Talk:RNA world/Archive 1

Title of first section
I've just removed the &ldquo;In the beginning&rdquo; from the first section; especially given the topic, it seems unwise deliberately to antagonise Jud&aelig;o-Christian believers.

The only other edit that might arouse controversy is linguistic: I've changed 'catalyze' to 'catalyse'; this isn't a U.S./U.K. thing (and I've left other '-ize' spellings), but 'catalyse' is a back-formation from 'catalysis', and there's simply no reason to spell it with a 'z'. I'll not revert it if someone feels strongly enough to change it back. Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 12:21, 18 Feb 2005 (UTC)


 * Agree with section title change - good move. However, it's been z since the beginning in 2001 so let's follow wiki spelling rules. Also do a simple search with catalyse on Google - the first two pages are French - nothing English there. -Vsmith 15:06, 18 Feb 2005 (UTC)
 * Yes, the French tend to be more careful about such things. But I'll grit my teeth and bear it. Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 15:14, 18 Feb 2005 (UTC)

Carl Woese
but the concept itself originated with Carl Woese in 1967.

I've just moved this here because, after checking nine article on Woese on the Web, I could see no evidence that it's true. before it goes back in the article, could anon provide a reference? Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 15:38, 18 Feb 2005 (UTC)


 * It was in his book The Genetic Code, New York: Harper and Row, 1967. Notice, he didn't call it RNA world, but he had the idea, i.e. that the first organisms were RNA.


 * More backup:


 * Ribozyme Engineering and Early Evolution BioScience 48(2), February 1998


 * The notion that RNA could be an enzyme was first proposed 30 years ago by Francis Crick and others (Woese 1967, Crick 1968, Orgel 1968) in an effort to explain the origin of life.


 * The RNA-World


 * In the late 1960s Carl R. Woese of the University of Illinois, Francis Crick, then at the Medical Research Council in England, and Lesley Orgel of the Salk Institute for Biological Studies in San Diego independently proposed that RNA based organisms might well have come before the DNA and protein based organisms that currently infest Earth. They established what is now called the RNA-World hypothesis; a world in which RNA catalyzed virtually all the reactions necessary for a precursor of life's last common ancestor to survive and replicate. The motivation for favoring RNA over DNA as the medium for coding genetic information is that RNA is considerably easier to synthesize than DNA. (Bold added)


 * Scientists Debate RNA's Role at Beginning of Life on Earth


 * Although the phrase "RNA world" is generally attributed to Walter Gilbert, Harvard University's Carl M. Loeb University Professor, in a short 1986 paper, the idea of RNAís importance at the beginning of life was discussed two decades earlier.


 * The RNA world hypothesis has fueled diverse research approaches, drawing from geology, biochemistry, and evolutionary biology. RNA world studies have been strong and steady for a decade. Researchers are re-creating early Earth conditions, discovering new RNA activities, and uncovering clues to life in the most ancient rocks.


 * Yet the central role of RNA at lifeís debut is hardly settled. "The world is divided into those who say it was RNA and those who say no because it is hard to make RNA nucleotides and conditions on the prebiotic Earth were not favorable for that," says Leslie Orgel, senior fellow and research professor at the Salk Institute for Biological Studies in San Diego. Orgel and, independently, Francis Crick at the University of California, San Diego, and Carl Woese at the University of Illinois in Chicago suggested a role for RNA in the origin of life in the late 1960s. (Bold added)


 * Would you please restore the sentence? 138.130.195.166 16:16, 18 Feb 2005 (UTC)


 * I'd already restored a version of it &mdash; see below. Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 16:42, 18 Feb 2005 (UTC)


 * Thanx. 138.130.194.229 06:13, 19 Feb 2005 (UTC)

anon has provided a refernce that seems to back up, if not the claim above, then a similar one (though the rerference was added with the disingenuous remark that an avowedly Intelligent Design-based criticism couldn't be seen as having any religious content...). Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 15:51, 18 Feb 2005 (UTC)


 * Nope, I challenged people to find any in the article concerned.  That should be all that matters when deciding whether the article belongs.  It has also been rightly pointed out that there are a number of evolutionists who have religious/philosophical motivations for their views too.  Dawkins readily comes to mind with this obsessive atheism 138.130.195.166 16:16, 18 Feb 2005 (UTC)


 * Well of course there are &mdash; and as an atheist, I find Dawkins, Atkins, and others extremely embarrassing. But then I shouldn't cite their writings as evidence in any scientific debate (I doubt that Dawkins would recognise the inside of a biology lab, it's been so long since he did any scientific work). Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 16:42, 18 Feb 2005 (UTC)


 * Despite our clear ideological differences, we seem to agree on something :) BTW, why have you transliterated &eta; as i instead of &#275;? 138.130.194.229 03:36, 19 Feb 2005 (UTC)


 * You're thinking of classical Greek; this is modern. It sometimes seems as though all the vowel sounds have become 'i' (though I should add that it's not my transliteration; I got it from some on-line dialogues on the philosophy of religion Is Nothing Sacred?). Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 10:17, 19 Feb 2005 (UTC)


 * All the same, the good thing about Et&#275;t&#275;s is that it's clear that the Greek is &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; -- some might pronounce it the classical way, others the modern way, but no one would ever think that the Greek is &Epsilon;&tau;&iota;&tau;&iota;&sigmaf; which most people would think of Etitis.138.130.194.229 16:04, 19 Feb 2005 (UTC)

Actually, I think that most people wouldn't know what on Earth '&#275;' meant... Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 16:12, 19 Feb 2005 (UTC)
 * Yeah, that's a point 138.130.194.229 02:42, 20 Feb 2005 (UTC)

Chemical objections
What was wrong with this:

A.G. Cairns-Smith argued that there were far too many chemical difficulties for any nucleic acid to arise abiotically (Genetic Takeover: And the Mineral Origins of Life ISBN 0-52123-312-7, (numbered list format added)):


 * The implausibility of prevital nucleic acid

....


 * Let us consider some of the difficulties.

First, as we have seen, it is not even clear that the primitive Earth would have generated and maintained organic molecules. All that we can say is that there might have been prevital organic chemistry going on, at least in special locations.

Second, high-energy precursors of purines and pyrimidines had to be produced in a sufficiently concentrated form (for example at least 0.01 M HCN).

Third, the conditions must now have been right for reactions to give perceptible yields of at least two bases that could pair with each other.

Fourth, these bases must then have been separated from the confusing jumble of similar molecules that would also have been made, and the solutions must have been sufficiently concentrated.

Fifth, in some other location a formaldehyde concentration of above 0.01 M must have built up.

Sixth, this accumulated formaldehyde had to oligomerise to sugars.

Seventh, somehow the sugars must have been separated and resolved, so as to give a moderately good concentration of, for example, D-ribose.

Eighth, bases and sugars must now have come together.

Ninth, they must have been induced to react to make nucleosides. (There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry-phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides (Orgel & Lohrmann, 1974).)

....

Eleventh, phosphate must have been, or must now come to have been, present at reasonable concentrations. (The concentrations in the oceans would have been very low, so we must think about special situations &#8212; evaporating lagoons and such things (Ponnamperuma, 1978).) Twelfth, the phosphate must be activated in some way &#8212; for example as a linear or cyclic polyphosphate &#8212; so that (energetically uphill) phosphorylation of the nucleoside is possible.

.... Fourteenth, if not already activated &#8212; for example as the cyclic 2',3'-phosphate &#8212; the nucleotides must now be activated (for example with polyphosphate; Lohrmann, 1976) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent must now have been fed into the system. Fifteenth, the activated nucleotides (or the nucleotides with coupling agent) must now have polymerised. Initially this must have happened without a pre-existing polynucleotide template (this has proved very difficult to simulate (Orgel & Lohrmann. 1974)); but more important, it must have come to take place on pre-existing polynucleotides if the key function of transmitting information to daughter molecules was to be achieved by abiotic means. This has proved difficult too.....

Seventeenth, all reactions must have taken place well out of the ultraviolet sunlight; that is, not only away from its direct, highly destructive effects on nucleic acid-like molecules, but away too from the radicals produced by the sunlight, and from the various longer lived reactive species produced by these radicals.

