Abiogenesis - Or Better Living Through Chemistry

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Originally posted by Quetzal:
My post is a synopsis of current research, and is part of a substantially longer essay I've been working on.

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Any plans to post it here when its complete?

[QUOTE]Originally posted by joz:
[B] Q/Doesn`t repeated drying and dillution (as would be experienced on a shoreline) of the biotic soup produce peptide bonded chains that exhibit limited self replication?[B][/QUOTE]

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It do indeed. In fact, Miller et al were sort of relying on this scenario to concentrate the chemistry. Unfortunately, complex long-chain macromolecules break down quickly in the presence of intense UV. Remember that at the ~4gya mark there wasn't any free oxygen (evidenced by ferrous - i.e., non-oxydized - iron in the oldest basement rocks). No O2 = no O-. Without the ozone shield, shoreline pools would be deleterious to these molecules. The only possibility would have been to suppose these reactions took place in the depths of the ocean - meaning that we'd have to assume an even higher percentage of organics in the primordial oceans - a difficult assumption. This is not an insurmountable problem, however. The "snowball Earth" hypothesis permits the concentration of biological macromolecules in shallow water because the ice provides the shielding. The evidence for snowball Earth to date is rather less than compelling, IMHO. ('Course, I'm one of those guys that needs to have his nose rubbed in something before he'll believe it .)

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Originally posted by joz:
Any plans to post it here when its complete?

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Errr, , the original intent was to develop an essay that answered some of the common creationist quibbles - to be posted in a forum such as this, or added to a website. It sort of takes things from the formation of the solar system to the edge of the Vendian and the diversification of bacteria, archaea, and eukaryotes. However, it has mostly become more of a hobby than a serious endeavor. IOW, the odds of ever actually completing it are rapidly growing vanishingly small. Reality check: I use it more as a "mine" for key points when I want to post something like the above. In addition, everytime I turn around there's more information to add...

Quetzal,Out of interest, how many "snowball earth" events were/are alleged?I'm aware of the one just before the Cambrian explosion, & am dimly aware it wasn't the first. My reading suggests it may have been life itself that prevented the next "post" cambrian snowball, due to a change in gas concentrations, particularly oxygen.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 03-04-2002]

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Originally posted by mark24:
Quetzal,

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Out of interest, how many "snowball earth" events were/are alleged?

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I'm aware of the one just before the Cambrian explosion, & am dimly aware it wasn't the first. My reading suggests it may have been life itself that prevented the next "post" cambrian snowball, due to a change in gas concentrations, particularly oxygen. Mark

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Besides the 600-700 mya series of glaciations (the Vendian snowball), I seem to remember Kirschvink claimed evidence for another period of "freeze-fry" series of consecutive disasters occurring 2.3 gya. He's postulating that arrangement of continents was the cause. George Williams (another bloody Australian) proposed that Earth was more oblique up to the end of the Proterozoic, leading to a fairly regular cycle of freezing. I don't think anyone's ever "proved" things one way or the other.Here's a good paper on the "snowball earth" idea: "The Snowball Earth".I don't have an answer for the "why not since?" question. Hoffman's conclusion in the paper seems to indicate there is no intrinsic reason why it couldn't. I don't think I'm going to lie awake at night worrying about it - if the timescales required are correct, the snowball is roughly every 1-1.5 billion years. We've got a ways to go before the next one...

And,to speak rightly, I mean correctly about this grand assymetry that was not a proximate exclaimation of one of Pasteur's students on a location in histology, I, BSM, have given this some thought concluding that if linear inertia be the content of any DNA information then base pariing whether chemcially (acridines) or not is rotation founding the inertia sort that works wholly in nature on the force of torque and could be the physico-chemical matrix from which any morphophemetrics has an acutally as opposed to mere affine geometric reality that may also help in working out in the equations of the electro-tonic state.This merely is the only force I am willing to accept in trying to think about any idea that connect life and non-life. I do not think it myopic. You may?

