How to make a ribozyme (using abiotic starting compounds)

Percy:That information (in particular a complex code / language) arises from intelligent guidance. Be it written language or spoken, the word itself testifies the fact (which is particularly rich as a theological point as you know).What you guys need to do (and have not) is show how a highly specified complex code can originate without intelligence. The fact that the code exists does not equate to natural causes. What are you going to mutate?You can't mutate something that does not exist. To change or rearrange something, that 'something' must exist...Your talking about creation... mutation is something that happens after the fact. It is the same point I made to Doddy in my last post. And I provided a link that explains with much detail the coherent arguments. You're free to study it if you like...Also, I don't think genetic diversity is equal to mutation. Mixing genes of the father and mother doesn't necessarily mutate anything. It rearranges into a utterly unique individual with essential worth; no carbon copies.And from what I understand, most of the genes are present in previous generations, but not all of them are expressed. So, in different generations, preexisting genes may be expressed in offspring that were not in the parent or vice versa.That is why it is so important that words objectively mean things Percy. So that we cannot misuse 'replication' in place of 'organization', or 'creation' in place of 'mutation'.Do you concur?Btw... since this relates to the issue of an increase in information and not simply a net change... this is one of my favorite questions... For Dr. Dawkins answer you can follow this link and watch for yourself: Richard Dawkins And The 11 Second Pause Edited by Rob, : No reason given.

Random mutation and natural selection.But, look, the code isn't actually that complex. Here it is:That's it. That's the whole code. Three codons specify an animo acid according to this chart. It's true for nearly every single organism (there are maybe a few families of organisms that use a slightly different set of codes.) You've correctly identified sexual recombination as a source of phenotypic diversity that doesn't rely on mutation; but the mother and the father have to have different alleles in the first place, right? The different alleles they have to recombine come from mutation, initially.If there were no mutation, all individuals would be clones - regardless of recombination. If everybody is recombining the exact same cloned alleles, there's no gain in diversity. Er, no. The only way you can have a gene neither of your parents possess is by mutation. You may be confusing dominance with inheritance. A false account based on misleading editing.

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1. According to Dawkins, he paused because the question revealed that the interviewers were creationists, that he had been duped about their motives. He paused to think about how to handle them, and the change of subject occurred due to the several minutes when he confronted them being omitted from the video (Dawkins 2003).

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2. The question is equivalent to asking how complexity could evolve, which Dawkins has covered in at least four books (The Blind Watchmaker, River Out of Eden, Climbing Mount Improbable, and A Devil's Chaplain). He has answered the question at great length.

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3. The ability of a single person to answer a question is largely irrelevant. The scientific literature is rife with examples of information increasing.

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CB102.1: Dawkins interviewed about evolution increasing informationIt's a good example, but not of what you think. It's an example of the fact that there's no dishonest act creationists won't stoop to to attack scientists and science.