....

Nineteenth, what is required here is not some wild one-off freak of an event: it is not true to say 'it only had to happen once'. A whole set-up had to be maintained for perhaps millions of years: a reliable means of production of activated nucleotides at the least. ....

This is an NPOV encylopedia so what was wrong with providing some comprehensive opposition to RNA world? However, some evolutionists evidently couldn't bear this, so just deleted this wholesale, then accused ME of vandalism, the hypocrites.

BTW, Cairns-Smith is an evolutionist, but it shouldn't make any difference whether he is or isn't because all that matters is whether his chemistry is sound.138.130.194.229 02:41, 20 Feb 2005 (UTC)


 * Sorry, I apologise for using the word "vandal" for this revision because this reviser has many times shown himself to be honorable, and the summary was fair.138.130.193.136 12:22, 23 Feb 2005 (UTC)

Please see Requests for comment/138.130.194.229. Dunc|&#9786; 16:48, 19 Feb 2005 (UTC)

Some cleanup
I've edited part of the "implications" sections for some cleanup and some ideas which are slightly inaccurate. Firstly, it was claimed that before the RNA world hypothesis, life was thought of purely in terms of DNA and proteins with RNA as inert messenger transfer. Although this is true for much of the time following the major discoveries of molecular biology, work carried out beginning around 10 years ago has shown that RNA plays a much bigger number of important and interesting roles - and so it is not correct to speak of the RNA world hypothesis revolutionising "today's" view of molecular biology - as "today's view" already emphasises the importance of RNA, and these disoveries were not really prompted by a desire to investigate the RNA world hypothesis. I've also removed:


 * requiring that we define life primarily in terms of RNA and the set of strategies that RNA has used to perpetuate itself.

This is (as mentioned below) essentially philosophy, not falsifiable science. What is meant by "defining" life? Molecular biologists only seek to describe and explain, not define life. Additionally, it assumes that the RNA world hypothesis has been robustly tested and supported by evidence - and while it is a interesting and plausible *hypothesis*, this simply has not taken place. Additionally, there is an error in discussing the structure of the ribosome:


 * with proteins playing only a structural role in holding the ribosomal RNA together

This is not correct. In prokaryotes, the ribosomal RNA consists of the 23S and 5S in the large subunit, and 18S in the small subunit. Because it is a covalent polymer, the rRNA holds itself together; the interface between the two subunits is conspicuous for its lack of protein; as is the interface between the 23S and 5S fragments. Hence, the proteins are structurally peripheral. --163.1.176.68 19:58, 12 July 2006 (UTC)


 * The RNA world hypothesis, if true, has important implications for the very definition of life. We may be too ready to define life in terms of DNA and proteins. After all, in today's world, DNA and proteins seem to be the dominant macromolecules in the living cell, with RNA serving, for the most part, as a mere messenger between them. But the RNA world hypothesis places RNA at center-stage when life originated, and therefore requires that we define life primarily in terms of RNA, and only secondarily in terms of DNA and proteins. If the RNA world hypothesis is true, life can be defined as the set of strategies that RNA polynucleotides have used and continue to use to perpetuate themselves.

Whether RNA was the first form of "life" or not is nice scientifically-falsifiable theory. But all these philosophical interpretations can't be automatically attached to the theory. Let's not forget that whenever group of organisms are totally dependent on each other in reproduction, and RNA, DNA and proteins crearly are, there is no conflict of interest between them and interpretation from POV of any of them is not any less good than interpretation from POV of others. So it doesn't need to have such philosophical implications. --Taw


 * I know I seem ignorant (I am), but how is the RNA world hypothesis a scientifically-falsifiable theory? I'm honestly, genuinely interested. I've been looking around the web for an answer for a long time. It states that life emerged from a self-replicating RNA molecule. What experiment could refute that? Would we need to map all the possible combinations of the RNA molecule in order to prove that it's not duplicating itself? That's surely impossible.--213.253.208.133 06:46, 4 October 2005 (UTC)


 * One doesn't need to prove that the hypothesis is without-a-doubt the mechanism by which life began. If that were the case, virtually no scientific theory would be valid.  Rather, one needs to demonstrate that, first, the hypothesis is consistent with itself and with the body of scientific knowledge as it stands today (i.e., it's possible), and second, that it is more plausible than any other hypothesis in the running.  That's all science asks.  Teflon Don 05:52, 18 February 2006 (UTC)

How long would an RNA molecule have to live in order to reproduce itself? Granted there are two answers (one for today's fragile RNA and one for the RNA-world-type RNA); just curious whether anyone's thought about how tough RNA would have to be in order to be evolutionarily successful. --RjLesch
 * There's presumably no reason today's "fragile" RNA couldn't be a self-replicating molecule... RNA is only fragile because of RNase, which are ubiquitous (to fight viruses and the like). Without these, it's considerably more stable (although maybe not as stable as DNA). I don't think anyone has yet formed an RNA that could self-replicate (or an RNA-only polymerase), though this would of course be a major, major boost for the theory... so if someone wants a Nobel prize... your work is cut out for you. Graft

Actually, RNA is fragile because the equilibrium favors the monomers. RNase merely accelerates the approach to equilibrium. But even without RNase, RNA readily breaks down. In the cell, there are many repairing enzymes. Even DNA, far more stable than RNA, breaks down very quickly. Svante Pääbo found that DNA fragments a few hours after death into chains 100–200 units long, that water alone would completely break it down by 50,000 years, and that background radiation would eventually erase DNA information even without water and oxygen, ‘Ancient DNA’, Scientific American 269(5):60–66, 1993. 220.244.224.8 02:39, 18 Feb 2005 (UTC)


 * My guess is this is an evolutionary defense mechanism to prevent us from coming back as zombies. Graft 02:55, 7 October 2005 (UTC)

I recall reading somewhere about a theory that the first life used PNA instead of RNA or DNA; that's "peptide nucleic acid", IIRC. The nucleotide bases were mounted on a backbone that was joined together with peptide (protein) bonds instead of sugar phosphates, which was much more stable than either DNA or RNA in open solution. Anyone know what I'm talking about, or am I remembering phantoms? -BD
 * Read the scientific American article you referenced - seems pretty weak, it basically suggests that PNA COULD be a progenitor molecule, but doesn't purport to show that it WAS - if it says anything it's only that some complementing polymer was the original genetic molecule. Graft

Some things a lay person asks upon reading this: who has worked on, supported, first described the hypothesis, and when did they do so?

So, i note that there's an "RNA World" article (which only evolution links to). Any thoughts on which should be the actual page? Graft 17:46 Oct 15, 2002 (UTC)


 * It looks like this has been resolved. AdamRetchless 21:21, 9 Jul 2004 (UTC)

Weak definition
I think that this article presents a strong definition of "RNA world hypothesis" that is almost certainly wrong -- that first life was just RNA. However, there is also a weaker statement of the hypothesis that is strongly supported-- that at some point in the history of life, RNA molecules served both genetic and enzymatic functions, predating the modern DNA-RNA-protein genetic system. Today, we know of RNA molecules that serve genetic functions, and RNA molecules that serve enzymatic functions, but we don't know of molecules that serve both functions. I'll have to look into this... AdamRetchless 22:05, 10 July 2005 (UTC)

Agreed on your first part. The first sentence definitely must be changed. I don't think most supporters of the RNA World would describe it as "the first life-form on earth." Rather, I believe the idea is that RNA may have possibly acted as both the genetic material and enzymes for the first life forms.Superdoggy 05:28, 14 July 2006 (UTC)

Age of Genetic Code Paper
Have you seen the article relating comparative sequence analysis of transfer RNA by statistical geometry indicating that the genetic code is not older, but almost as old as our planet. That would put it some 4.57 billion years old and the first bacterial fossils then at 3.5 billion years in pillow lavas and stromatolites. The genetic code would predate the first cells by 1 billion years. Maybe it should be added for support of possible RNA world and for NPOV? GetAgrippa 00:23, 8 September 2006 (UTC)

Of course there are the harsh environment papers, carbon dioxide environment, and how salt water is incompatible with primordial soup reactions or RNA world. Although a new paper adding hydrogen with carbon dioxide changes the equation to favorable reactions. It keeps yo yoing. Still the recent paper of the age of the genetic code maybe worthy of mention. GetAgrippa 00:32, 8 September 2006 (UTC)


 * and the paper is......where?--Deglr6328 04:40, 8 September 2006 (UTC)

It is an old Science paper: Science 12 May 1989 244: 673-679. It does get me thinking about theories of the origin of the genetic code. I was always intrigued by the coevolution theory of the genetic code and genes and the role that transfer RNA like hairpins and their ability to carry amino acids was essential to that evolution. Some of that information would be supportive of an RNA world origin of life and the genetic code.We should also mention ribozymes strongly support the notion of an RNA world origin.GetAgrippa 09:47, 8 September 2006 (UTC)

Magnetitie chains forming RNA?
I once came across a paper that proposed magnetitie chains formed, through decades of evolution, RNA.