Good exposition Quetzal
A question: During the time of prebiotic evolution, Earth was under an intense bombardment of spatial debris. Some of the impacts were so big as to evaporate all the water and eradicate the incipient life. Perhaps the possibility of life surviving (or even surging) in subterranean niches, should be added to the list.

Quote by John Paul

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We also have no evidence that DNA can form anywhere outside of a living cell, and the cell itself represents IC (irreducible complexity):

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It looks like only life can beget life.

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Actually, even if it were not beside the point in your arguement it is misleading in another area. RNA and/or RNA analogs have not only been demonstrated to form but they polymerize and can perform a number of catalytic functions. One really neat thing is that these polymers prefer to form in a homodimeric strand.
M. Bolli, R. Micura and A. Eschenmoser, Pyranosyl-RNA: Chiroselective self assembly of base sequences, Chemistry and Biology (1997) Vol 4 no 4 pp309-320
where the chiroselectivity apepars to be more a function of kinetics, probably based on the stabalization from stacking of the pyranosides.Another good one is
JP Ferris et al, Synthesis of long prebiotic ligomers on miernal surfaces, Nature 1996, vol 381 pp59-61.Sorry John Paul but you are rather behind on the research.------------------
"Chance favors the prepared mind." L. Pasteur
Taz

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Originally posted by Andor:
Good exposition Quetzal
A question: During the time of prebiotic evolution, Earth was under an intense bombardment of spatial debris. Some of the impacts were so big as to evaporate all the water and eradicate the incipient life. Perhaps the possibility of life surviving (or even surging) in subterranean niches, should be added to the list.

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Thanks Andor. I do remember reading something about that theory - do you have a link or reference? I seem to remember not being that enamored of it, at least for OOL, because the authors sort of glossed over any mechanism for concentration of precursor molecules. There's no question that during the Hadean period cometary and debris impacts could very easily have wiped out any potential replicators. The impact that created the moon nearly cancelled the entire experiment. However, by about 4 gya, most of the major impacts were over (based on moon samples, IIRC). With the bombardment period over, the atmosphere stabilized, the dust settled, we have the first Dawn, and life can start rocking.

Quetzal, I've read two books on the matter: "The deep hot biosphere" by Thomas Gold, and "The fifth miracle" by Paul Davies. There are some Astrobiology web pages that mention the hypothsesis: http://www.pathwaysforinquiry.com/studentpapers/wallacebigidept2.htmlhttp://waynesword.palomar.edu/ploct97.htmhttp://www.spacedaily.com/news/life-01zd.htmlI have read somewhere that big sterilizing impacts could have lasted as late as 3,8 billions years ago. Any way, if by 3,5 billion years forms of life as complex as cyanobacteria (stromatolites) were already present, the time for life to evolve seems a little scarce. Here is where the possibility of life surviving underground fits nicely.

[QUOTE]Originally posted by Andor:
I have read somewhere that big sterilizing impacts could have lasted as late as 3,8 billions years ago. Any way, if by 3,5 billion years forms of life as complex as cyanobacteria (stromatolites) were already present, the time for life to evolve seems a little scarce. Here is where the possibility of life surviving underground fits nicely.[/B][/QUOTE]I read a couple of articles concerning the last big group of impactors, and by big group I mean what are generally called sterilization events, and I remember a range of 3.8 to 4.1 Byr ago. That would have given life (not killed) by the impactors 300 to 600 million years to start. Several of them concerned the generation of organics through the heat of impact, this one is the only reference that I still have Nature 1992, 355: 125-132. If I can find the originals I will post references to them.------------------
"Chance favors the prepared mind." L. Pasteur
Taz

