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Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
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Author | Topic: How to make a ribozyme (using abiotic starting compounds) | |||||||||||||||||||||||
Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Ok,
I'm really interested in organic chemistry, and so to brush up on my skills, I decided to see if I could find a way to build an RNA enzyme from prebiotic chemicals. Theoretically of course. So, the first step was to make some ribose. Now, I believe that using the Formose reaction using Pb (II) as the catalyst, one can make aldopentoses like ribose in high yield. However, that would require methanal (H2CO). The only ways I know how to make that is as follows: Method 11. CO2 + 3 H2 ’ CH3OH + H2O 2a. 2CH3OH + O2 ’ 2H2CO + 2 H2O 2b. CH3OH ’ H2CO + H2 The problem is, this appear to require a heavy metal catalyst (like Ag or V). Also, one of the above pathways requires oxygen, which most assume didn't exist freely in prebiotic earth. Method 2 1. 3CO2 + 12H2 ’ 3CH4 + 6H2O 2. 3CH4 + 3O2 ’ 3H2CO + 3H2O But this method also uses oxygen, and exotic catalysts (like V and Se). So, does anyone know a way to make formaldehyde/methanal without requiring oxygen and catalysts? I think the best bet would be to look for alternative methods for the dehydrogenation of methanol, to see if we can get some room temperature reactions going (UV light or electric sparks?). Or do I have to 'appeal to space' to send me some on comets from oxygen-rich areas before I can make some ribose? Once we've done that, then we can start talking about getting some hydrogen cyanides to make nucleotides. As for forum section, methinks Origin of Life would be the best bet to get the organic chemists involved. Edited by Doddy, : mistake in stoichiometry Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Matt P writes: It's formed through a number of high-energy processes, most starting with CO (exact chemical pathways aren't clear, but probably ion-molecule or radical reactions). Yes, I did originally notice that, but that just leads to questions about how much carbon monoxide would have been present in prebiotic earth (I know it is made in volcanoes and meteor impacts). In comparison to methanol or hydrogen, what composition would carbon monoxide be in the prebiotic atmosphere?
Matt P writes: It could be formed naturally at 10^-8 atm under equilibrium in an O2-poor atmosphere (like on the early Earth), and enriched to ~10^-4 through non-equilibrium processes in a CO2 atmosphere with water or H2 (lightning, meteor infall). I also have noticed that UV radiation can produce formaldehyde from CO2 and H2), via carbon monoxide (CO) and H2 intermediates.(Pinto JP, 1980: Science 210, pp183-184). Ok, now we have some probable models of the formation of formaldehyde, we move onto the formose reaction.
Matt P writes: Alternatively, you could mix it with borate minerals to select specifically for ribose and associated pentoses (see Steve Benner's work- e.g., Ricardo et al. 2004, 1 page article in Science). You could also mix it with a bit of ammonia and some trimetaphosphate, and get ribose phosphates (a la Krishnamurthy et al. 1999). Interesting. I had found that going in the direction of phosphates made the coming chemistry (formation of nucleosides) a little harder though, so I'm not tempted to go that way yet. In my research, I noticed that a Pb+2 could catalyze the formation of ribose quite readily in alkanine solutions, even at low temperatures (35oC, though it is much faster around 60oC) (Zubay, G.: 1998, Studies on the Lead-Catalyzed Synthesis of Aldopentoses, Origins Life Evol B 28, 13-26). This is useful because while lead isn't as common as iron, calcium or magnesium, it is still a very common ion in minerals. So, we now have ribose. I assume we can keep it stable while we set about the difficult task of making nucleosides. I say difficult because it appears we are going to require nitriles. Purines appear to be most likely a product of hydrogen cyanide (HCN) and pyramidines perhaps from hydrated cyanoacetylene C3HN, both fairly common in space, but could they have been produced on Earth? Edited by Doddy, : formatting Edited by Doddy, : minor correction Edited by Doddy, : correcting the correction Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
I only said it was hard because that is one of the main fronts of abiogenesis where creationists like to attack - synthesis of nucleobases.