Has anyone any information on this? or the concept?

Any information would be appreciated. 69.76.192.205 02:53, 27 December 2006 (UTC)

Cleanup Feb 07

 * Sorry to put this at the top, but i think it has to be noticed!

I have carried out a large restructuring of this article, no information has been removed, and added information on the properties of RNA and its role as a ribozyme/information store etc. Hopefully this gives the article a more NPOV as it simply presents the facts of what is possible with RNA.

Unfortunately the article is still a mess! Particular attention needs to be given to the "Support"/"Difficulties" sections to provide a clear set of points both ways. The "Details of the RNA world" section also needs lots of help, unfortunately Im no expert so have left this alone.

Lets put this article on the road for a long, prosperous, NPOV future! - Zephyris Talk 13:55, 25 February 2007 (UTC)


 * Further to my previous comments there seems to be a fundamental misunderstanding of the role of the RNA world hypothesis in the history and origin of life. The RNA world hypothesis refers to the possibility that in the past the world was dominated by RNA based life, not DNA+protein based life. It is not, as this article suggests, a common explanation for the origin of life. - Zephyris Talk 15:23, 25 February 2007 (UTC)

Citations?
AFAIK, Walter Gilbert's article in Nature was published in 1986, not 1968. However, I don't know to correct the source. --193.2.69.113 12:59, 4 April 2007 (UTC)
 * Indeed - fixed and the DOI corrected too Codec 14:16, 4 April 2007 (UTC)

Theory or Hypothesis
Look at the first sentence of the article:

“The RNA world hypothesis is a theory…”

Well, which is it? You can’t have it both ways. Rather than trying to decide for yourselves (original research), I would suggest looking at what some of the sources cited here call it, and following their example.

Xargon666x6 01:46, 14 June 2007 (UTC)

Pseudoscience
How are we to write articles about pseudoscientific topics, about which majority scientific opinion is that the pseudoscientific opinion is not credible and doesn't even really deserve serious mention?

If we're going to represent the sum total of human knowledge, then we must concede that we will be describing views repugnant to us without asserting that they are false. Things are not, however, as bad as that sounds. The task before us is not to describe disputes as though, for example, pseudoscience were on a par with science; rather, the task is to represent the majority (scientific) view as the majority view and the minority (sometimes pseudoscientific) view as the minority view; and, moreover, to explain how scientists have received pseudoscientific theories. (Note to Deglr and other censors: doesn't mean chopping off articles he doesn't like, even if can get a majority to support him. Nor does it mean that those who insert minority viewpoints are "vandals" 220.244.224.8 07:16, 18 Feb 2005 (UTC)) This is all in the purview of the task of describing a dispute fairly.

There is a minority of Wikipedians who feel so strongly about this problem that they believe Wikipedia should adopt a "scientific point of view" rather than a "neutral point of view." However, it has not been established that there is really a need for such a policy, given that the scientists' view of pseudoscience can be clearly, fully, and fairly explained to those who might be misled by pseudoscience. 220.244.224.8 07:16, 18 Feb 2005 (UTC)


 * And this applies to the article how? It's a scientific topic, not a pseudoscientific one. --Carnildo 07:59, 18 Feb 2005 (UTC)


 * We have a fairly standard way of dealing with such things. We need to report the current scientific paradigm, and thus we accept that this is science.  Criticism from creationists is then worth mentioning, it is relevant becaue of the social effect science has.  Censorship is not the way forward.  It needs to come in its own separate paragraph at the end of the article, to save obfuscating the earlier parts, and it needs to be proportional to the rest of the article; i.e. 3-4 sentences max should suffice.  It needs to be couched in appropriate language "Creationists argue that... ...though the scientific community does not accept these criticisms".


 * Which scientific community? Kenyon is part of the "scientific community" and he disagrees with you.  I've looked at all the furious edit wars, and as yet, no one has demonstrated a single error.  It's pathetic so simply assert what an alleged community would do without showing why.


 * It also needs to be accurate

I've seen a lot of back and forth, but not once has any of the detractors bothered to demonstrate an error. For the moment, this would seem to be good justification for putting the link back in.


 * (Creationists have a nasty habit of bending the truth),


 * What crap. Never mind all the evolutionary hoaxes eh?  (Piltdown and Nebraska Man, Archaeoraptor ...


 * Wait a little. Piltdown Man was hoaxed to damage the researcher who subsequently "discovered" it. Nebraska Man was not a hoax, it was an error; its discoverer found out the next year that it was a pig and published this. "Archaeoraptor" was made for money. Many of the farmers in Liaoning who find most of the fossils there glue together incomplete fossils to make more complete and therefore more expensive ones. Also, you seem to be blissfully unaware of the fact that the bird part of "Archaeoraptor" is Yanornis, a bird with, for starters, lots of teeth and a pubic symphysis (the hipbones meet in the middle, unlike in modern birds), while the tail belongs to the counterpart of the first Microraptor specimen that was found, Microraptor being a tiny feathered dromaeosaurid… reality is way cooler than the hoax!
 * I wouldn't call it "bending the truth". I call it ignorance: not knowing reality. David Marjanović (talk) 00:07, 5 December 2007 (UTC)


 * and relevant to the article.


 * Chemical criticisms of the RNA world would seem to be completely relevant to this article. 138.130.195.166 15:12, 18 Feb 2005 (UTC)


 * We have reached rough agreement on other pages, and lets hope we can on this one. Anons IPs should Log in otherwise there are people on here who will give them short shrift, particularly if they are spouting nonsense and trying to push their POV. Dunc|&#9786; 09:51, 18 Feb 2005 (UTC)


 * Please do not interweave your comments into mine. Being offensive will get you nowhere, and ultimately we will ignore you and treat you as a vandal unless you are courteous.  Trolling is forbidden, and please stay on topic.  Now, onto the article, we need two things.  Firstly, a few words into the ideas surrounding this hypothesis, paradigm shifts, debates, discussions and controversies within the scienctific community as to its merits compared with other hypotheses (and "straw man hence goddidit" isn't an option).  No-one is going to trust you to provide this, since you are not going to get the POV right at all.  Secondly, we need an accurate report of what creationists say, as long is it is relevant to the article in question, I have no problem in reporting that.  If you like, try speaking to Philip J. Rayment he's quite reasonable, or maybe even putting your work on his creation wiki, where no doubt it will be welcomed.  Dunc|&#9786; 16:22, 18 Feb 2005 (UTC)


 * Don't be so precious. You blatantly called creationists liars, then play the crybaby when you're called to task on it.  And if you want "trolling", what about the users who vandalized the perfectly reasonable link and heavy-handedly put the author on the vandals list -- on this grounds alone. 138.130.194.229 03:35, 19 Feb 2005 (UTC)


 * I have added comments to Requests for comment/138.130.194.229, so won't say too much more here. However, I support user 138.*'s edits, and although I've contributed to CreationWiki, it is most certainly not "mine".   Philip J. Rayment 11:03, 20 Feb 2005 (UTC)


