A Question on Abiogenesis

[Wavicle]

My point is that there was confidence in the scientific community during the 1950s that things were falling into place nicely for the creation of life to occur in a laboratory. And, if the universe were truly random, there is no reason to believe that it would not have. Now, however, after massive technological progress during the past 54 years, we appear to be back to Square One when it comes to creating life. Doesn't that make you wonder just a tad if the creation of life really was a random process?

To be fair, we really do not know how life began. In the 1950s the belief was that the fundamental component that started life on earth was amino acids. There is an increasing suspicion that amino acids are just a very advantageous mutation. So advantageous that protein-using life completely out competed non-protein-using life.

The fundamental component is now suspected to be RNA. One strong piece of evidence for this is that the ribosome, the guy who translates RNA into peptides, is mostly RNA (well, the functional parts anyway). The hypothesis is that ribosomes are very primitive and still contain components from a time when all organelles were made up of RNA. In fact the ribosomes of eukaryotes and prokaryotes are quite similar to one another.

Thus the hypothesis of the 1950s was probably wrong. Having lots of amino acids hanging around is nice, but not likely to start life. So yeah, when it turns out we were barking up the wrong tree, we do have to go back to square one, BUT we now know which direction NOT to take.

 

[Schneibster]

My problem with your analogy is that it's clear that if you throw two dice enough times snake eyes eventually will come up. However, it's not clear that life from non-life will ever come into existence from a random process. So, first you need to show that such an event is possible.

Oh, really? Why is it not clear? I guess I'm not quite clear on why you think it's not clear. Why don't you be specific about that.

Why do you say that the 1950s understanding of physics was far from reality? It seems to me that what has happened since that time have been refinements, rather than a revolutionary new approach.

Oh, really? Do you know what renormalization is? Did you know that it was not proven physically justifiable until the 1970s? Do you know what the Weinberg-Salam-Glashow electroweak theory is? Have you ever heard of quarks? Are you familiar with quantum chromodynamics?

None of these things except renormalization were even conceived in 1960, much less 1950- and Feynman and Dirac argued against renormalization until the 1970s. And if you don't know about these things, not only can you not be a physicist today, but you don't even understand what experimental physicists are DOING today. And you don't even want to have nightmares about the theoretical physicists; they're off inventing new branches of mathematics because the mathematicians didn't pay enough attention to what they were doing in the 1960s, 70s, 80s, and 90s. In both experimental and theoretical physics, the differences between each of those four decades are as stunning as the difference between 1899 and 1901; before the beginning of the twentieth century, physicists thought they had everything all figured out; by the end of the second year of the new century, the foundations of quantum mechanics and relativity had been laid, and nothing would ever be the same.

The progress of technology and science is accelerating; but that doesn't mean it's infinite. But boy oh boy has a hell of a lot of water gone under the bridge since 1995, not to even TALK about 1965 or 1950. That was like, the Stone Age or something.

My point is that there was confidence in the scientific community during the 1950s that things were falling into place nicely for the creation of life to occur in a laboratory.

No, that's not your POINT; it's your ASSERTION. And an unproven one.

And, if the universe were truly random, there is no reason to believe that it would not have.

Wrong. There are enormous reasons to believe that it would not have, starting with that whole probability thing you're having so much trouble with, and tried to ignore in my last post.

Now, however, after massive technological progress during the past 54 years, we appear to be back to Square One when it comes to creating life. Doesn't that make you wonder just a tad if the creation of life really was a random process?

No, not really. You see, I've observed that the same equations that describe the regular growth of a cabbage also describe the irregular spreading of ink in water; that the same equations that govern the random rolls of dice govern the random recombinations of sexual reproduction.

We are nowhere near square one. In the 1950s, we had no idea that complexity (by which I mean mathematical complexity, also known as dynamical systems or non-linear analysis) even existed; the discovery of the first clearly identified complex system was not made until Edward Lorenz discovered a curious fact about the behavior of a simple weather simulation he was running on a computer in 1961. Non-linear dynamics was not being taught in schools until the 1970s, only one school in the US for most of that decade, and there still are old hard-liners who don't accept it as "real mathematics," despite its demonstrated successes in physics, biology, and mathematics itself.

In the 1950s we had no idea how phospholipids could self-organize into membranes spontaneously when put into water.

We did not know what DNA was until 1953, and we did not understand what it did until 1957; and the final details of how it and RNA interact to create proteins were not understood until the 1970s or later; the actual structure of the RNA in a ribosome was not worked out until the year 2000. That RNA was created from DNA by RNA polymerase was not announced until 1965; and the mechanics of expression, that is, the transcription by RNA polymerase of DNA sequences into the complementary sequences in mRNA, followed by the translation of that mRNA into a protein by ribosomes, also made of RNA, and supplied with amino acids by tRNA, was not known until the late 1960s at the earliest. Without even knowing how this mechanism worked, how can anyone have had any realistic idea of how a cell worked? And until the invention of the scanning electron microscope in 1964, biologists had never seen the organelles inside a eukaryotic cell; even then, special techniques had to be used, and only partial information was available.

We did not understand the full role of proteins in life until the 1990s; and even today we are still learning how they work. We simply didn't know enough physics until then.

You see, this is why it's so unreasonable of you to expect us to know everything. We don't have a theory of everything in physics; and we don't have powerful enough computers to do the research into complexity, or non-linear or dynamical systems, or whatever you want to call it, that we need to do in order to understand more details about how life works; the heck with life, we don't even understand turbulence properly yet. Gonna tell me jebus has a hand in turbulence?

Hey, the Rolamite bearing wasn't even invented until the 1960s, and that's been described as the only fundamental mechanical invention of the 20th century! And guess what? Here we are in 2007 and nobody's using the rolamite for anything! It's like the story of the switch-mode power supply. And most like the Cuk converter; I've seen, now, four consumer products that had Cuk converter power supplies. Out of hundreds of thousands that could use them. So if we can't even figure out how to use stuff we already know, and have known for thirty years or more, why would you expect we'd know enough that you can RULE OUT random chance?