[QUOTE]Originally posted by Quetzal:
[B]Apologies in advance for the length of this post. Enjoy!Even though abiogenesis — the origin of life from non-life — is not related to the validity or falsehood of evolutionary theory, it is an interesting subject in its own right. Although evolutionary theory does not rest on the truth of abiogenesis, creationists in particular seem to demand that a non-supernatural origin of life be proven before evolution can be accepted.I suppose your right, there is theistic evolution. But surely, if, hypothetically, it becomes clear that abiogenesis is not feasible by natural means, then there is no reason to accept materialistic evolution. Once a Creator is established as a neccessary condition for life, would not Creation make a lot more sense than evolution?Quetzal: The modern chemical composition of the Earth is mostly Fe, Mg, Si, and O, with the other elements contributing 5% of the total. Life originated as a result of chemical reactions occurring (largely) in the atmosphere followed by reactions in the primeval oceans and lakes. The atmosphere at the end of the Hadean Period (~4-4.2 gya) is primarily composed of variable amounts of CO2, N2, SO2, H2S, S, HCl, B2O3, and smaller quantities of H2, CH4, SO3, NH3 and HF (but no O2), due partly to outgassing from volcanoes, and partly to the reaction of condensing water vapor (formed as the Earth cooled) with minerals such as nitrides (hence NH3), carbides (hence CH4, CO, etc.) and sulfides (hence H2S). There was no free oxygen (any free O2 ...Bart007: What if there was free O2, would that have any adverse affect on the formation of life's molecules, or are you simply pointing out that there simply was not any O2 in the prebiotic atmosphere?

Bart - these are both excellent questions that deserve a response longer than I have time for (I'm jumping on a plane in about an hour, and have to finish packing). However, I didn't want to you to think I was ignoring your post. If you'd like, I'll try and respond more substantively when I return. In the interim, hopefully someone else will pick up the slack.

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Originally posted by Bart007:

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Q: Even though abiogenesis — the origin of life from non-life — is not related to the validity or falsehood of evolutionary theory, it is an interesting subject in its own right. Although evolutionary theory does not rest on the truth of abiogenesis, creationists in particular seem to demand that a non-supernatural origin of life be proven before evolution can be accepted.

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B: I suppose your right, there is theistic evolution. But surely, if, hypothetically, it becomes clear that abiogenesis is not feasible by natural means, then there is no reason to accept materialistic evolution. Once a Creator is established as a neccessary condition for life, would not Creation make a lot more sense than evolution?

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Hypothetically? "Creation" and a "creator" isn't necessarily the default hypothesis if chemical abiogenesis is "proven impossible". I suppose it could be one of the hypotheses. OTOH, in this case (where abiogenesis is impossible for some reason), positive evidence must be presented to support the creator version. IOW, you can't validate a theory by falsifying another. You can only validate a theory by providing positive evidence for it. Falsifying abiogenesis does nothing except falsify abiogenesis. It doesn't validate creationism. (sorry for the short answer)

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Q: The modern chemical composition of the Earth is mostly Fe, Mg, Si, and O, with the other elements contributing 5% of the total. Life originated as a result of chemical reactions occurring (largely) in the atmosphere followed by reactions in the primeval oceans and lakes. The atmosphere at the end of the Hadean Period (~4-4.2 gya) is primarily composed of variable amounts of CO2, N2, SO2, H2S, S, HCl, B2O3, and smaller quantities of H2, CH4, SO3, NH3 and HF (but no O2), due partly to outgassing from volcanoes, and partly to the reaction of condensing water vapor (formed as the Earth cooled) with minerals such as nitrides (hence NH3), carbides (hence CH4, CO, etc.) and sulfides (hence H2S). There was no free oxygen (any free O2 ...

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B: What if there was free O2, would that have any adverse affect on the formation of life's molecules, or are you simply pointing out that there simply was not any O2 in the prebiotic atmosphere?

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Neat question. I'm not really sure I have the answer to that - my guess would be that significant free atmospheric O2 would change the chemistry postulated as necessary for what are thought to be the first replicators. Until the much-later-appearing cyanobacteria evolved the capability to synthesize superoxide dismutase around 2.2-1.9 gya, significant free 02 would have been pretty poisonous - as in fact it was (look up the "oxygen holocaust" in the mid-late Proterozoic - a lot of prokaryote families went extinct, and even the cyanobacterial families which had not developed this capability were also strongly effected).OTOH, chemical analysis of the lowest basement rocks show the presence of non-oxydized iron (greenstone or banded iron formations) - indicating that whatever 02 was available either through outgassing or dissociation of water and other compounds was pretty quickly snatched up by other elements. It wasn't until the cyanobacterial waste built up in the atmosphere that we see evidence of free 02 (about 2-3%). There are a couple of very good geologists on this board that might be able to provide details.Sorry about the short and reference-less reply. I really do have to run.