 * I'm a non-religious scientist, and I have to say I am glad to see Cairns-Smith's objections represented on the RNA World Hypothesis page. I was talked out of the "standard" RNA World idea both by Cairns-Smith and by Robert Shapiro in his excellent book "Origins."  It amazes me how many molecular biologists dismiss the chemical difficulties with a wave of the hand when they are honestly insurmountable from any realistic chemical point of view.  If there was an RNA World of any sort it arose inside metabolizing cells.  In other words, proteins came first.  Freeman Dyson, Cairns-Smith, Shapiro and others describe this as "genetic take-over."  I believe in the RNA World as a stage in the development of life, but certainly not as the original state of life.  Origins, Robert Shapiro, Simon and Schuster 1986.  Origins of Life, Freeman Dyson, Cambridge, 1999.  Seven Clues too the Origin of Life, A. G. Cairns-Smith, Canto 1985, all popularized science books that anyone could read.User:Affenbart 18:49, 2 Mar 2005 (UTC)

DNA evolution
I remember reading that there was evidence that DNA evolved multiple times (several surviving lineages), so leading to credence for an RNA world. If someone can source that, it should be added to this article. 76.66.195.63 (talk) 11:53, 25 November 2008 (UTC)

Recent achievements
Here. Yosef1987 (talk) 18:37, 23 December 2008 (UTC)


 * Just the link because I don't like to embark on articles and start editing right away, just to discuss where to add the new research etc. Yosef1987 (talk) 18:48, 23 December 2008 (UTC)

More.

Perhaps someone who knows the subject could add details about the following development - http://www.sciencedaily.com/releases/2009/01/090109173205.htm Jooler (talk) 23:44, 10 January 2009 (UTC)

Catalysts lowering energy of reaction?
I read in the article:

"However, some sequences of base pairs have catalytic properties - catalytic properties which lowers the energy of that same chain being created."

However I am quite certain that I've learnt somewhere that catalysts actually do not change the energy of chemical reactions, rather they speed the reaction towards equilibrium. Can anybody back me on this? If so the section would read:

"However, some sequences of base pairs have catalytic properties - catalytic properties which increases the likelihood of that same chain being created in a shorter amount of time." or something of the sorts...


 * It should probably say 'activation energy' instead of 'energy', which would make it kosher. However, the whole section is really rather badly written and somewhat dubious. In any event the remarkable property of RNA is not that it polymerizes easily (lots of things do that spontaneously), but that it is an information-retaining molecule that can self-replicate. So that entire paragraph about spontaneous polymerization should really be whacked. Along with a whole bunch of this article. Someday someone (probably me) ought to sit down and read the literature on this thing and make a decent article out of it. Graft 18:47, 9 Jul 2004 (UTC)


 * Also catalysts are not "used up" in the chemical reaction, meaning that any templating of RNA towards its self replication would have to include a final disscoiation step - this being the difference between autocatalytic and self replication. Additionally, I don't think RNA is self replicating per se. Semantically, a self replicating reaction templates the synthesis of *itself*, RNA templates the synthesis of its opposite nucleotide chain (which then goes on to template the synthesis of itself. Spuddddddd 12:28 25Nov08 —Preceding unsigned comment added by 131.111.116.107 (talk) 12:31, 25 November 2008 (UTC)

Criticisms
Wikipedia is supposed to be NPOV, but some evidently want to censor the purely scientific criticisms of the RNA world hypothesis. The censors are committing the genetic fallacy in trying to discredit the science by noting that it comes from an intelligent design website. What about all the pro-chemical-evolution work coming from atheists, who likewise have a religious axe to grind? 220.244.224.8 01:25, 18 Feb 2005 (UTC)


 * Yeah, wikipedia IS supposed to be NPOV and this information is from a highly POV creationist website (the infamous "Access Research Network") that does NOT belong in the article at all. If you insist on including this religiously influenced nonsense into wikipedia do it in the creationism or "intelligent design" article or mention it in the origins of life article's creationism section, not here. For more information on the sordid academic career of the author, Dean Kenyon, see here.


 * This article was by a philosopher with no scientific qualifications. Seems as ignorant of chemistry as Deglr.


 * Can we please take a vote here on who wants this bilge included in a perfectly good scientific article? Obviously everyone here knows I think it needs to go. (furthermore, I can't believe we're wasting our time arguing with an IP address. someone who cares so little for wikipedia he hasn't even bothered to take the 2 minutes to get a username.)--Deglr6328 03:59, 18 Feb 2005 (UTC)


 * Dean Kenyon was a leader in chemical evolutionary research. He co-authored the influential textbook Biochemical Predestination.  Later, he concluded that his theories were inadequate to explain the origin of life from non-living chemicals.  But he was verboten by his university from presenting his scientific objections to chemical evolution in class.  Academic freedom is evidently only for atheistic leftists, e.g. to claim that the Twin Tower victims were "little Eichmanns" (Ward Churchill), but not to challenge the materialistic paradigm.  Here is a more balanced article on Kenyon, unlike the rabidly atheistic source of Deglr6
 * Frankly it's a joke that Deglr6328 thinks he is in a position to dismiss the science of a former leading chemical evolutionist, when he thinks that a link on self-reproducing PEPTIDES is the only link that belongs here. Yet he doesn't even realise that if DNA won't last more than 105 years, then RNA would not even last THAT long.  DNA instability is FAR more relevant to the RNA world page than self-reproducing peptides, and since Deglr6 doesn't even know that, his vote is worthless. 220.244.224.8 06:24, 18 Feb 2005 (UTC)


 * Wow, need we more evidence this guy is a rabidly rambling nutter?--Deglr6328 06:34, 18 Feb 2005 (UTC)


 * As usual, censors are incapable of rational argument but have to resort to name-calling and quashing contrary evidence. We still have yet to see the slightest evidence of scientific error in the paper.


 * I think my contributions show that I am reasonably knowledgeable about the topic. All  Deglr has done is censor real scientific criticisms, and show that he doesn't understand the chemisty. 220.244.224.8 07:07, 18 Feb 2005 (UTC)


 * I would be interested in knowing Deglr6328's reasons for including the link to peptides on the RNA world page. I see that when it was first removed, it was added to the origin of life page.  So in that case, it was not censorship. 138.130.195.166 15:37, 18 Feb 2005 (UTC)

Note that 138.130.195.166 is actually 220.244.224.8 and he is also 138.130.194.62.--Deglr6328 18:35, 18 Feb 2005 (UTC)
 * Note that no reason is given for this claim, and it would seem to be disputable. Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 12:49, 20 Feb 2005 (UTC)

VOTE

Should the section: "The RNA World: A Critique (Origins & Design 17(1):9&#8211;16, 1996) (Intelligent Design publication, co-authored by Dean Kenyon, former leader in chemical evolution)" be included in this article?


 * Oppose - Links to highly POV creationist dogma and religiously influenced material do not belong inside this article. Also it appears to be original research, which is not permitted.--Deglr6328 03:59, 18 Feb 2005 (UTC)
 * Quoi? Original research WITHIN an article is not permitted. Links to original research are fine. With that said... Graft 05:52, 18 Feb 2005 (UTC)