Because here's the thing:
Fundamentally, your post in this thread is dishonest. Here is why:
1. You did not announce in clear language what your position is.
2. Your initial argument places the burden of proof on "random chance;" however, random chance is a proven operation, as I showed. The REAL burden of proof is on YOU, and it is to prove that there is something other than chemistry going on in a cell. Because that is what you have to prove to prove that a cell cannot occur by random chance; if it is just all chemistry, then anything can happen at any time, and given a long time and a lot of space, then anything WILL happen. It is only if there is "something extra" above and beyond the chemicals and their interactions that it won't.

So, now you get to prove the existence of that something extra. How about a look in a microscope? Oh, yeah, that's right, that didn't work out too well for you guys with Galileo and the telescope, yes? Pretty bad propaganda there. Not to mention the evocation of the image of our Imperious Leader bumbling around looking under his desk for WMD. While the soldiers he was supposed to be commanding were dying.

Besides, there have been thousands, nay millions of pictures taken with microscopes, of cells, and no one has ever seen anything in there but chemicals. So I don't think you're going to find anything. You are of course welcome to look; but until you can pull that something extra out and show it to me, I'm going to exercise my option not to believe in things that no one can prove exists. Just like I do with all the rest of that horsepucky made up by the neolithic sheep herders.

 

[Dancing David]

Rodney,

Have read the history of the Manhattan Project? Are you aware of the complexity and the expenditure of money and human hours that went into that project?

Now you make this argument regarding abiogenesis, and it seems to be based upon some distorted thinking.

1. Abiogenesis is a theory, at this point it discusses things like the likely mechanisms for the possibility of life arising from the random motion of molecules.

2. It is a huge falacy to state that because the theory of abiogenesis states it is possible that life arose from the random motion of molecules, humans shouls be able to recreate the process in the laboratory and this is needed to somehow prove the theory.

3. If the theory of abiogenesis makes predictions and those can be observed or tested then it would be evidence that it is likely to be a correct theory.

If we take intelligent design to be the case, what evidence would even remotely support that theory? Is there evidence that if you place a lot of chemicals in a flask that angels and miracles arise?

Schneibster stated this all very well.

posted by Rodney
You're still begging the question. No one has ever demonstrated that life can form from a random process and so, until someone does, probability arguments are unavailing.

Abiogenesis does rely upon random action of particles, do you realise that the theory of how fusion occurs in the sun requires the same action? For the atoms, or stripped down protons, to fuse there has to be the quantum randomness! The Coloumb Effect states that as two particles of like chages approach each other the reulsive force increases and will drive the particles apart. For fusion to occur one of the proton , or both, have to quantumly and randomly appear next to each other. Then the fusion can occur.

Do you have some sort of problem with this? It is random, and it requires that quantum effects are random or chaoticly complex. Do nuclear physicists have to prove the random effect? Do they have to make fusion occur in a laboratory for this to occur?

NO, a theory to be useful has to make predictions about the behavior of observations. So if quantum theory can explain how fusion occurs and the Coloumb effect is gotten around, it matches observation and therefore is a likely theory.

A theory is only an appoximation of how reality might work, for a theory to be true it must be able to accurately predict reality.

 

[Rodney]

Oh, really? Why is it not clear? I guess I'm not quite clear on why you think it's not clear. Why don't you be specific about that.

My point is that, if the universe is truly random, life did not have to come into existence at all. Therefore, your dice-throwing analogy is not apt because it is inevitable that snake eyes will eventually come up.

Oh, really? Do you know what renormalization is? Did you know that it was not proven physically justifiable until the 1970s? Do you know what the Weinberg-Salam-Glashow electroweak theory is? Have you ever heard of quarks? Are you familiar with quantum chromodynamics?

None of these things except renormalization were even conceived in 1960, much less 1950- and Feynman and Dirac argued against renormalization until the 1970s. And if you don't know about these things, not only can you not be a physicist today, but you don't even understand what experimental physicists are DOING today. And you don't even want to have nightmares about the theoretical physicists; they're off inventing new branches of mathematics because the mathematicians didn't pay enough attention to what they were doing in the 1960s, 70s, 80s, and 90s. In both experimental and theoretical physics, the differences between each of those four decades are as stunning as the difference between 1899 and 1901; before the beginning of the twentieth century, physicists thought they had everything all figured out; by the end of the second year of the new century, the foundations of quantum mechanics and relativity had been laid, and nothing would ever be the same.

The progress of technology and science is accelerating; but that doesn't mean it's infinite. But boy oh boy has a hell of a lot of water gone under the bridge since 1995, not to even TALK about 1965 or 1950. That was like, the Stone Age or something.

Depends on your perspective. If you look at the history section of the Wikipedia physics article -- http://en.wikipedia.org/wiki/Physics#Theoretical_and_experimental_physics -- not that much space is devoted to the last 54 years. I think developments in physics during the first half of the 20th Century were more revolutionary than anything that has happened since.

No, that's not your POINT; it's your ASSERTION. And an unproven one.

Check science books and science articles in newspapers written in the decade or so following publication of Miller's experimental results in May 1953 and see what you find.

Wrong. There are enormous reasons to believe that it would not have, starting with that whole probability thing you're having so much trouble with, and tried to ignore in my last post.

I didn't ignore your probability analysis, I just don't think it's appropriate to the issue at hand.

No, not really. You see, I've observed that the same equations that describe the regular growth of a cabbage also describe the irregular spreading of ink in water; that the same equations that govern the random rolls of dice govern the random recombinations of sexual reproduction.

We are nowhere near square one. In the 1950s, we had no idea that complexity (by which I mean mathematical complexity, also known as dynamical systems or non-linear analysis) even existed; the discovery of the first clearly identified complex system was not made until Edward Lorenz discovered a curious fact about the behavior of a simple weather simulation he was running on a computer in 1961. Non-linear dynamics was not being taught in schools until the 1970s, only one school in the US for most of that decade, and there still are old hard-liners who don't accept it as "real mathematics," despite its demonstrated successes in physics, biology, and mathematics itself.

In the 1950s we had no idea how phospholipids could self-organize into membranes spontaneously when put into water.