We already know that the creation of information does not require intelligent guidance. That was why I provided the example of mutation. Mutations, which represent the addition, subtraction or modification of information, arise in almost every reproductive event without any intelligent intervention whatsoever.In other words, additions, subtractions and modifications of information occur just by matter and energy following known physical laws. Mutation and natural selection (and allele remixing for sexual species) are all that is necessary to produce the diversity of life around us today, and the entire history of life represented by fossils in the ground. What other causes are there besides natural causes? Do you have evidence of something non-natural ever being the cause of something happening in the natural world? Of course not. (In the context of this question, people are of course part of the natural world.)We don't know the details of the origin of life, may never know the details given that it happened around 4 billion years ago, but the genetic code arose through the natural process of change and selection we're familiar with today, only with predecessor molecules of DNA rather than modern DNA.This is the answer to your later question about what is it that is mutating for pre-life: DNA predecessors, and the predecessors before them, and before them, and so forth until you reach a time when there were only relatively simple organic molecules. Yes, that's right, but I think what you probably meant to say is, "I don't think allele remixing is the same as mutation," and that is correct, they are not the same. Genetic diversity is just a measure of the richness of variety in the alleles of a species gene pool.Allele remixing is what happens in sexual species. In single-celled non-sexual species there is no such thing as allele remixing during reproduction. When a bacteria divides, the two resulting bacteria probably each have a small number of mutations. Bacteria can also perform a type of allele remixing called conjugation, where two existing bacteria temporarily meld to share genetic material.In sexual species, the difference of offspring from parents is caused primarily by allele remixing, but nearly every offspring also contains a small number of mutations. In other words, allele mixing and mutation are not mutually exclusive. I don't know, since I can't think of anything I said that this could be a response to, so it's completely out of context for me. All I can say is that scientists don't think of "creation" as a synonym for "abiogenesis", and I don't see anyone confusing terms except you, as you just did with genetic diversity and allele remixing. This is famous. Your website even provides the correct explanation for the pause: In other words, once the question was asked and the interviewers had been revealed to have misrepresented themselves, Dawkins was no longer thinking about the question. And by the time he answers he had evidently forgotten the question, because his answer is unrelated to the question.The question actually has a very simple answer. There are a number of different processes that add to information in the genome (though biologists don't usually think of genomes in terms of information, that perspective is much more common in ID). One of the simplest to explain processes, though not the most common one, is gene duplication. Occasionally cell division errors cause duplication of an entire gene. With two copies of the gene, one of them is now free to mutate independently to carry out a modified or even a new function, because the other gene is still there to perform the original function.--Percy

Percy:How so?Percy:I did not say that an intelligence was directly (or even indirectly) guiding every step of the process. I am not talking about intervention...The point is that 'the process of mutation' cannot explain the existence of the information that is mutating.Percy:Are you asking for materialistic evidence for the existence of the non-material? Kind of a no-win for me isn't it? Nice ground rules... Is philosophical coherence legitimate evidence to you? It is after all, non material.Percy:You seem to be stating fact here... I am thankful that even though there is much disagreement, that Matt P, and Doddy (as two examples) are much more responsible in their description and beliefs. You could learn a few things from the more responsible and candid among us. I know I must strive to remember that myself...Percy:It is interesting (rather telling) that you call it an error.But the next time I see a kid with down syndrome, I'll remember that it is only nature doing her thing. Or is it an error?I could say more, but we're not going to agree. You believe what you must for the sake of your lifestyle demands (that is clearly what this is really all about... I won't name names... but I can read between the lines).I am not buying. In some ignorant and childish way, I might have liked to a point... being molested as a kid, but I wanted to believe the lies out of curiosity for 'more knowledge'.I have no such illusions now.

Down's syndrome isn't caused by gene duplication, but rather by improper assortment of chromosomes during meiosis.It has nothing to do with mutation. Evolution doesn't justify any sort of lifestyle. Indeed, if people like Ted Haggard are any indication, it's hardly necessary to be an evolutionist or even abandon fundamentalist Christianity to live hedonistically.Percy, like the rest of us - indeed like the vast majority of scientists - accepts evolution because of the vast weight of scientific evidence that supports it.

Crash:Thank you for that...What do you mean by improper?Is the syndrome a disorder, or just 'evolution' working it's random marvels?

The human body is chemistry. It's processes are stoichiastic. In meiosis, chromosomes assort equally into two daughter cells. Sometimes they don't. One cell gets one extra and the other gets one too few. Down's syndrome isn't heritable, so it really doesn't have anything to do with evolution. It's just a chromosomal disorder - not an example of the gene duplication that Percy was talking about.