 * Favor - The article is well-written and sound, regardless of who wrote it. Although I think it's a bit of a strawman to say that the RNA World is an "established" hypothesis. Graft 05:52, 18 Feb 2005 (UTC)
 * No one doubts that the article is fairly well written, just that pseudoscience shouldn't be included within it. Also I don't recall anyone ever using the phrase "established hypothesis"--Deglr6328 06:22, 18 Feb 2005 (UTC)
 * Kenyon does: The RNA World hypothesis is another matter. We see no grounds for considering it established, or even promising... Also, what is the pseudoscience within his article? Graft 06:53, 18 Feb 2005 (UTC)
 * Oppose - In my opinion creationism/intelligent design is Pseudoscience created to push a religious point. -- Chris 73 Talk 05:40, Feb 18, 2005 (UTC)
 * Favor - The article should be judged on its scientific merits. Instead, the opposers resort to the genetic fallacy, trying to discredit the article by tracing it to its source.  OK, let's remove all articles by people who might be motivated by theistic religious beliefs -- provided that we remove all articles by people who might be motivated by atheistic religious beliefs!! 220.244.224.8 05:57, 18 Feb 2005 (UTC)
 * It is POV to put a title on the section "religiously motivated" unless you're prepare to mark much evolutionary material as "atheistically motivated".   E.g. demonstrate that the following is religiously motivated:
 * But each of these four ribonucleotides is built up of three components: a purine or pyrimidine, a sugar (ribose), and phosphate. It is highly unlikely that any of the necessary subunits would have accumulated in any more than trace amounts on the primitive Earth. Consider ribose. The proposed prebiotic pathway leading to this sugar, the formose reaction, is especially problematic. If various nitrogenous substances thought to have been present in the primitive ocean are included in the reaction mixture, the reaction would not proceed. The nitrogenous substances react with formaldehyde, the intermediates in the pathways to sugars, and with sugars themselves to form non-biological materials. Furthermore, as Stanley Miller and his colleagues recently reported, "ribose and other sugars have suprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents.138.130.194.229 02:41, 20 Feb 2005 (UTC)
 * I'm still waiting for Deglr or Duncharris to demostrate a single scientific error in the article. Try even the above paragraph. But it's laughable that an optics technician like Deglr thinks he's in a position to judge the chemical arguments of a biochemist who was one of the worlds leading chemical evolutionists.  I doubt that Duncharris is in any more of a position to do so.138.130.193.19 13:20, 21 Feb 2005 (UTC)


 * Oppose. This is a scientific article.  A link to a religious (intelligent design) site does not belong here. --Carnildo 07:03, 18 Feb 2005 (UTC)
 * Oppose. Agree with Chris 73.-gadfium 21:30, 18 Feb 2005 (UTC)
 * Favour. I agree that the source of the article is dubious, and that the motivations of the author are likely to be the same &mdash; but it's surely not acceptable to judge an article on the motivations of the author rather than on its content.  Moreover, I see no pseudoscience in the article (again, whatever its origin), though the conclusion bears no relation to the content of the article, being a mini-sermon which missed the point of the scientific enterprise.  That's not enough, in my opinion, to exclude it. Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 21:45, 18 Feb 2005 (UTC)
 * My main objection to its inclusion here is that websites which are linked to from wikipedia should be accurate, informative and scientifically correct. This website (arn.com) is none of those things and in addition seems highly disreputable. --Deglr6328 11:58, 19 Feb 2005 (UTC)
 * But is the link to a site, or to an article? If this is the sticking point, could permission be gained to reproduce the article on a neutral Web site, so that the Wikipedia link could point there? Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 12:28, 19 Feb 2005 (UTC)
 * This is acceptable to me, though I would like to see just a bit more verification of the articles/author(s) validity.--Deglr6328 18:50, 19 Feb 2005 (UTC)
 * But this is silly. Not a single point of the article will be changed, whether it's on ARN, Talk.Origins, or girlguides.com  Articles must stand on their own merit.  Evidently Deglr wants to have a blacklist of websites.138.130.194.229 12:40, 20 Feb 2005 (UTC)
 * Yes, it's silly (and Deglr6328 acceptance of the suggestion does indeed bring out the fact that it's prejudice and not the scientific method that drives him here), but wouldn't you rather have the article linked to than not? Mel Etitis ( &Mu;&epsilon;&lambda; &Epsilon;&tau;&eta;&tau;&eta;&sigmaf; ) 12:49, 20 Feb 2005 (UTC)
 * That's a good point. Even sillier is the way they chopped out the Cairns-Smith quote, and for that they didn't even have the excuse that he is creationist.  So I'm not sure if Deglr would even accept your recommendation, because to him, any site that hosted it would be pseudoscientific.138.130.193.19 13:18, 21 Feb 2005 (UTC)
 * If it is prejudice against charlatanism and pseudoscience you speak of, I'm proudly guilty as charged. I was truly unaware that to demand the source of a scientific article be reputable and professionally respected was currently considered 'silly' on wikipedia. Silly me.--Deglr6328 17:13, 20 Feb 2005 (UTC)
 * Ah yes, the optics technician hath spoken, and we must heed, because what would a former leading chemical evolutionist know about the chemical problems of obtaining prebiotic RNA compared to the almighty Deglr? Yeah, "silly you" is right.138.130.193.19 13:18, 21 Feb 2005 (UTC)
 * Are you referring to yourself? If so, very little apparently. You've made several obvious errors in your posts thus far.--Deglr6328 14:02, 21 Feb 2005 (UTC)
 * For those of thus that must be blind to his errors, perhaps you could enlighten us as to some of those "obvious" errors? Philip J. Rayment 01:19, 23 Feb 2005 (UTC)


 * Oppose This is a science article. The link in question is on a creationist site and the concluding mini-sermon essentially negates its validity here. Also the main POV pushing anon user(s) likes to have discussions with himself(s), I find this to be offensive sock-puppetry and reason enough to invalidate the link pushed by the puppet(s). -Vsmith 14:25, 19 Feb 2005 (UTC)
 * Favor. on point, good stuff.  the science/pseudoscience distinction is a pov which can be attributed, but cannot reasonably be used as a basis for deletion of attributed views and links thereto.  Ungtss 17:01, 19 Feb 2005 (UTC)


 * Favor. Very on point, and I think it is quite nonsensical to label an article pseudoscience merely because it is contrary to your pov. Of course I favor, no reason not to. Infocat 13:28, 20 Feb 2005 (UTC)

For the record, I originally labeled the article as being from a Creationist web site simply because I think that readers should be aware of the potential biases of any given source on something like this. Labeling something as "Creationist" means two things to me: 1. it is probably not supported by the mainstream scientific community, 2. it identifies their motivating ideology. It doesn't mean it is "wrong" and it doesn't mean it is not worth reading, it simply lets the reader know these two facts before they read something on a subject. They can still come to their own conclusions, I expect. This is of course alltogether different from the question of whether it should be in the article at all, but I thought I should make this clear since this appears to be what set off this little edit war (which it was not intended to do, mind you. I didn't think the Creationists would be so uncomfortable in being labeled as such). --Fastfission 00:52, 21 Feb 2005 (UTC)
 * 2. it identifies their motivating ideology.
 * The problem with this is that is presumes that a creationist's motivation is suspect, whereas an evolutionist's motivation (evolutionary articles are not normally so labelled) is not.
 * Your first reason, that it is not mainstream, may be a legitimate reason. However, note that (a) our anon user did not object to this (except to label it ID rather than creationist), and your edit was not the start of the dispute.  The dispute started (if you discount the anon editor's original insertion) nearly two and a half days earlier with Deglr6328 deleting it with the edit comment that it was "religious".  So you conscience can rest easy.  :-)
 * Philip J. Rayment 01:29, 21 Feb 2005 (UTC)
 * If you'd like to identify sites which are created by mainstream scientists as such with a warning, I'd fully support it on pages like this (where such a distinction is the cause of radically different POVs). Of course, I'm not sure how generalizable I think that ought to be, but I think this is a place such a thing could apply. If the contention is that they are ID and "not" Creationist (I have always thought that ID was a form of Creationism, but I think it matters little), then that would be fine to use a label by me. From what I see in the edit log, it seems that it went from me adding the warning, to an anon user wanting to "clarify" the warning (Creationist -> ID), and then account for a perceived inferiority of being labeled as non-mainstream by placing a long string of credentials on the warning, which led to a number of ridiculousnesses. But anyway. Whenever this gets resolved, perhaps someone can come up with a nice way to insert a source notice/warning after any inline links (it is easy enough to make such things clear in the external links section using subheads as is done on most controversial pages). --Fastfission 03:14, 21 Feb 2005 (UTC)
 * OK, so let's identify any pro-evolution sites by Dawkins as "Rabidly fundyatheist" because that describes his motivation accurately.138.130.193.19 13:18, 21 Feb 2005 (UTC)
 * Are you saying that saying the ID is "Creationist" is the same thing as saying that mainstream biology is "Rapidly fundyatheist"? Surely you're not that ashamed of the term "Creationist", are you? As I said, I'm happy with labeling which sites are considered a "mainstream" as well as the ones which are considered to not be on pages of this sort, and I'm happy with pointing out that Dawkins has his own philosophical baggage. As it is, though, none of the sites linked to on this page currently look like they are owned and operated by Dawkins. --Fastfission 18:02, 3 Mar 2005 (UTC)

It's high time that this page was unblocked. A vote has rejected the charge of "vandalism", so it's clearly Duncharris' own POV talking. The real vandalism was deleting the Cairns-Smith ref while voting was still in progress.