We did not know what DNA was until 1953, and we did not understand what it did until 1957; and the final details of how it and RNA interact to create proteins were not understood until the 1970s or later; the actual structure of the RNA in a ribosome was not worked out until the year 2000. That RNA was created from DNA by RNA polymerase was not announced until 1965; and the mechanics of expression, that is, the transcription by RNA polymerase of DNA sequences into the complementary sequences in mRNA, followed by the translation of that mRNA into a protein by ribosomes, also made of RNA, and supplied with amino acids by tRNA, was not known until the late 1960s at the earliest. Without even knowing how this mechanism worked, how can anyone have had any realistic idea of how a cell worked? And until the invention of the scanning electron microscope in 1964, biologists had never seen the organelles inside a eukaryotic cell; even then, special techniques had to be used, and only partial information was available.

We did not understand the full role of proteins in life until the 1990s; and even today we are still learning how they work. We simply didn't know enough physics until then.

You see, this is why it's so unreasonable of you to expect us to know everything. We don't have a theory of everything in physics; and we don't have powerful enough computers to do the research into complexity, or non-linear or dynamical systems, or whatever you want to call it, that we need to do in order to understand more details about how life works; the heck with life, we don't even understand turbulence properly yet. Gonna tell me jebus has a hand in turbulence?

Hey, the Rolamite bearing wasn't even invented until the 1960s, and that's been described as the only fundamental mechanical invention of the 20th century! And guess what? Here we are in 2007 and nobody's using the rolamite for anything! It's like the story of the switch-mode power supply. And most like the Cuk converter; I've seen, now, four consumer products that had Cuk converter power supplies. Out of hundreds of thousands that could use them. So if we can't even figure out how to use stuff we already know, and have known for thirty years or more, why would you expect we'd know enough that you can RULE OUT random chance?

I think you're unwittingly making my point. What we've learned during the past 54 years is that the creation of life was vastly more complex than we previously believed it to be. All that believers in a random universe can do is speculate that somehow a whole slew of extraodinary events somehow conspired to bring life into existence through an unknown mechanism.

Because here's the thing:
Fundamentally, your post in this thread is dishonest. Here is why:
1. You did not announce in clear language what your position is.
2. Your initial argument places the burden of proof on "random chance;" however, random chance is a proven operation, as I showed. The REAL burden of proof is on YOU, and it is to prove that there is something other than chemistry going on in a cell. Because that is what you have to prove to prove that a cell cannot occur by random chance; if it is just all chemistry, then anything can happen at any time, and given a long time and a lot of space, then anything WILL happen. It is only if there is "something extra" above and beyond the chemicals and their interactions that it won't.

So, now you get to prove the existence of that something extra. How about a look in a microscope? Oh, yeah, that's right, that didn't work out too well for you guys with Galileo and the telescope, yes? Pretty bad propaganda there. Not to mention the evocation of the image of our Imperious Leader bumbling around looking under his desk for WMD. While the soldiers he was supposed to be commanding were dying.

Besides, there have been thousands, nay millions of pictures taken with microscopes, of cells, and no one has ever seen anything in there but chemicals. So I don't think you're going to find anything. You are of course welcome to look; but until you can pull that something extra out and show it to me, I'm going to exercise my option not to believe in things that no one can prove exists. Just like I do with all the rest of that horsepucky made up by the neolithic sheep herders.

I'm having a little difficulty following the connection between abiogenesis and WMD, but maybe that's just me. However, my fundamental point is that, 54 years ago, believing that random factors brought life into existence was far more consistent with the facts than it is now.

 

[Schneibster]

My point is that, if the universe is truly random, life did not have to come into existence at all. Therefore, your dice-throwing analogy is not apt because it is inevitable that snake eyes will eventually come up.

And my assertion is, if life is a result only of the laws of physics, which produce chemistry, then life is an inevitable result of those laws, because we see it. HOW it is an inevitable result of those laws is still not entirely known; but the more we find out, the closer we get to knowing the details. What you are basically saying is that, since we don't know the details NOW, we never will.

Depends on your perspective.

No, it doesn't. It depends on whether, knowing only what we knew in, say, 1955, you could pursue a career in physics today- and the answer is, no, you could not.

Check science books and science articles in newspapers written in the decade or so following publication of Miller's experimental results in May 1953 and see what you find.

It's not mine to prove- it's yours, you have already been challenged three times on this point and have failed all three times to provide that proof.

I didn't ignore your probability analysis, I just don't think it's appropriate to the issue at hand.

And without it, you don't UNDERSTAND the issue at hand.

I think you're unwittingly making my point. What we've learned during the past 54 years is that the creation of life was vastly more complex than we previously believed it to be. All that believers in a random universe can do is speculate that somehow a whole slew of extraodinary events somehow conspired to bring life into existence through an unknown mechanism.

No, that's not all they can do. What they are in the process of doing is proving that in fact, life is inevitable given the laws of chemistry and the presence of appropriate and highly likely simple constituents, in the appropriate and highly likely environment.

I'm having a little difficulty following the connection between abiogenesis and WMD, but maybe that's just me.

Oh, really? Fine, it's a bummer having to explain jokes but I guess it figures.

Here you go: you, bumbling around looking for some magic principle inside cells over and above the chemistry happening in them; Shrub bumbling around looking for WMD under his desk; and both of you ignoring what's really going on. Happy now?

However, my fundamental point is that, 54 years ago, believing that random factors brought life into existence was far more consistent with the facts than it is now.

Well, it doesn't look like you have anything to point to, and it also looks like you're not very aware of what's going on in chemistry, physics, or molecular biology since the 1950s. You'll pardon me, but I think your fundamental point isn't a point, but just another unproven (and as far as I can see, unprovable) assertion. Which means it doesn't have anything to do with science. Which is what I thought when I first saw it.

 

[smaxwell]

50 Years of Ambiogenesis Research: Life Origins Remain A Mystery

In the 1950s, prebiotic earth environment was believed to be made up primarily of the reduced gases methane, ammonia, hydrogen, and water. In a non-reducing atmosphere containing more oxygen and less hydrogen, the formation of significant amino acids by the Miller-Urey process is very scant to nonexistent. The serious problem with the Miller-Urey hypothesis is that the atmospheric ammonia and methane, which are reducing agents critical to the process of forming amino acids, would not have been stable in the prebiotic environment. The eventual degradation of the methane and ammonia with the resulting release and escape of the hydrogen from the atmosphere would have resulted in the reducing atmosphere becoming more oxidizing.

