don't know on the basis of evidence, but even if we're wrong, assuming that answer will likely lead us in the right direction.
(There are inductive reasons to expect that abiogenesis was materialistic, but that's a little too subjective to be knowledge--it's more of a belief at this stage, and different people have different beliefs about what to apply induction to.)
[ 23. May 2004, 04:34: Message edited by: Rex Kerr ]
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charlie d.
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posted 23. May 2004 08:48
quote:
Fine. But you guys are going to have to point out what laws and chance hypothesis I should be considering, aren’t you? Can you see that all three of you are positing that I fail to apply laws where there is no law? If the debaters on your side know of a law that would cause proteins to jump together, pray tell the others what this law is.
Please list them so we can discuss them.
Jerry, there is no substitute to hard work. If you are interested in abiogenesis, go read the relevant literature, and critique what's there. Asking a bunch of guys on the internet to please digest a quarter century of modern abiogenesis research in a neat little post for you simply does not cut it. Educate yourself. Until you do, your calculations are meaningless.
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Jerry D. Bauer
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posted 23. May 2004 18:28
But I do know there are not any laws that would cause proteins to come together within an organism before there were ribosomes and mRNA. I’ve studied chemistry and physics. It’s the people debating me on this thread that claim these laws exist, or might exist. Shouldn’t it be up to them to state what they are?
I would think it might even be dangerous to scientific truth to surmise that laws exist where we have no evidence to suggest this.
REX:
*****The difference between Evan's example and Jerry's coin flips is that in Evan's example, you get to roll multiple times. In Jerry's example, you only get to try once.*****
Actually the difference between our two analogies is that Evan bases his on intelligence and mine is based on chance.
You’re also using intelligence with your coin flips. If I get to keep the coins I want and keep flipping the ones I don’t, I’ll have a 100% chance of reaching the goal. You guys can go with intelligence for this initial design if you want, I’m an Idist and you probably won’t get much argument from me.
Let’s see if I can answer your questions for you, or at least take a stab at it:
In your first question I’m not sure if you mean racemic amino acids or chiral proteins. But I’ll run with the acids. The answer is yes. Amino acids found in nature are racemic. And the ones Miller produced were racemic. The chirality of the amino acids we are built from are only L or only D depending what tissue we are examining. Interestingly, when an organism dies, its amino acids decay into the D form until an equal amount of L and D are present. And weirdly, in a meteorite only a slightly racemic mixture was found. I’m aware of one where a 9% dominance of Ls were discovered.
EDITED to add, depending on who you are reading.
These guys say this: "all living organisms are now composed predominantly of L-amino acids. Nobody knows why, where and how nature selected L-amino acids, or whether the selection of L-amino acids had a logical reason or was a chance occurrence. However, it is clear that only one of the enantiomers could be selected because polymers which consist of many diastereoisomers of amino acids would not be able to be folded into a proper structure like a current protein. Therefore, homochilarity is essential for life. Once the L-amino acid world was established, D-amino acids were excluded from living systems. For this reason, the presence of D-amino acids in living organisms has not been studied in the life sciences for a long time. However, D-amino acids were recently detected in various living organisms in the form of free amino acids, peptides, and proteins."
http://hlweb.rri.kyoto-u.ac.jp/fl/eng/english.html
We must assume that early life is not much different than lower order life (not the right term, but I think you’ll get it) we see today because we have no evidence to show the contra. Plus, if common descent occurred, then one is necessitated to assume it was similar to our cells.
No, proteins cannot work in our cells constructed of racemized Aas.
There is little or no scientific evidence that proteins can self catalyze in nature from the papers I‘ve examined on it and short polymers are relevant to life but not by themselves. Some proteins in muscle tissue run up 27,000 Aas.
The bottom line here, Rex, is that the laws of physics haven’t changed since day one. Oh, we learn more about them over time and discover quantum mechanics and the like, but there were no laws back then that we don’t have today.
It’s interesting that you note that no one knows what happened back then and this is true. But we can use science and math to push and probe and we can calculate the possibilities to suggest what happened. I feel that’s all I’m attempting.
But don’t you feel that if the truth of origins is ever derived it will be by Idists not afraid to think out of the Darwinian box? I certainly do.
[ 23. May 2004, 19:35: Message edited by: Jerry D. Bauer ]
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Rex Kerr
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posted 24. May 2004 06:23
Jerry said
quote:
Actually the difference between our two analogies is that Evan bases his on intelligence and mine is based on chance.
But Evan explained how physical law could substitute for intelligence.
In my coin flip example, maybe the target is all heads, and maybe the material is ferromagnetic and the coins are actually dipole orientation of local domains during a cooling phase.
So Jerry may want to re-evaluate what the difference is.
Jerry claims
quote:
I do know there are not any laws that would cause proteins to come together within an organism before there were ribosomes and mRNA.
If we take a current organism and throw away all the protein synthesis machinery, obviously no proteins will get made. But if we stick in, somehow, a solid-phase peptide synthesis cycle using t-Boc, trifluoroacetic acid, and so on, we could do it. (We certainly use that method labs to synthesize peptides.)
Early chemistry wasn't like the inside of a cell with the protein synthesis machinery ripped out, and it wasn't like the inside of a solid-phase protein synthesis column. What was it like?
I think the key problem is in this statement:
quote:
We must assume that early life is not much different than lower order life (not the right term, but I think you’ll get it) we see today because we have no evidence to show the contra.
But this isn't a good assumption to make. We know that conditions were drastically different then--no oxygen, lots of different chemicals, no life on the surface!
If we flip the question around, it would be stated like this: the first self-catalyzing polymeric reaction to exist would multiply and continue essentially unchanged through four billion years of Earth's history through a number of dramatic changes in the planetary environment. That sounds pretty unlikely, doesn't it?
Therefore, the assumption we should make is that we don't really know what early life was like past a certain point. (We can guess parts of it from homologous genes shared by different kingdoms.) I'd say we can be pretty sure that it was fairly different from anything alive now, given how different the conditions were. But it's hard to know just what the differences were.
I've studied chemistry and physics too. I agree that physical laws haven't changed, but physical conditions have.
I don't even know what reactants I should be starting with. Do you? If so, how do you know? If not, how do you know the reactants can't react to give self-catalyzing polymers?
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Daniel S. Rose
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posted 10. September 2004 18:58
If I may jump in on a single point, as far as I'm aware, oxygen levels of the atmosphere and oxidation of the lithosphere of early earth is controversial. While the level of C02 seems more accepted and doesnt contribute much to the success of abiogenesis theories.
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Jerry D. Bauer
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posted 23. February 2005 07:49
Readers: Please note that Dr. Elsberry has rebutted my refutation of the paper here
[ 23. February 2005, 07:50: Message edited by: Jerry D. Bauer ]
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