Also, it's interesting that Duncharris has added a link by an overtly creationist author, Jonathan Sarfati. This brings up another point. Sarfati seems to be a highly qualified chemist, and is arguing against the abiotic synthesis of cytosine based on the chemical evidence of the evolutionist Shapiro. So on what grounds is Sarfati pseudo-scientific and Shapiro not, when both have raised the same chemical objections? Could it be that Sarfati uses this as evidence against chemical evolution and for creation, an unprovable belief; while Shapiro maintains that chemical evolution occurred anyway despite the hurdles he raised, which is equally unprovable?

This reinforces the point that creationists are denounced NOT because of their science but because they refuse to play by materialistic rules of the game.138.130.192.82 12:06, 2 Mar 2005 (UTC)

Back to the vote, I think that the creationist criticisms should be deleted, the article already discusses the scientific difficulties with the RNA world. It obvious that creationist are going to have criticisms about any evolutionary theory and these are well covered already on the Creation vs evolution articles on wikipedia.--nixie 12:12, 11 Mar 2005 (UTC)


 * Oppose, Origins and Design is a non-PubMed indexed journal with no clear peer-review process, no listed editors and published by Access Research Network, an organisation with a clear ideological bias. This is consequently not a reliable source for science and should not be cited on Wikipedia except to illuminate the unusual beliefs of the contributors. Tim Vickers (talk) 22:53, 14 January 2009 (UTC)

Scripps implications?
Very recently (I'm writing this on 23-Jan-2009), a team at the Scripps Research Institute in La Jolla, California managed to synthesize self-replicating RNA ribozimes. (Later experiments showed they competed for resources and were subejct to both mutation and natural selection, but that's not relevant to the issue of how they got started in the first place.)

Were these ribozymes better self-replicators than any that had previously been encountered? If so, it would be the first answer to the question of whether high fidelity self-replicators are possible. -- Rogermw (talk) 20:21, 23 January 2009 (UTC)


 * Yes. They were generated by molecular competition, and this is the simplest self-replicating system to date. With a replication time of 1 hour, this has massive potential research implications. I have already introduced this into the article (reference 19 in the current version).Novangelis (talk) 20:41, 23 January 2009 (UTC)

Is the sugar phosphate backbone really necessary?
Is the sugar phosphate backbone really necessary? wouldnt it be much simpler to suppose that the original rna-like molecules consisted entirely of nothing but bases? is there any research in this direction? just-emery (talk) 09:07, 28 June 2009 (UTC)
 * There are researchers looking at PNA as a possibility. I don't think there is anything terribly conclusive yet. Especially given the recent synthesis by Powner et al.

Section "Support and difficulties" Needs to be cleaned up.
The 3rd paragraph states:

"Since there are no known chemical pathways for the abiogenic synthesis of nucleotides from pyrimidine nucleobases cytosine and uracil under prebiotic conditions, it may be the case that nucleic acids did not contain the nucleobases seen in life's nucleic acids."

And then the 4th:

"Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by a sequence of reactions which by-pass the free sugars, and is assembled in a stepwise fashion by going against the dogma that nitrogenous and oxygenous chemistries should be avoided. In a series of publications, The Sutherland Group at the School of Chemistry, University of Manchester have demonstrated high yielding routes to cytidine and uridine ribonucleotides built from small 2 and 3 carbon fragments such as glycolaldehyde, glyceraldehyde or glyceraldehyde-3-phosphate, cyanamide and cyanoacetylene."

I'm suggesting that the 3rd paragraph in the section be re-worded or removed.

67.193.56.126 (talk) 22:29, 28 July 2009 (UTC)

Riboswitch
These aren't mentioned at the moment but I guess that they should be, there must be a reference somewhere too. Smartse (talk) 16:19, 9 November 2009 (UTC)


 * I'm an idiot, was reading this which states just that.... Smartse (talk) 16:21, 9 November 2009 (UTC)


 * I've added this under "RNA as a regulator", feel free to change the title if you can think of a better way of saying it. Smartse (talk) 21:25, 9 November 2009 (UTC)

Section "Alternative hypotheses"
Hello, I understand that there is another theory regarding the creation of RNA.

In the Lipid World, aggregates/micelles of lipids can exhibit evolution to reach an optimal composition.

Could I ask for further information and/or references about this? This is brifly mentioned in Abiogenesis

Thanks! Omer website link removed 16:01, 21 December 2009 (UTC)

RNA-first vs. RNA-later
There is strangely no mention of this distinction, I'm going to work it in but it will require restructuring of the article (e.g. alternative hypotheses would fall under RNA-later; pre-biotic synthesis under RNA-first). There could also be substantial expansion of studies to produce RNA... there's no mention of the formose reaction, borate stabilisation, montmorillonite regiospecificity. I am planning to add this information but am posting here first, in case there are any objections to these big changes  Jebus989 ✰ 10:32, 4 May 2011 (UTC)

RNA world hypothesis?
DNA based - LUCA - last universal common ancestor (LUCA) it is the most recent common ancestor of all current life on Earth. It is estimated to have lived some 3.5 to 3.8 billion years ago http://en.wikipedia.org/wiki/Last_universal_ancestor (Tales23 (talk) 15:19, 14 January 2009 (UTC))
 * There was no reason to place this at the top of the discussion. This has nothing to do with the RNA world hypothesis. Origin of life and last ancestor are unrelated.  Please read Coatrack. The term "debunk" is flagrantly biased unless you can document fraud. Novangelis (talk) 15:34, 14 January 2009 (UTC)
 * Thanks Novangelis, for this answer, which been asked a view times (see above comments - all unanswered) --Tales23 (talk) 15:38, 14 January 2009 (UTC)
 * Novangelis, I don't see the word "debunk" in the post you replied to above, so I'm not sure how that verb being biased is relevant to this thread. The Mysterious El Willstro (talk) 01:01, 24 April 2012 (UTC)

Dates of references and their implications
I wonder about the POV of this article, based on its use of old citatations. To insert a final summary from an 1989 article is not reasonable. I think the first step to clarifying the matter is to add the dates for all the references, which can be done in a number of ways, besides the rather simple one I used. Not that the latest paper is always right, but on a topic such as this at least giving the year does distinguish the current consensus. In discussing philosophy it may not be the best guide for the reader, but it is in science. I'm also going to look for some 2006 review articles; citing these is more to the point than a few of the many research papers. This shouldn't look like a debate even though we don't know the answer. We don't support or oppose hypotheses such as this, we try to find information that would support it or not.
 * Many of the WP articles on evolution systematics etc. etc don't mention the rna world at all, and I plan on updating them, so I'd like to get this one right. DGG 04:28, 24 September 2006 (UTC)
 * Actually, a few of the references are as recent as 2008, 2009, and 2011. As long as some references are fairly recent, I don't see a problem with also having some old ones. The Mysterious El Willstro (talk) 01:06, 24 April 2012 (UTC)

RNA/DNA comparison figure is misleading
Hi,

I find the introductory figure quite misleading. First thing, the difference between RNA and DNA isn't so much in U/T as it is in ribose/deoxyribose. And second, RNA may be double stranded just like DNA, so that's not even a difference -- this criticism is especially strong in the context of the RNA World Hypothesis. (Pretty much the same is said in the "Comparison of DNA and RNA structure" paragraph of the article.)

Would be nice if it could be changed!