Moreover, Ohmoto et al (2006) and many others have assimilated compelling evidence that the earth’s atmosphere was oxygenated as early as 3.8 billion years ago, in agreement with a wide range of studies that the atmosphere of the earth was oxidizing during pre-biotic times. The atmosphere of the early earth would have likely come from out gassing of the mantle, and we know that such gasses are uniformly oxidized, ruling against the likelihood of a neutral atmosphere composed of carbon dioxide, water, nitrogen, and some trace hydrogen. Thus, the accumulated evidence for the presence of oxygen in primordial times does not support the spontaneous formation of amino acids in the pre-biotic earth environment.

There are other problems with a spontaneous amino acid polymerization model. A pre-biotic soup of amino acids has been calculated to be too dilute to be involved in spontaneous assembly into proteins. For instance, present concentrations of the most abundant amino acids in the mid-Atlantic ocean only range between 10 to 100 micrograms/liter, concentrations too low to produce spontaneous amino acid polymerization. As predicted in the Miller-Urey experiment, large amounts of non-biologically produced nitrogenous tarry material as a by-product would have been found in the Precambrian and earlier sediments but no such tarry material has been recorded as observed in the geological records.

A dilute primordial soup poses substantial problems for protein polymerization. Amino acid polymerization generates water as a product and thus is only efficient in the absence of water molecules. Experiments have shown that significant polymerization is virtually impossible in aqueous solution with very high concentrations of amino acids.

An attempt was made by a chemist, Sydney Fox, to get around this water problem for polymerization by heating pure crystalline amino acids, thus driving off the water. After heating the mixture for several hours, some polymers of amino acids were generated with some properties of proteins. These amino acid polymer products were called proteinoids and were proclaimed to be the macromolecular bridge to cell transition. However, a number of serious problems have been revealed with the proteinoids that have invalidated the proteinoids as being a contender for the origin of life. First, proteinoids are not true proteins because they contain many non-peptide bonds and un-natural chemical crosslinkages. Second, proteinoids contain beta-bonds whereas biological proteins are made up of alpha-peptide bonds. Third, the starting materials in the Fox reaction were pure amino acids that would nowhere resemble the primordial dilute soup. Fourth, the ratio of Glu and Asp amino acid concentrations required for success of protenoid synthesis has no similarity to the considerably higher ratio of Gly and Ala in primordial origin of life experiments. Fifth, no information is contained in the proteinoids leading to any known catalytic or functional activities.

The use of clays has been tried in amino acid polymerization and have generated some polymers consisting of about a dozen basic amino acids. The biological relevance of these types of polymers is in doubt based on the following: (1) Although peptide bonds are formed in the polymers, no information is present. (2) The clays show a preference for basic amino acids. (3) No polymerization occurs with free amino acids. (4) In order for the polymerization to proceed, pure amino acids attached to adenine must be used and this adenylated amino acid molecule is not likely to have been floating in a primordial soup. (5) The polymers are three-dimensional rather than linear. These issues make the clay-catalyzed process highly unlikely to have generated biologically functional proteins in a primordial soup.

Many problems are encountered when considering RNA in origin of life scenarios. Could RNA ribozymes be created by random chance in a primordial soup? Substrate recognition by the Azoarcus ribozyme depends on the existence of a single accessible CAU triplet for effective recombination. Unfortunately, the right conditions to create the nucleosides, consisting of both purine (A & G) and pyrimidine (C,T, & U) nucleosides, required to produce a functional ribozyme is very specific and probably did not apply for prebiotic Earth, because the prebiotic conditions seem to only favor the creation of purine nucleosides and not pyrimdines C, T, and U.

More problems confront the concept of RNA being a mechanism for origin of life. The production of precursors of RNA by pre-biotic conditions has so far been less than promising. Ribose is a rare sugar produced in formaldehyde polymers, the mechanism believed to have given rise to sugars. The presence of any nitrogenous substances such as amino acids would inhibit the synthesis of sugars. The concentration of formaldehyde solutions required to produce sugars is far higher than what would be likely in a primordial soup. The formaldehyde reaction conditions that tend to produce the sugars in turn will degrade them, and sugars tend to make complicated molecules in the presence of amino acids.

In a scenario to produce a nucleoside, condensation of a sugar with a nitrogenous base will produce a mixture of optical isomers, most of which will inhibit the polymerization of nucleotides. Then of course we have the problem of phosphorylating the 5’ hydroxyl of the nitrogenous base to produce a nucleotide able to undergo polymerization. Modern nucleosides are phosphorylated by kinases and ATP in a stepwise process to produce nucleotides. Hydrolysis of the triphosphate between the alpha and beta phosphates is required to generate the energy required for covalent bonding to the 3’ hydroxyl residue of another nucleotide for polymerization. While only 3’-5’ polymers are found in biological systems, prebiotic-type synthetic reactions generate predominantly 5’-5’ and 5’-2’ polymers. A formidable problem in RNA prebiotic mechanism schemes is the ability to synthesize an RNA molecule that can copy itself and then perform some function relevant to life.

The lability of RNA in aqueous solutions effectively rules out its role as an origin of life mechanism. Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific base catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. Autocatalytic and self-replicating RNA experiments are conducted under very controlled conditions to maximize the stability of the RNA, and these conditions nowhere resemble a prebiotic soup. Thus any RNA that is postulated to have formed in a primordial soup would have been effectively degraded very rapidly, essentially preventing any significant accumulation of autocatalytic and self-replicating RNA molecules.

As indicated in Trevors and Abel (2005, Theor Biol Med Model. 2: 29), “One of the biggest problems for the pre-RNA World model is finding sequences that can simultaneously self-replicate and catalyze needed metabolic functions. For even the simplest protometabolic function to arise, large numbers of such self-replicative and metabolically contributive oligoribonucleotides would have to arise at the same place at the same time……Nucleic acid prescription of function cannot be explained by "order out of chaos" or by "order on the edge of chaos". Physical phase changes cannot write algorithms. Biopolymeric matrices of high information retention are among the most complex entities known to science. They do not and can not arise from low-informational self-ordering phenomena. Instead of order from chaos, the genetic code was algorithmically optimized to deliver highly informational, aperiodic, specified complexity. Specified complexity usually lies closer to the noncompressible unordered end of the complexity spectrum than to the highly ordered end. Patterning usually results from the reuse of programming modules or words. But this is only secondary to choice contingency utilizing better efficiency. Order itself is not the key to prescriptive information.”