Hi Rob,It's a little hard to track your reasoning in your opening couple points, so rather than replying directly just let me try to clarify the point I was making.I was under the impression that one of your points was that the creation of information requires an intelligent source. This is untrue, as mutations (errors in copying during reproduction, a natural process) add, subtract and modify information.If that wasn't really one of your points and you already understand that, then that's a good thing. Sure it can. Consider a single bacterium, just to keep it simple. This bacterium was the product of a cell division which likely produced a few mutations, so this bacterium likely possesses a few differences in its DNA from the original bacterium, call it the parent bacterium.Now the parent bacterium was also the product of a cell division which likely produced a few mutations, so the parent bacterium likely possessed a few differences in its DNA from it's parent bacterium, which we'll call the grandparent bacterium just to keep the names unique.In turn, the grandparent bacterium was also the product of a cell division which likely produced a few mutations, so it was different in its DNA from the great-grandparent bacterium.And the great-grandparent bacterium was different in its DNA from the great-great-grandparent bacterium.In other words, the information that is mutated in each generation came from the previous generation, and the previous generation's information came from the generation before that, and so forth. I don't know if it's a no-win situation for you, because I don't understand your argument. You said the fact that the DNA code exists does not equate to natural causes. The DNA code exists in the natural world. If you believe the DNA code came about through non-natural causes, and if you believe there can never be any evidence for things in the natural world that have non-natural causes, then you are invoking a cause for which you have no evidence.And that's why I said you have no necessity for resorting to claims of non-natural causes, because natural causes are not only sufficient to explain what we observe in nature, we actually have real world evidence for them. But you're ignoring the point, which is that the same process of change and selection observed today is also believed to have caused simple organic molecules to gradually acquire the self-replication capabilities that led to life and eventually all the diversity we know today. Mutations are the result of copying errors during reproduction, there's no secret about that. Mutations can also be caused by radiation. Theories become accepted based upon the degree to which they're supported by and explain the evidence, as well as they're demonstrated predictive power over time. Evidence is something you lack for your non-natural causes.--Percy

[Adminnemooseus persona]
Can anyone tell me what rob's posts and subsequent replies have to do with (a) this thread in general and (b) the "Re: Synthesis of Nucleotides" sub-thread? If you're going to go off on another ROB tangent at LEAST give it a new subtitle ...
[/Adminnemooseus persona]

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Just a reminder: this topic was intended to ask a specific question of those who had knowledge in organic chemistry.The past dozen or so posts have drifted to a recurring topic which is, well, off topic. Unless everyone is agreed that the original has run its course, please allow the thread focus to stay close to what you would expect to find under the title.

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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.gifNote 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

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Doddy: Heat only provides the correct environment for the processes. So you need energy for the environment, and then energy to sysnthesize.The soure of energy for these reactions is stuff like ATP and GTP. Not that I am very knowledgeable about it all.So why don't you explain just one step in the procedure for me...How do you synthsize AMP?Remember, as Percy said, we'll keep it simple... we won't even talk about a bacteria though...Just 'AMP' will suffice. More importantly (and one step back into more complexity, not less)... how do you make the ATP used to synthesize ADP?It's sooooo simple.http://www.emc.maricopa.edu/...farabee/BIOBK/BioBookATP.htmlEdited by Rob, : No reason given.

Nope. http://www.arxiv.org/pdf/q-bio.PE/0501013Of course modern ATP synthase didn't exist back then. Nobody's claiming it did. Except you, I mean.Furthermore. The polymerization was probably catalyzed. Catalyzation of this sort has been done in the lab. The catalyzed polymerization rate was greater than the uncatalyzed polymerization rate by a factor of 10e9. (Gosh darn it! What's the code for "superscript"? I hate this whole 10e9 business.) Anyway. That's a billion to you and me.The catalyzed polymerization rate is really thermodynamically favored. That means that the reaction is going to be "pushed" in the direction of polymerization. ATP is not necessary. Actually, nothing else is necessary. It's like putting a ball on the side of a mountain. It's gonna roll down hill. The energy state of the ball at the bottom of the hill is lower than the energy state of the ball on the side of the mountain. So it will happen.



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