For fuck’s sake, Gaspode, can you simply get over the fact that Ben misspoke/was wrong when he said that CO[sub]2[/sub] was organic? I mean, the definition everyone is given in general chemistry is “a compound is organic if it contains carbon.” I don’t think I’ve ever been explicitly told that there are exceptions to this rule. I had to pick it up in context, when professors would say things like, “inorganic substrates, such as phosphates, carbonates, sulfates, etc.”
Even your quote above (published by Random House? WTF?) shows that there IS no hard-and-fast rule. Look at the wording, “are considered for convenience.” To me, that’s saying, “Yes, there is a rule saying that if it’s got carbon, it’s organic, but sometimes we re-define this rule, as with…” It’s all definition, semantics, and convention. Surely, you’d be ridiculed if you called acetonitrile (CH[sub]3[/sub]CN) inorganic, even though it does contain the cyanide/nitrile group.
Bottom line–let it go. Ben says that he’s a molecular biologist. Hey, they deal with large molecules anyways I doubt if he has to know the molecular formula of anything he works with. The molecular formula for most of the stuff he works with is probably indeterminate, anyways. Making a simple error does not wreck his credentials, and it’s not him clouding the issue. If anyone is clouding the issue, it’s you, by refusing to get past it.
Ok, you can get back to your argument from incredulity now. My other quick interjection–Avagadro’s number is 6.022 x 10[sup]23[/sup]. Even at concentrations of 10[sup]-7[/sup], we’re still talking about billions and trillions of molecules. Makes those odds seem much more reasonable, to me.
The line you are drawing between organic and inorganic is not as clear as you make it. If you ask any organic chemist whether -CN is organic, they will tell you, “Of course it is.” That is because organic chemists deal with the cyanide all the time. Look in the front cover of any organic chemistry group and cyanide is listed as an organic functional group. Often times the division depends on the context. For example most chemists would agree that Cr(CO)[sub]6[/sub] is inorganic. But most would say that the -CO[sup]+[/sup] is an organic group.
The definitions you are giving are useful for biologists. They like to track where carbon can enter the bioshpere. If a carbon compound can be easily metabolized (like carbohydrates), it is considered organic. If a carbon compound cannot be metabolized, or can only be metabolized by very special processes (the fixing of CO[sub]2[/sub] in the Calvin Cycle) the compound is considered inorganic.
To a chemist these lines seem rather arbitrary since often there are many chemical reactions that we can do to introduce carbon into a complex molecule using so-called “inorganic” sources. Since organic chemistry is the study of the chemistry of carbon many organic chemists consider any carbon containing compound as organic.
This is why I believe Ben misspoke and was not intending to decieve. Most chemists don’t care about the precise definition of organic. They only care about the starting materials, the products, and what happens in between. Besides, I belive it is pointless to harp on this point any longer. Ben already admitted he made a mistake several posts ago. As a general rule, if someone says something you disagree with, and you call them on it, and they admit their error, then that should be the end of it.
I thought Sidney Fox was the one who did the experiment where he synthesized amino acids from primordial organic compounds using electric sparks. Turns out, Fox had nothing whatsoever to do with that experiment – it was carried out by Urey and Miller.
Sidney Fox was the one who took amino acids, baked them under ultraviolet light, and discovered that this created short chains of amino acids called proteinoids (some of which had catalytic properties). Later, in the 1970s, Fox discovered that by taking a lump of hot proteinoids and soaking it in a salt solution for a few minutes, these microscopic (1 micron across) balls would break loose from the lump of proteinoids and float around in the solution. He called them “proteinoid microspheres.” They share much of the behavior of common bacteria – they “eat” material from their surroundings, they grow, and they even divide, though they carry no genetic information along with them.
Theoretically, since proteinoid microspheres can be created abiotically, and RNA can be created (and self-replicate) abiotically, some proteinoid microspheres might have “eaten” some RNA and been unable to “digest” them, whereupon the RNA continued to “live” inside the proteinoid microspheres symbiotically – in much the same way that mitochondria inhabit eukaryotic cells today. This microsphere/RNA symbiosis may have been the first cells.
For all your protestations, Gaspode, it seems to me that you are clearly- and falsely- ascribing bad motives to me in this thread. As has already been pointed out, for all the verbiage you have expended on this point, I have apologized for an error which was already entirely irrelevant to the point at hand. To say that I “decided to cloud the issue” is entirely uncalled for.