Still more problems confront spontaneous chemical origins of life models. Molecules such as nucleotides and amino acids exhibit symmetry and exist in right- or left-handed forms, which are mirror images of one another. In non-biological materials, equal numbers of right- and left-handed molecules are found, whereas in biotic life, one handedness is preferred over another. For instance, the RNA and DNA molecules that form the backbone of nucleic acids in biotic life contain only right-handed sugars. Amino acids in proteins are only left-handed. The synthesis of new RNA and DNA molecules is inhibited in the presence of equal amounts of right- and left-handed because molecules of the wrong orientation terminate the reactions. Organics found in comets and meteorites contain nearly equal proportions of left- and right-handed molecules, whereas only earth terrestrial biotic life displays handedness.

DNA and in particular RNA have to be protected by an enclosed membrane in order to have originated cellular life. The membrane also would function to keep a cell’s RNA and DNA distinct and separate from other cells. One important property of a cell membrane is that it must be selectively permeable to various inorganics and organic compounds to initiate a replicating unit.

Some scenarios to explain the origin of cell membranes include the heating of amino acids that can spontaneously form small spherical membranes, thus sequestering the complex nucleic acid molecules inside. It has been observed that the heating of various organic polymers can lead to the formation of organized clusters that can enclose organic molecules. However, modern cell membranes are not anything resembling these in composition or structure. The origins of modern membranes is thus a mystery.

Compartmentalization is indispensable for the emergence of RNA origin of life, since natural selection would not be able to operate with an efficient replicating RNA molecule that replicates other less efficient RNA types indiscriminately. Segregation from other RNAs by a membrane compartment is required before natural selection can confer a reproductive or replication advantage.

Claudia Ginanni (Medical Research Institute for Infectious Diseases[FONT=&quot]) [/FONT]summed up the current state of RNA origin of life scenarios as follows: “A rare point of agreement about the RNA World is that no amount of research can actually prove that it ever existed: it can only suggest whether such a scenario was possible. And there seems to be no convergence towards agreement on fundamental principles. Molecular biologists who have spent untold hours researching and speculating about the RNA World hold opinions about the origin of life ranging from a solid belief that the evolution of life was the inevitable product of laws of nature to an equally firm conviction that it could not have happened without some kind of outside intervention.”

Arthor Chadwick (Professor of Geology and Biology, Southwestern Adventist College) puts the random chance of the origin of life in this perspective:
“Let us try another approach---forget the cell, forget the membrane---what would be required as a base minimum just to make a protein molecule. We could imagine proteins smaller than modern proteins, say 100 amino acids long, using less than 20 of the proteinous amino acids, a less than perfect polymerase system, perhaps as few as 100 specific proteins total, maybe even 80. Let’s even suppose they could also use non-proteinous amino acids, and that either enantiomer would work. All of these assumptions are ludicrous with respect to life origins. Since we are playing this game lets make it even worse. Of the 80 proteins we said we needed, lets allow the first 60 to have any sequence of amino acids at all. Of the remaining 20 proteins, the first has one amino acid specified. The other 99 can be any amino acid. The second has two specified, and so on until the twentieth has twenty amino acids specified. We will let the ocean be two miles deep over the entire earth and the concentration of amino acids 1 molar for each species. We will divide the ocean into one liter increments and consider the feat accomplished when any one liter produces all of the requisite proteins. We will allow the proteins to be made at the rate of a million tries per liter per second. We will assume the same probability for nucleic acids. With all these assumptions made in favor of producing our exceedingly liberal primitive cell, we will achieve the intended result with a 50% probability once in 10186 years.” A probability of one in 1050 can be considered as impossibility.

After a careful review of the abiogenic research scene, J. Brooks and G. Shaw (1973) concluded: "These experiments...claim abiotic synthesis for what has in fact been produced and designed by highly intelligent and very much biotic man."


Consider the following article:

Trevors JT and Abel DL (2004) Chance and necessity do not explain the origin of life. Cell Biol. Int. 28:729-739

Chance brings about randomness. Laws bring about order. Purposeful direction brings about organization. And organisms are organized. DNA language encodes and transmits organization. All languages are forms of message intent devised by intelligence. By induction and inference, life had intelligent origin. It’s the only viable explanation that we currently have to account for the origin of life information, language, organization, and complexity.


Human DNA contains more organized information than the Encyclopedia Britannica. If the full text of the encyclopedia were to arrive in computer code from outer space, most people would regard this as proof of the existence of extraterrestrial intelligence. But when seen in nature, it is explained as the workings of random forces
- George Sim Johnson

Embracing the theory of naturalism (physical laws are the only things that govern the origin and evolution of the universe and biology) would have me believe that:

1.Nothing produces everything
2.Non-life produces life
3.Randomness produces fine-tuning
4.Chaos produces information
5.Unconsciousness produces consciousness
6.Non-reason produces reason

Why should a bunch of atoms have thinking ability? Why should I, even as I write now, be able to reflect on what I am doing and why should you, even as you read now, be able to ponder my points, agreeing or disagreeing, with pleasure or pain, deciding to refute me or deciding that I am just not work the effort? No one, certainly not the Darwinian as such, seems to have any answer to this…. The point is that there is no scientific answer.
–Darwinist philosopher Michael Ruse

We have always underestimated the cell. The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. Why do we call them machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts
-Bruce Alberts, National Academy of Sciences

Scientists who utterly reject Darwinism may be one of our fastest growing controversial minorities…Many of the scientists supporting this position hold impressive credentials in science
- Larry Hatfield in Science Digest

 

[Dancing David]

Rodney:
Does the sun shine?

Does it rely on random processes?

 

[Dancing David]

There are other problems with a spontaneous amino acid polymerization model. A pre-biotic soup of amino acids has been calculated to be too dilute to be involved in spontaneous assembly into proteins. For instance, present concentrations of the most abundant amino acids in the mid-Atlantic ocean only range between 10 to 100 micrograms/liter, concentrations too low to produce spontaneous amino acid polymerization.