I thought most exobiologists today now believe that it wasn't a reducing atmosphere? As John agrees at this site?

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For a long time it was thought that the early Earth had a reducing atmosphere. A reducing atmosphere contains reductants, or molecules saturated with hydrogen atoms, which are able to reduce other molecules. Many scientists believed that the atmosphere consisted of CH4, NH3, and H2. This is the mixture of gases Miller and Urey used in 1953 to mimic the conditions of the early earth. Their experiment showed that abiotic molecules could be used to create important biotic compounds thought to be necessary for the origin of life.

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However, most of the scientific community now believes that the early Earth's atmosphere was not reducing. Instead, scientists beleive the atmosphere was full of oxidants, such as CO2 and N2. An oxidizing atmosphere is essentially neutral, and does not permit organic chemistry to occur.

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There is much known about the environment and composition of the early earth. However, there is even more which is uncertain and not known. Because of this, scientists are studying and searching for the conditions which they believe were present when life began. If we know these conditions then perhaps we can discover the building blocks from which life came. --http://www.chem.duke.edu/...ise_chem/Exobiology/PBearth.html

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[I got this site off John]

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Originally posted by Quetzal:

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Originally posted by joz:
Great post Quetzal, thanx.....

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Q)I was under the impression that one of the problems with The Biotic Soup Hypothesis of abogenesis was the low abundance of sugars produced and the lack of long chain fatty acids (in the Urey/Miller experiments). Has anything new cropped up that makes this less of a problem?

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Wow, try and get some work done for one day, and look what happens! I'll try and answer everyone's posts (or quibbles) as I get the opportunity.

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Anyway, joz, you're absolutely correct. One of the crucial problems with the experiments was their apparent inability to synthesize complex sugars, specifically ribose. Ribosomal RNA, of course, was the autocatalytic self-replicator that Cech discovered. It wasn't so much that they didn't get sugars or that the chemistry wasn't correct (after all, you get HCHO forming photochemically in the atmosphere today, then by Formose reaction you get isomers like formaldehyde (CH2O)6 [detectable in modern rainwater]. It's a fairly simple step to re-arrange things into C6H12O6). Getting from there to ribose is mostly a question of concentration and energy with the right catalyst.

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Miller's biggest problem was (and remains) trying to get rRNA to form spontaneously. That and the fact that RNA couldn't be the first replicator simply because it is really unstable and formed in very tiny quantities. It wasn't until only a couple of years ago that it was found peptides (which are REALLY easy) were able to bond to the 5' site on the nucleic acid forming a stable hybrid polymer: pRNA.

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You still have major problems with concentration and getting the nucleic acids to line up properly - something that hypothesis 2 and both 3's accomplish by using inorganic templates. Fe4S4][SFeS]2), which is structurally identical to the active center of ferredoxin (the Fe4S4).

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Dear Quetzal.I believe every experiment you refer to was intelligently designed and controlled to get the intended results. That none of these experiments were every done replicating actual prebiotic atmosphere conditions. Peptides may form easily in the presence of amoni acids, but none that are of any use to life.To make life, we need amino acids, sugars, bases, and phosphates. This gives us other catch 22's. You need formaldehyde to make sugars, but formaldehyde fixes amino acids so that they do not react. Methane
polymerizes formaldehyde, but must be present to make amino acids.
Amino acids plus bases destroys formaldehyde. Calcium and magnesium in
our oceans destroy phosphates, you can't get phosphates in oceans. Heat needed to make amino acids also destroys the amino acids.You have presented abiogenesis in the best light possible. I will post a new topic on abiogenesis and which will reflect why I believe abiogenesis is impossible as based upon scientific considerations only.I will write a second topic