In fact, you are the one “clouding the issue with incorrect and misleading statements.” Here’s your summary of some earlier points in the conversation:
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If you simply look at the original context of my statements to which Gaspode is referring, you’ll see that he’s done some mixing and matching. I made two statements: one, that some experiments had shown that prebiotic conditions can produce RNA. Two, that starting from random RNA sequences, selection in the laboratory can produce functioning ribozymes. Gaspode has taken these two statements of mine out of context and juxtaposed them so as to make it appear that I brought up the second experiment in response to Gaspode’s request for more information about the first, when in reality, I mentioned both experiments in my original post! Gaspode then goes on to say that as a professional biochemist, I should know that the experiment involving selection of RNA strands doesn’t prove that RNA can be created under prebiotic conditions. Not only did I never claim it did, I also explained more than once, including in my original post, that the selection experiment only showed that the chances of a pool of random sequences containing a functional ribozyme are quite high!
Sorry, Gaspode, but I think my original statements were quite clear. The reason that you are the only person who has a problem with them is because you’re the only person who can’t keep straight what I actually said.
The random RNA strands to ribozyme experiments are called SELEX. This is how it is performed, to initially select for RNA sequences which bound a protein[sup]1[/sup] :
Start with a random poool of RNAs.
Perform multiple rounds of RNA-binding to protein of interest. This is done by affixing protein of interest to plastic beads, and then incubating said beads with proteins. Various wash conditions are done to eliminate non-specific RNA binding.
Tuerk and Gold. “Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.” Science 1990 Aug 3; 249(4968):505-10
SELEX has been used many times. Go to PubMed and type SELEX. 133 hits. It has been used to do all types of things. To explain how this may happen in a primitive world for auto-replication, step 1) could be creation of many mono- and poly- nucleotide chains of RNA or “proto-RNA.” Steps 2) - 4) would be replaced by the auto-replication of RNA out of the pool of mononucleotides. RNA is of course synthesized from nucleotides, but SELEX is done by individual selection, hence Ben’s use of the term “evolution.” Just like humans are made from proteins but evolution acts on individuals. The criterion for selection in this case is of course replication.
This is done by affixing protein of interest to plastic beads, and then incubating said beads with RNAs. Various wash conditions are done to eliminate non-specific RNA binding.
Actually, in the experiments I heard about they selected for more than just protein binding- specifically, for RNA polymerase and restriction activity.
I don’t understand your problem here. Scientists have duplicated in the lab their best approximation of the state under which these reactions were to have taken place, then ran the experiment. Considering that the atmosphere and biosphere are radically different now, how do you propose that they run the experiment without such shelter? What, exactly, is the experiment sheltered from that you think it should have been exposed to?
I’m staying out of the biochemistry debate but I will weigh in on if evolution is provable or not…I’'d weigh in on the yes it is provable and without the need for a Megayear long experiment or a time machine.
For examples see:
A) <B>Bacteria and antibiotic resistance</b>. IIRC in less than 5 years after theintroduction of Penicillin the first strains of bacteria resistant to penicillin appeared. If that isn’t a case of evolution in action. and a very direct proof that could be proved in the lab.
B) Central American High Elevation Arboreal Pitvipers in particular the <i>Botriechis nigroviridis</i> complex. They used to classify them as one species from Chiapas to Costa Rica until someone took a close look at their taxonomy and found out that they could interbreed with each other. All the species are remarkably close in appearance but differ in genetics. All of them are isolated at high elevations above 1,800 meter in rain forests.
C) <b><i>Rana catesbiana</i> complex in the Americas.</b> <i>Rana catesbiana</i> used to be considered as one species ranging from Canada to South America. it wasn’t till someone tried breeding frogs from populations that were separated by more than 1,000 miles that they found out they were dealing with differing species. in fact frogs from the middle of the range could not breed period with frogs from either extreme of the range. The end result was that the <i>Rana catesbiana</i> complex was split into multiple species.
D) <b><i>Drosophila melanogaster</i> (Fruit flies)</b>. I seem to recall reading about some experiments that where done in Australia on fruit flies in which they selected for certain traits in 2 experimental groups of flies. I do not specificly recall what triats where selected but they were related to reproductive biology. The end result was that by the end of the experiment neither group of flies could crossbreed with the other.
I doubt if he has to know the molecular formula of anything he works with. The molecular formula for most of the stuff he works with is probably indeterminate, anyways. Making a simple error does not wreck his credentials, and it’s not him clouding the issue. If anyone is clouding the issue, it’s you, by refusing to get past it.