So there are no salt deposits from early ocean either, because they are too dilute to crystalize. i don't suppose that ponds, or tide pools exist either.

As predicted in the Miller-Urey experiment, large amounts of non-biologically produced nitrogenous tarry material as a by-product would have been found in the Precambrian and earlier sediments but no such tarry material has been recorded as observed in the geological records.

How much of the mantle that old exists on the surface of the earth?

The use of clays has been tried in amino acid polymerization and have generated some polymers consisting of about a dozen basic amino acids. The biological relevance of these types of polymers is in doubt based on the following: (1) Although peptide bonds are formed in the polymers, no information is present.

Duh, abiogensis would say that there is not information until it is postbiotic.

(2) The clays show a preference for basic amino acids.

Yeah so? Self catalyzing sets don't require clay bases.

(3) No polymerization occurs with free amino acids. (4) In order for the polymerization to proceed, pure amino acids attached to adenine must be used and this adenylated amino acid molecule is not likely to have been floating in a primordial soup.

Not likely, what leads to this conclusion, data and sources please?

(5) The polymers are three-dimensional rather than linear. These issues make the clay-catalyzed process highly unlikely to have generated biologically functional proteins in a primordial soup.

A bunch of assertion, any sources any data, nope might as well just say "I think so".

Many problems are encountered when considering RNA in origin of life scenarios. Could RNA ribozymes be created by random chance in a primordial soup? Substrate recognition by the Azoarcus ribozyme depends on the existence of a single accessible CAU triplet for effective recombination. Unfortunately, the right conditions to create the nucleosides, consisting of both purine (A & G) and pyrimidine (C,T, & U) nucleosides, required to produce a functional ribozyme is very specific and probably did not apply for prebiotic Earth, because the prebiotic conditions seem to only favor the creation of purine nucleosides and not pyrimdines C, T, and U.

Duh, I don't suppose that RNA could have arisen from the abiogenic mess when it was already biotic. Gosh no. Any reason to say it couldn't have?

Why the varieties on RNA in existance?

More problems confront the concept of RNA being a mechanism for origin of life. The production of precursors of RNA by pre-biotic conditions has so far been less than promising.

More assertions.

Ribose is a rare sugar produced in formaldehyde polymers, the mechanism believed to have given rise to sugars.

So, what data do you have, a sample of the earth 3.5 billion years old? Does formaldehyde exist in space in huge molecular clouds?

The presence of any nitrogenous substances such as amino acids would inhibit the synthesis of sugars.

Inhibits means prohibit? there is a zero chance that protons will come close enough to fuse in the sun. Hmm, maybe they do , huh?

The concentration of formaldehyde solutions required to produce sugars is far higher than what would be likely in a primordial soup.

More assertion.

The formaldehyde reaction conditions that tend to produce the sugars in turn will degrade them, and sugars tend to make complicated molecules in the presence of amino acids.

Oh, just one flask the size of a liter, how about a pond , how about a shallow tide pool that is only filled at high tide.

In a scenario to produce a nucleoside, condensation of a sugar with a nitrogenous base will produce a mixture of optical isomers, most of which will inhibit the polymerization of nucleotides. Then of course we have the problem of phosphorylating the 5’ hydroxyl of the nitrogenous base to produce a nucleotide able to undergo polymerization. Modern nucleosides are phosphorylated by kinases and ATP in a stepwise process to produce nucleotides. Hydrolysis of the triphosphate between the alpha and beta phosphates is required to generate the energy required for covalent bonding to the 3’ hydroxyl residue of another nucleotide for polymerization. While only 3’-5’ polymers are found in biological systems, prebiotic-type synthetic reactions generate predominantly 5’-5’ and 5’-2’ polymers. A formidable problem in RNA prebiotic mechanism schemes is the ability to synthesize an RNA molecule that can copy itself and then perform some function relevant to life.

I don'y suppose you could have self catalyzing set that are not RNA lead to RNA in a biotic fashion. You don't have to have RNA to be biotic.

I don't suppose there were horse drawn carriages because now we have only cars.

The lability of RNA in aqueous solutions effectively rules out its role as an origin of life mechanism.

How about within cell walls?

Under neutral or alkaline pH conditions, the dominant pathway for RNA degradation is an internal phosphoester transfer reaction that is promoted by specific base catalysis. As expected, increasing the concentration of hydroxide ion, increasing the concentration of divalent magnesium, or raising the temperature accelerates strand scission. Autocatalytic and self-replicating RNA experiments are conducted under very controlled conditions to maximize the stability of the RNA, and these conditions nowhere resemble a prebiotic soup.

So i suppose cell can't manage it either? What about biotic forms that possibly lead to RNA? Do cells have RNA?

Thus any RNA that is postulated to have formed in a primordial soup would have been effectively degraded very rapidly, essentially preventing any significant accumulation of autocatalytic and self-replicating RNA molecules.

It would be unlikely that RNA arose in a soup, how about in primitive biotic forms?

As indicated in Trevors and Abel (2005, Theor Biol Med Model. 2: 29), “One of the biggest problems for the pre-RNA World model is finding sequences that can simultaneously self-replicate and catalyze needed metabolic functions.

No you don't, all you need is self catalyzing sets that become entrapped in a lipid layer and have the capability of supporting the lipid layer.

For even the simplest protometabolic function to arise, large numbers of such self-replicative and metabolically contributive oligoribonucleotides would have to arise at the same place at the same time……Nucleic acid prescription of function cannot be explained by "order out of chaos" or by "order on the edge of chaos".

More assertion.

Physical phase changes cannot write algorithms. Biopolymeric matrices of high information retention are among the most complex entities known to science. They do not and can not arise from low-informational self-ordering phenomena.

More assertion.

Instead of order from chaos, the genetic code was algorithmically optimized to deliver highly informational, aperiodic, specified complexity.

Goofy informational, redundant and prone to error. And a lot of nonsense and garbage.

Specified complexity usually lies closer to the noncompressible unordered end of the complexity spectrum than to the highly ordered end.

OOOH, magic words, hold the demon at bay.
More assertion.

Patterning usually results from the reuse of programming modules or words.

Snowfalkes don't exist either, not does hematite or diamond.