Have a look at this page: No webpage found at provided URL: http://www.godandscience.org/evolution/rnamodel.php (never mind the fact that their references are almost all from the same person). Anyway, back on topic. I'll quote something from Leslie Orgel's 2004 paper "Prebiotic Chemistry and the Origin of the RNA World"
quote: So taking this route for now, we have the following reactions: Synthesis of PurinesPolymerisation of hydrogen cyanide to produce both adenine and guanine. Adenine - C5H5N5 5HCN + NH3 ’ C5H5N5 + ? Guanine - C5H5N5O 5HCN + NH3 + H2O ’ C5H5N5O + ? Synthesis of PyrimidinesPolymerisation of cyanoacetaldehyde in urea to produce cytosine, followed by hydrolysis of cytosine to uracil. Cytosine - C4H5N3O C3H3NO + (NH2)2CO = C4H5N3O + H2O Uracil - C4H4N2O2 C4H5N3O + H2O ’ C4H4N2O2 + NH3 Next step, and also quite difficult (scientifically, not in terms of creationist attack this time) is the formation of nucleosides - we have to join that ribose to our freshly made nucleobases. You'd better be quick too - creationists have evidence that these bases will only last for a few decades! Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Matt P writes: Alternatively, you could use formamide (HCONH2) coupled with TiO2 to form nucleobases in pretty good yield (Saladino 2003). Interesting. I have also noticed that one could use 90%N2-10%CO-H2O gas mixture in , producing guanine, uracil and cytosine (Miyakawa et al, 2000; "Abiotic synthesis of guanine with high-temperature plasma." Orig Life Evol Biosph 30:557-566.)
Matt P writes: heating nucleobases with ribose for a few minutes at 130-160 C will form nucleosides Ok, well adenosine (thus probably guanosine too) can be formed by the simple heating and dehydrating reaction, but what about the others? Adenosine - C10H13N5O4 C5H5N5 + C5H10O5 ’ C10H13N5O4 + H2O Seeing as many researchers haven't found a simple method for prebiotic synthesis of pyrimidine nucleosides, and have even proposed that perhaps the modern pyrimidine nucleosides are not the same as those of ancient life, then perhaps we shall have to skip over this problem.
Matt P writes: I'm anxiously awaiting your next step/question, since that's one I did my dissertation on! Next step is phosphorylation (although it may have occured before the formation of nucleosides) of the 5' carbon on the ribose. If that's something you know a lot about Matt, then I'll hand over to you. Edited by Doddy, : minor correction of html Edited by Doddy, : spelling Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Ok, that will be enough to create nucleotide triphosphates, I take it?
I'll just provide one reaction, as most will be much the same. This is a phosphorylation using an orthophosphate, such as calcium phosphates (found in minerals like hydroxylapatite), under acidic conditions. According to Lohrmann and Orgel (Science, 1971), this reaction is catalysed by urea at 100oC, especially in the presence of ammonium chloride. Adenosine Triphosphate (ATP): C10H16N5O13P3 C10H13N5O4 + 3PO43’ +9H+ ’ C10H16N5O13P3 + 3H2O Let us not forget also that this may not have been the way it happened, and ribose may have been phosphorylated before being incorporated into the nucleobase. Next step: polymerisation Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
You do have a point Rob - the conditions that chemists can create are likely to be far more favourable to the creation of life than was present primordially. I once read that it was like a golfer putting a golfball into the hole, then surmising that wind, rain, tornadoes and earthquakes could have done the same, given enough time.
However, it isn't especially likely that life originated in this manner. Not only are these steps quite probably not the ones that occurred, but a ribozyme might not even be the first sort of life (if the RNA world isn't true). But then, a few humans have only looked at this problem for a few dozen years, whereas there were billions of years and billions of planets for this to occur randomly. I don't care how smart you think humans are, or how dumb you think chemical reactions are - I have no problem believing that this would have happened. Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes:
The very definition of life, as proposed by Schrdinger, is something that organised itself - negative entropy. However, negative entropy is not restricted to life. Snowflakes are an example, but I think a better one is galaxies - the force of gravity caused them to organise, forming a lower entropy state. It isn't to hard to imagine, at least for myself, that such a low entropy state would happen upon a formation that could indeed become reproducible (in that life must grow).
it is 'counter emperical' to believe that nature organizes anything. Nature tears down. Rob writes:
As Dr Jones* tried to point out, albeit slight erroneously, life itself isn't prohibited by the second law. DrJones* was right in that the particular interpretation of the second law stating "everything tends to a higher entropy state" only applies to closed systems, although the law has no problem dealing with open systems - you just need to factor in the enthalpy change too.