Regards, — Preceding unsigned comment added by 2A01:E35:8B2E:25C0:1B7:F3DF:77EB:FFC (talk) 22:32, 10 October 2013 (UTC)

Self-Assembling Molecules
http://www.wired.com/wiredscience/2014/02/rna/ Just granpa (talk) 10:19, 14 February 2014 (UTC)

User:Dienerto Edits: ok - or not?
 Copied from => Talk:Viroid: User:Dienerto Edits: ok - or not?

Seems User:Dienerto (contribs), without discussion, has been rewriting several articles (ie, Viroid; RNA world hypothesis; Potato spindle tuber viroid; Circular RNA; Non-cellular life) - in order to promote himself, his own studies and his own WP:POV - in addition - seems the editor is attempting to remove references to other studies, again without discussion, that may not agree with his own studies or WP:POV - the editor may (or may not) be correct in the contents - a closer look at the edits may be indicated - nonetheless - possible issues of WP:COI, WP:PROMO, WP:OWN, and WP:SPA may apply - comments welcome - in any case - Enjoy! :) Drbogdan (talk) 13:08, 16 November 2014 (UTC) Please discuss this at => Talk:Viroid - in any case - Enjoy! :) Drbogdan (talk) 13:08, 16 November 2014 (UTC)

Assessment comment
Substituted at 23:29, 26 June 2016 (UTC)

Sutherland-Patel paper — RNA World or Peptide-RNA World?
Note 5 in the intro currently cites a recent paper by John D Sutherland, Bhavesh H Patel and others "Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism" as supporting the concept of an RNA World. The paper does support one part of the RNA World model, the part that says RNA appeared early in the process of abiogenesis. However, it also supports the view that the precursors of proteins (and lipids) appeared at the same time, in fact from the same network of reactions. This is calls into question another major plank of the RNA World as generally understood (and presented on this page), the idea that there was a time when RNA operated without help of peptides. In short, the Sutherland-Patel paper seems in line with the general idea of a Peptide-RNA World, an idea mentioned in the section "Alternative Hypotheses" (or perhaps one should say an RNA-Peptide-Lipid World), rather than an RNA World in the usual sense. Kalidasa 777 (talk) 04:19, 3 August 2015 (UTC)


 * Some of the papers under alternative hypotheses also point in that direction. Do you think the Sutherland paper should just be added there, or does this merit something more major, like re-creating the peptide-RNA world article? --HighFlyingFish (talk) 02:11, 15 August 2015 (UTC)


 * I agree it would be good to mention the Sutherland-Patel paper in the "Alternative hypotheses" section. Also think we need to look at the way earlier research by Sutherland and his team (in 2009) is covered in the section "Support and difficulties". At present it says "This was hailed as strong evidence for the RNA world". Following the citation given (a report in Nature News), it turns out that one scientist, Donna Blackmond, did say this about Sutherland's work; but the same article also quotes Robert Shapiro as disagreeing. I found another report about the same research (in Chemistry World) where Sutherland gives his own view about how his work relates to the RNA world hypothesis: " 'The RNA world is a very restrictive, hypothetical arrangement and one shouldn't necessarily interpret our results as just supporting an RNA world,' explains Sutherland.  'Our work doesn't preclude metabolism being important, but it suggests that nucleic acids would be central to any early origin of life idea.' Kalidasa 777 (talk) 23:01, 15 August 2015 (UTC)


 * References 4 and 5 really shouldn't be used for the RNA world statement, since 4 is a news report and 5 is a primary research paper. For Sutherland, ideally we should first establish the significance of the work in question by citing reliable secondary sources, e.g. academic review or textbooks. (WP prioritizes these sources for a number of reasons, but the important idea here is that the amount of coverage we provide about a given subject is determined by the amount of coverage in reviews, textbooks, and similar sources.) Recreation of the Peptide-RNA world article would also need to address the sourcing concerns raised at the AfD, and an additional primary study isn't likely to have an impact on that. However, if there's been a decent-quality review article about the peptide-RNA world, then I'd go for it. :-) Sunrise (talk) 02:52, 15 August 2015 (UTC)


 * About secondary sources for Sutherland's recently published research... Too early for textbooks, I think, since the work was only published March this year, and possibly too early for academic reviews. However, there is a news report in Science Mag, which is not based only on the researchers' press release, but also on comments by other scientists working in the same field. Another secondary assessment is by science writer Michael Brooks in New Statesman, who goes so far as to compare the importance of this work to the Big Bang Theory... Kalidasa 777 (talk) 23:49, 15 August 2015 (UTC)


 * Regarding sources for the general concept of a "peptide-RNA world", it seems writers who refer to the concept don't necessarily use that exact term. Another term used is "RNA-peptide coevolution". For instance in the book From Suns to Life, a chronological approach to the history of life on Earth, by Muriel Gargaud and others (Springer 2007). It has a section by Robert Pascal, on Prebiotic Chemistry, which compares three scenarios — a "peptide world" in which peptides were originally replicators as well as catalysts; an "RNA world" in which RNA originally did all the catalysing as well as the replicating; and "RNA-peptide coevolution", where RNA and peptides emerged together from simpler molecules (the part about coevolution begins on page 163). Perhaps "RNA-peptide coevolution" would be a more appropriate name for a recreated WP page than "peptide-RNA world"? Kalidasa 777 (talk) 01:16, 16 August 2015 (UTC)


 * Science News is a good secondary source for this, if reviews aren't available. I'd have no objection to adding a sentence or two to the article about this. One thing I'd keep in mind is that best practice would be to reflect the coverage in the secondary sources, because it tells us what the outside observers thought was important.
 * On whether the concept deserves a separate article at this point, I can't say for sure. WP has highly intricate guidance on all sorts of things like this, and I only have passing familiarity with the article creation standards (for which the main page is WP:N, if you weren't already aware). Pascal et al does seem to be a good secondary source as well, but with the caveat that the publisher is a planetary science journal. A journal is generally considered reliable only for information within its scope, and this doesn't seem to be the journal's usual material (e.g. see the articles in the most recent issue), so it may be open to opposition on those grounds. Sunrise (talk) 05:41, 17 August 2015 (UTC)


 * Glad we're agreed that Science News is a good secondary source. Regarding your point about Pascal's article being published by a planetary science journal (Earth, Moon, and Planets), one can approach the topic of abiogenesis from two different directions. One can either start from the living cell today (which puts abiogenesis in the field of biochemistry), or from the chemistry of Earth soon after the formation of the Solar System (which puts abiogenesis in the field of planetary science). It really belongs in both these fields, surely? Kalidasa 777 (talk) 23:47, 17 August 2015 (UTC)


 * It depends on what information is being cited. I agree that for some statements regarding abiogenesis, a planetary science journal (even this same review article) would be appropriate. However, for information about the evolution and chemical composition of replicators in the primordial ocean, I really think there should be better options available. That said, I recognize that the boundaries are potentially arguable, which is why I worded my previous comment the way I did. Sunrise (talk) 05:28, 18 August 2015 (UTC)

Ribose synthesis
This research is making the rounds in the news outlets. I am not sure how to use it in this article so I will just leave it on your desk: Cheers, BatteryIncluded (talk) 14:46, 10 April 2016 (UTC)
 * Making ribose in interstellar ices Science journal
 * Complex sugars cooked up from 'comet ice'. BBC News.

Plagiarism
I made some legit changes, but also some that maybe I should not have.

I deleted a sentence in one section and a paragraph in another because they were, in my view, plagiarism. They were word-for-word direct quotes from sources, but were presented as though they were not (they were not in quotes, for example). In one case the reference was not even to the correct source: the reference was copied from the correct source as part of the plagiarism!!

I just made those deletes, so if someone wants to undo my 2 plagiarism-based deletes, it should not be hard to find them. — Preceding unsigned comment added by 2601:442:C180:3E13:E094:2427:C161:7BFE (talk) 04:05, 25 December 2015 (UTC)

Molecular chemists Dream/Nightmare
This whole section needs to be completely redone. If nothing else, blow it completely away and start from scratch.