But this is only secondary to choice contingency utilizing better efficiency. Order itself is not the key to prescriptive information.”

Still more problems confront spontaneous chemical origins of life models. Molecules such as nucleotides and amino acids exhibit symmetry and exist in right- or left-handed forms, which are mirror images of one another. In non-biological materials, equal numbers of right- and left-handed molecules are found, whereas in biotic life, one handedness is preferred over another.

Oh I see so self catalyzing sets can't have a preference?

For instance, the RNA and DNA molecules that form the backbone of nucleic acids in biotic life contain only right-handed sugars. Amino acids in proteins are only left-handed. The synthesis of new RNA and DNA molecules is inhibited in the presence of equal amounts of right- and left-handed because molecules of the wrong orientation terminate the reactions. Organics found in comets and meteorites contain nearly equal proportions of left- and right-handed molecules, whereas only earth terrestrial biotic life displays handedness.

In cell walls , correct?

DNA and in particular RNA have to be protected by an enclosed membrane in order to have originated cellular life.

yeah, so biotic form with cell walls might have arisen before RNA and DNA. Duh.

The membrane also would function to keep a cell’s RNA and DNA distinct and separate from other cells. One important property of a cell membrane is that it must be selectively permeable to various inorganics and organic compounds to initiate a replicating unit.

Some scenarios to explain the origin of cell membranes include the heating of amino acids that can spontaneously form small spherical membranes, thus sequestering the complex nucleic acid molecules inside. It has been observed that the heating of various organic polymers can lead to the formation of organized clusters that can enclose organic molecules. However, modern cell membranes are not anything resembling these in composition or structure. The origins of modern membranes is thus a mystery.

Cars and horses again.

Compartmentalization is indispensable for the emergence of RNA origin of life, since natural selection would not be able to operate with an efficient replicating RNA molecule that replicates other less efficient RNA types indiscriminately. Segregation from other RNAs by a membrane compartment is required before natural selection can confer a reproductive or replication advantage.

Yeah, so biosis occurs before RNA, big whoop.

Embracing the theory of naturalism (physical laws are the only things that govern the origin and evolution of the universe and biology) would have me believe that:

1.Nothing produces everything

No something came from something, the Big band Event, is not something from nothing. Are balck holes nothing?

2.Non-life produces life

Yeah so? cars make carbon dioxide, does that mean they are alive.

3.Randomness produces fine-tuning

No, constrained variability produces fine tuning, as apossible mechanism.

4.Chaos produces information

You don't understand chaos theory , do you. Order produces chaos.

5.Unconsciousness produces consciousness

No, non-consiousness leads to behaviors we assume to be consious, can you prove that you are consious. can you prove that electrons are conscious.

6.Non-reason produces reason

Not at all, reason is an illusion at best. It varies from person to person and culture to culture.


Very erudite post! i comend you. it is well composed but needs more work. Too many assertions, but a definite B+

 

[Schneibster]

Chance brings about randomness. Laws bring about order.

And randomness brings about chaos- but chaos is not without laws.

Purposeful direction brings about organization.

So does chaos, according to the laws of chaos, that is, the laws of behavior of non-linear dynamical systems. Which we have been studying since the first such system was quantified in 1961.

Like Dancing David said, you don't know very much about chaos, do you?

 

[Foster Zygote]

No something came from something, the Big band Event, is not something from nothing. Are balck holes nothing?

Good point. I'm no expert in cosmology but I understand enough to see this fundamental error made by many people. Big Bang theory doesn't say that the universe sprang into being from nothing. It says that at one point the universe, all energy, matter, space, time, everything, existed as a singularity, but it was all still there. Plus there isn't even a "before" the Big Bang. The way we think about time makes it hard to conceive that you can't keep rolling time back to the Big Bang and then keep going further back. Time starts at the Big Bang. It's really weird to think about, but in a sense the Big Bang singularity is "still there" at one end of the time dimension of the universe.

 

[Schneibster]

Actually, you've got the right idea but not quite a firm grasp on the details, Foster. The Big Bang theory says that all matter and energy in the universe was compressed together very closely, but the singularity that follows from assuming that that compression continues to infinity is a mark of the fact that our theory of physics cannot currently adequately describe what immediately preceded that time. The most popular current hypothesis is something called the "inflationary universe scenario of the Big Bang theory," which says that the universe underwent expansion of the three space and one time dimensions that we now see around us; before that, all the dimensions were small, on the close order of the size of the Planck Length (which you should google up). The Wikipedia article on the inflationary universe is something you'd probably find interesting about now.

Incidentally, once that expansion happened, it's important to remember that the dimensions became large- and that the incredibly dense hot state of the universe wasn't very small, it was everywhere in the universe. It's just that everything for as far out as we can see was compressed together into a very small area- not that the entire universe was.

And the mechanics of what happened when the time dimension expanded are pretty spooky- and time isn't well dealt with in some ways in our current understanding, anyway. But it is probably accurate to mark the instant prior to the beginning of that expansion as "the beginning of time," or perhaps the moment just after the expansion stopped.

 

[Rodney]

Big Bang theory doesn't say that the universe sprang into being from nothing. It says that at one point the universe, all energy, matter, space, time, everything, existed as a singularity, but it was all still there.

How do you suppose it got there?

 

[quixotecoyote]

How do you suppose it got there?

To 'get' anywhere requires a point in time where it was somewhere else. If there are no previous points in time, the question is meaningless.

 

[Foster Zygote]

How do you suppose it got there?

Well, obviously God put it there. Of course that leads to the vexing question of how God got there.

 

[Foster Zygote]

Actually, you've got the right idea but not quite a firm grasp on the details, Foster. The Big Bang theory says that all matter and energy in the universe was compressed together very closely, but the singularity that follows from assuming that that compression continues to infinity is a mark of the fact that our theory of physics cannot currently adequately describe what immediately preceded that time. The most popular current hypothesis is something called the "inflationary universe scenario of the Big Bang theory," which says that the universe underwent expansion of the three space and one time dimensions that we now see around us; before that, all the dimensions were small, on the close order of the size of the Planck Length (which you should google up). The Wikipedia article on the inflationary universe is something you'd probably find interesting about now.