The information that we do have (ie emperical) says no. In particular the 2nd Law of Thermodnamics. Rob writes:
To discuss this in depth would drag the thread off topic, but suffice it to say that supernatural things are not only beyond the scope of science, but indeed one must presuppose their non-existence if one intends to investigate the natural world. Else, one can never be sure if one is observing the natural or the supernatural world, thus making all experiments meaningless.
To presuppose (unscientifically but rather philosophically) that everything is material in origin is also falacious. To exclude philosophical coherence as a valid test, purely on philosophical grounds does not follow. It is utterly illogical. Rob writes:
The fact that certain conformations of RNA are able to reproduce others is precisely what drives the RNA world hypothesis. That is why I asked to make a ribozyme, as it is an RNA molecule that can make another RNA molecule. It is DNA that is dependant on RNA, not the other way around, as a strand of DNA cannot, IIRC, be created by itself, but must extend from an RNA molecule (which is then degraded to be replaced with DNA).
Especially since every component in the cell, is produced by the code in the DNA in conjunction with the other macinery in the cell. Even RNA is transcribed from the DNA, no? So what good is RNA on it's own. Rob writes:
It is unlikely that current life-forms are the simplest form of replication that can exist. Just as I would say that current media players (eg an iPod) are unlikely to be the simplest that exist (a record player? a phonograph?). It is only those lifeforms that are complicated enough to survive for billions of years that will be seen today, not the simplest ones.
What are the implications if no other form exists (a negative affirmation that cannot be proven)? But for arguments sake... what are the implications? Rob writes:
But we do have evidence for one - we see a self-replicating cycle, and it is only extrapolation backwards that leads to the assumption of one existing. It's an entirely different thing with supernatural beings, but I fear dragging this thread off the rails if I elaborate.
Why can't we assume that no other self replicating cycle exists, because we have no evidence of one? Rob writes:
Oh yeah, that is the case. It's not extremely unlikely, but I wouldn't have money on it, personally. After all, the areas where one RNA molecule would exist are likely to be friendly to others. It is also likely that this didn't occur in a vast ocean, but a small pond or something. But yeah, it's not likely, but it's possible.
You end up needing a whole bunch of different but coincidentally compatible RNAs (in some form) that converge in the same time and space. I know your familliar with all of this... I just confess complete incredulity. Rob writes:
Bold words coming from a self-organizing system such as yourself!
There's just no such thing as self-organizing. Rob writes:
As I said above, a self-perpetuating low entropy anomaly violates no known law of physics, whereas a perpetual motion machine does.
And to me it is just as unlikely as a perpetual motion machine, that not only perpetuates, but also grows. It's a bad analogy... but it makes the point. Rob writes:
Why not? Knowledge is good. All of this aside, let's assume that you (or anyone else) were able to solve this problem. I can't help but wonder... why do you want to solve it?[ Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes:
I'm sorry, but that is the entirety of it. Speaking for myself, however. I'm just curious about this stuff. I'm sure much the same reason applies to other scientists. Plus, it helps me learn about organic chemistry. I must say Doddy... I would have expected such anti-depth from the script of a low budget flick... but not from you. I didn't ask that question for my benefit... but your own. What answer did you expect? "We want to learn about this so that we can better support our materialistic worldview by explaining how life doesn't need a creator." Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes:
Extrapolation is scientific. It is assuming something without any evidence from which to extrapolate or interpolate that isn't.