It is full of statements that are (1) from anti-science, religious sources, (2) incorrect (as one example, these religious nuts don't know the difference between a DREAM and a NIGHTMARE!), and (3) are plagiarized (word-for-word copy and paste, without the statements being enclosed in quotes).

This section does not come from a NPOV, nor is its information correct; and at least in my view, parts are illegal/immoral (plagiarized). — Preceding unsigned comment added by 2601:442:C180:3E13:E094:2427:C161:7BFE (talk) 00:12, 28 December 2015 (UTC)
 * Yes, it indeed looks like Gerald Joyce and Leslie Orgel are attacking the RNA world hypothesis. They merely discuss the problems in terms of first genetic system in the RNA world. The statements mentioned are only half of what they actually said. For example It does not reflect Joyce's explicitly remark "There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life," or that of Orgel "It is now generally accepted that our familiar biological world was preceded by an RNA world." Of course the source is from Origins & Design, an ID journal. Chhandama (talk) 02:33, 27 August 2016 (UTC)
 * Gerald Joyce and Leslie Orgel are NOT attacking the RNA world hypothesis. These are all twisted words and lies spread by creationists. Please see the original papers and you will see what they said in reality.91.158.251.58 (talk) 17:19, 28 August 2016 (UTC)

Definition is wrong: I fixed it, but someone undid that
"The RNA world refers to the self-replicating ribonucleic acid (RNA) molecules hypothesised to have been the precursors to all current life on Earth"

No, it does not. The self-replicating RNA molecules would be replicase ribozymes, not the RNA world.

My edit, that was tossed for some reason, is better:

“The RNA world refers to a time in life’s early history on Earth, before genetically encoded proteins had evolved, when RNA performed two of the major functions required for minimal life: storing genetic information and catalyzing chemical reactions, including catalyzing the replication of the genetic information." — Preceding unsigned comment added by 2601:442:C180:3E13:8437:6BFF:2A42:913F (talk) 02:58, 15 January 2016 (UTC)

Self-replication change removed: who is running this show?
I had made a completely valid and contributor change to the self-replication part, noting ...

In 2013, scientists evolved the 'first polymerase ribozyme capable of catalysing the accurate synthesis of an RNA sequence longer than itself (adding up to 206 nucleotides)

And gave the reference Attwater, James (2013). "In-ice evolution of RNA polymerase ribozyme activity". Nature Chemistry 5: 1011–1018. doi:10.1038/nchem.1781

But it was removed. Why?

Another change of mine removed: who is running this show?
I had made a correction to another part, and it was removed also.

Originally, the first sentence mentioned only RNA, but the paper it used as support for the statement was about DNA. So I made the first sentence more accurate by noting that what it was talking about applied to both RNA and DNA. In addition, the last sentence in the paragraph seems to imply that the problem applies only to RNA and not to DNA, which would be wrong. My additions helped eliminate this misinformation too.

The chemical properties of RNA (and DNA) make large nucleic acid molecules inherently fragile, and they can easily be broken down into their constituent nucleotides through hydrolysis. These limitations do not make use of RNA as an information storage system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current 'DNA optimised' life, it may have been acceptable for more primitive life.

The reference they used was: Instability and decay of the primary structure of DNA

What's the difference between a dream and a nightmare? Apparently, only I know
Another of my corrections was undone.

The section titled "Molecular biologist's dream" is wrong. Joyce and Orgel had coined two cute terms: "Molecular biologist's dream" and "Molecular biologist's nightmare". As one can imagine, they are not the same thing. The paragraphs discuss the nightmare, but it is labeled as the dream.

I had fixed this too, but this correction of mine - like the others - was also tossed out.


 * No need to start a new section for each comment. :-) I haven't been active on this article for the last month or two, but I will check over recent edits at some point. Just commenting here so it doesn't seem like nobody's listening to you! Sunrise (talk)</i> 10:35, 19 January 2016 (UTC)

January 2019
This article needs revision. The problems with Pyrimidines are described in two different sections, without (afaik) any rationale. The 11-Jan-2019 issue of Science (magazine) contains an article which states "In 2009, for example, Sutherland ...reported a plausible prebiotic reaction for making C[ytosine] and U[racil]...Then, in 2016,...a plausible way to make A[denine] and G[uanine][was reported]...What's more, those steps can produce all four nucleosides in one pot, offering the first plausible explanation for how all four RNA letters could have arisen together". This directly contradicts some of the claims in the Wiki. article.(workshop paper not peer reviewed, afaik.) This article also seems to lack the coherence it needs. Life's origins require 3 things: Metabolism, Memory, and Separation. What the order of those are isn't clear. The coupling between memory (homeostasis of template) and metabolism (replication of templates) is obviously closely related while pre-cellular (possibly via lipids) separation/concentration/assembly/protection of the pre-biotic system might have occurred before, after or simultaneously with the other two requirements. RNA, Proteins, and RNA+Proteins are all possible as the 'first' step for metabolism and memory. Whether these reactions occurred inside a (cascade of) pool(s) or in lipid vesicles, or in ocean mud (or somewhere else) isn't known. We have no good reason to believe that abiogenesis didn't occur on Earth but it is unlikely that we can ever prove that it did. We do not know what the initial ingredients were to the primordial soup, nor where (on Earth) that soup was located. RNA world hypotheses suppose that the ingredients were purines, pyrimidines, ribose and phosphate - or (importantly) their chemical precursors. It doesn't seem to me that this is made clear in the article,and it should be. As an aside, this article conflates chemical "evolution" with Evolution. Everything "evolves"; meaning everything experiences time and, with time, changes. The key factors of "Evolution" are replication with (natural) selection. The prebiotic 'soup' may have existed (and changed and been dispersed as various precursors) for millions of years prior to the assembly of the components able to replicate. During this time, there may have been no "selection". 72.16.99.93 (talk) 23:04, 17 January 2019 (UTC)

Problematic word in Section 3
In the article’s current Section 3 "Support and Difficulties" there is a problematic word, but my correction has its own potential inaccuracy. The text now reads (underline mine)"Others have questioned whether ribose and other backbone sugars could be stable enough to find in the original genetic material" The context of find seems to necessitate the passive voice: "stable enough to be found"—but it occurs to me that this use of "find" may have been an error, and that "bind" was the author’s intent, as in "stable enough to bind." I am boldly replacing "find" with "be found" yet if one with a better understanding finds my edit to be a step in the wrong direction, please correct my mistake. catsmoke (talk) 21:38, 21 March 2021 (UTC)

Alanine World
The article currently ends with the following:

Setting aside that we should let people decide for themselves whether what follows is 'interesting', and ignoring that the paragraph is a bit of a jargon soup inpenetrable to a naive reader, it doesn't actually say anything whatsoever about RNA or the RNA world. If we are to mention this hypothesis at all in this article, it needs to be explicitly related to the article topic, and it needs to have a sufficient explanation to make it clear, else it can just be a 'See also' link (if that). The associated figure does mention the RNA world, but in such a tangential manner that the naive reader will have no idea that the nature of the link is, or what all of those 'worlds' shown in the figure are supposed to mean from the perspective of the RNA world. I will leave time for someone to fix this, but if it doesn't get addressed I will just remove it. Agricolae (talk) 17:22, 20 October 2021 (UTC)


 * Nobody has addressed this, so I am removing it. Agricolae (talk) 21:07, 8 November 2021 (UTC)

Please update with: "A prebiotically plausible scenario of an RNA–peptide world"
I think it would be good to add some brief info about this to the article and/or the article abiogenesis. It's currently featured in 2022 in science like so:

Scientists close a missing link in the potential origin of life from a RNA world – synergistic formation of peptides and ever-longer RNAs or peptide-decorated RNA, leading to a protein world.

Concerning the first reference used there: the paper didn't say it helped grow "ever-longer RNAs" or did it? Another thing that may be good to clarify is whether there were separate peptides, normal RNAs and peptide-decorated RNAs or just a few of those. The paper is so unclear about it, it may obvious/self-explanatory to some but I haven't read all of the study just to find that out.

Prototyperspective (talk) 19:42, 3 July 2022 (UTC)