Incidentally, once that expansion happened, it's important to remember that the dimensions became large- and that the incredibly dense hot state of the universe wasn't very small, it was everywhere in the universe. It's just that everything for as far out as we can see was compressed together into a very small area- not that the entire universe was.

And the mechanics of what happened when the time dimension expanded are pretty spooky- and time isn't well dealt with in some ways in our current understanding, anyway. But it is probably accurate to mark the instant prior to the beginning of that expansion as "the beginning of time," or perhaps the moment just after the expansion stopped.

Thanks! Very cool!

 

[Schneibster]

How do you suppose it got there?

Generation of our cosmos from a quantum fluctuation in an empty, dimensionless, timeless nothingness has been proposed and shown to be consistent with the development of the cosmos we see around us. The title of the paper was, IIRC, "Is the universe a quantum fluctuation?" and I think Alan Guth might be one of the authors.

 

[CapelDodger]

Why should a bunch of atoms have thinking ability? …. The point is that there is no scientific answer.
–Darwinist philosopher Michael Ruse

Nothing to with abiogenesis, but a chance to quote a Darwinist. OK, referring to a completely different matter, but it might suggest to the unwary that you're approaching this matter with an open mind. Which is, I suppose, your intent?

 

[Schneibster]

In the 1950s, prebiotic earth environment was believed to be made up primarily of the reduced gases methane, ammonia, hydrogen, and water.

I challenge the assumption implicit in that "In the 1950s" part. I'd like to point out that neither is there any evidence that that has changed, nor is there any evidence that the Earth's atmosphere before life started was not- then or now. And finally that there is a large and detailed body of evidence that in fact, it was like that. In other words, the presentation of a single data point that claims otherwise is not sufficient proof to overturn the large and detailed body of evidence that that is precisely how it was. Which given the false assumption you have started with, I have to guess you are going to try to disprove, in precisely that fashion. LATER: Looking it over, I find that is exactly what you have attempted; there is one and only one actual data point given, and it does not say what you say it does. Unfortunately, the assumption that begins the sentence I am replying to here is merely the first in a long list of factual errors.

In a non-reducing atmosphere containing more oxygen and less hydrogen,

Two points: where did the FREE oxygen come from? Note: FREE oxygen, not oxygen in a compound. Oxygen is highly reactive with most other elements; one that it does not react strongly with is nitrogen, which is why there is so much nitrogen in our atmosphere. The FREE oxygen in our atmosphere is, as far as scientists can tell, and that is very far indeed, an artifact of the existence of life, specifically plant life, on Earth. If all the plants died, the free oxygen in our atmosphere would be gone quite quickly, a matter of a few million years at most (a blink of an eye compared to the four and a half thousand million years the Earth has existed- but long in terms of the existence of human civilization, and even in terms of the existence of humans, period).

the formation of significant amino acids by the Miller-Urey process is very scant to nonexistent.

So what? You haven't shown either a source for free oxygen or any proof that there WAS free oxygen, and below you cite only one paper, and that paper does not say what you claim it does.

The serious problem with the Miller-Urey hypothesis is that the atmospheric ammonia and methane, which are reducing agents critical to the process of forming amino acids, would not have been stable in the prebiotic environment.

Why not? They're perfectly stable on Jupiter and Saturn, and you've shown no evidence to overturn the large and detailed body of evidence about the early Earth's atmosphere not having free oxygen in it, only a single source was cited and that source does not say what you claim it does.

The eventual degradation of the methane and ammonia

What "eventual degradation of the methane and ammonia? The one you haven't proven exists?

with the resulting release and escape of the hydrogen from the atmosphere

Congratulations! You've actually said something that makes sense! That's the first (and probably the last) time in this post, but I thought it was worth noting!

would have resulted in the reducing atmosphere becoming more oxidizing.

Why? Where did the oxygen come from?

Moreover, Ohmoto et al (2006) and many others

What others? Cites?

have assimilated compelling evidence that the earth’s atmosphere was oxygenated as early as 3.8 billion years ago,

No, they haven't. This is a specious claim, as can be shown by examining the first sentence of the abstract of the referenced citation, which says: "The ca. 2.2 Ga Hekpoort paleosol of the Transvaal Supergroup in southern Africa has been considered a type example and the youngest iron-depleted paleosol..." Nice try. But this is evidence either of direct dishonesty, or of acceptance of statements by someone who was dishonest without checking their facts.

in agreement with a wide range of studies that the atmosphere of the earth was oxidizing during pre-biotic times.

You have provided no proof of this. The only article you have cited does not say this, nor is there any "wide range of studies" that say this.

The atmosphere of the early earth would have likely come from out gassing of the mantle,

FREE oxygen from the mantle? Are you out of your ever-lovin' MIND?

For reference: THERE ARE NO GIANT VOLCANOES SPEWING FREE OXYGEN INTO THE ATMOSPHERE. Dude, where do you come up with this stuff?

and we know that such gasses are uniformly oxidized,

No doubt you mean like the hydrogen sulfide? Or perhaps you were referring to hydrogen chloride or hydrogen fluoride. All of which are no doubt HUGH!!11! sources of oxygen.

ruling against the likelihood of a neutral atmosphere composed of carbon dioxide, water, nitrogen, and some trace hydrogen.

Well THAT'S certainly interesting! Did you see that everybody? Water and carbon dioxide are removed from the atmosphere by oxygen.

Thus, the accumulated evidence for the presence of oxygen in primordial times does not support the spontaneous formation of amino acids in the pre-biotic earth environment.

I don't think there's any point in going on. This is a complete waste of time. You have made exactly one statement that even approached being factual, and that statement had nothing to do with the subject you are attempting (feebly) to address in this post. You can't come on a site filled with skeptics and make a post like this and expect that anyone is going to believe you, respect your opinion, or even read your second post afterward.

I don't really want to discourage newbs, so I'll hold off adding to my ignore list for now. You might say something intelligent eventually. But the number of chances you have to do so has just dwindled by one, for whatever that's worth.

 

[CapelDodger]

How do you suppose it got there?

Since "there" was everywhere and had never been anywhere else, it didn't have to get "there". In the Beginning were the Words, and the Words were "It was like that when I got here".

 

[Foster Zygote]

In the Beginning were the Words, and the Words were "It was like that when I got here".

That would be great on a T-shirt.