But it is exactly this 'extrapolation' that is purely 'theo' and is not science (even in terms of the current convention of methodological naturalism). Rob writes:
What is the difference? In order for something to replicate, it must go from one organised entity to two organised entities. Thus, it must have a mechanism of organisation - anabolism ('organising' reactions). Replication is just one major form of this type of metabolism. So replication is self-organization. I think we must distinguish between a self replicating cycle, and a self organizing cycle. A self replicating cycle is easy really, but it comes after the organization of the system. What do you think? It is possible that anabolism precedes replication, but this thread shall assume otherwise for the reason that most research has been done on the replicator-first hypothesis. Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes: The 'mechanisms' and preplication is regulated by a preexisting code and organization. What is the origin of the order which dictates the replication? Excellent question! I'm sure you know that biological information is not the only order in the universe. Look at the orderly rotation of the heavenly bodies, for instance. Why shouldn't biology ultimately be driven by physical laws? Thus, the origin of order is not a topic for this forum, but for the Big Bang forum section, where you can discuss the origin of the laws of the universe to your hearts content. Right, let's get back on to the current topic in this organic synthesis. This is probably the one that creationists go on and on about, so be warned. In my last post (way back in post 12), I had accepted the explanations of Matt P and my own research into the field of synthesis to the extent that I showed it wasn't impossible that the bases of RNA could have formed. We might not have pursued the correct biochemical pathway, but at least it's not inconceivable. Now, the next step is to join the RNA bases together. I'm sure everyone knows that RNA is joined together by phosphodiester bonds between the 3' carbon atom of one ribose and the 5' carbon of the other? That's two carbons joined together by not one oxygen (an ester) not two (a diester) by two oxygens and a phosphorus, as part of a phosphate (a phosphodiester). See this image if unsure on that: No webpage found at provided URL: http://www.ktf-split.hr/glossary/image/rna_en.gif Note also that unlike in DNA, the 2' carbon atom of RNA also has an -OH group, allowing it to form 2'-5' linkages as well as 3'-5' linkages. Now this is what a normal RNA nucleotide trisphosphate looks like - this is Adenosine Triphosphate (ATP): C10H16N5O13P3:
When two nucleotide trisphosphates polymerise, the excess phosphates (and the hydrogen of the hydroxyl group of the ribose) are released. In aqueous solution, this polymerisation reaction is not thermodynamically favoured, however, so there must be a source of energy. It doesn't take much, even moderate temperatures can enable a net polymerisation reaction to proceed, although this is a very slow process. As such, it isn't really known how far this polymerisation can go (who wants to wait for decades to get a paper out of this?). Regardless, this reaction doesn't need to synthesise a large molecule - a ribozyme may only be a few hundred nucleotides in length. Single stranded molecules will influence the synthesis of their complement, as the hydrogen bonding between complementary nucleotides will increase the probability of their ligation (in the same way that your friend's partner and your partner are more likely to meet than if they were just loners). dsRNA naturally forms helical structures. The problem that creationists bring up, however, is the likelihood of a given ribozyme occurring by random polymerisations reactions. I think that will be a good next topic, given that that is the last step for this discussion. Edited by Doddy, : clarify Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes:
You're confused. ATP is an energy medium. ATP is no more a source of energy than a battery is a source of energy. That is, in local systems, you can consider a battery to be a source of energy, but ultimately the energy came from somewhere else. The only ways that an organism can gain energy from the environment are listed there.
Why do they not mention ATP? Could it be because they don't want to confuse you with the facts?Rob writes:
Because it doesn't make sense. Given that we know that animals alive today aren't the same as they were 300,000,000 years ago, why shouldn't we assume the same is true of metabolic processes? Anyway, this is digressing.
Why, if we know what exists now, can't we assume that the same processes existed then? Rob writes:
I wish we knew. It's a mystery. But we can make intelligent hypotheses about what could have gone on, try to replicate it or compare it to known reaction parameters to corroborate the hypotheses, and use those to make some more hypotheses. That's science. As for origins, we simply don't know, except that you... do know... Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others. Registration not needed, but if desired, register here!
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Doddy Member (Idle past 5929 days) Posts: 563 From: Brisbane, Australia Joined: |
Rob writes:
You can have devices that run directly off the mains. So, likewise you could have primitive organisms that don't store energy. And the current batteries aren't like they used to be, and indeed soon may be replaced by fuel cells or similar. Likewise, it is unlikely that living creatures always used exactly what is present today.
Of course... I assumed you would understand why I mentioned ATP. the issue is one of converting the 'raw energy' into a useable biological form. How is that done without the complex functions we see in life. Rob writes:
That is perhaps a flaw in my aralogy, but the main point of it rests untouched. ATP, and other nucleotide triphosphates too, do indeed 'just happen' to provide energy to the cell. Or rather, energy to the cell 'just happens' to use nucleotide triphosphates. It's quite possible to have another form of energy. A battery doesn't just happen to provide energy to a machine. It exists for that purpose. We seek contributors with a knowledge of Intelligent design to expand and review our page on this topic. Registration not needed for editing most pages (the ID page is an exception), but you can register here!
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