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Author Topic:   Self-sustained Replication of an RNA Enzyme
greyseal
Member (Idle past 1363 days)
Posts: 464
Joined: 08-11-2009


Message 1 of 52 (547754)
02-22-2010 9:52 AM


I found a fascinating (if shallow) article on "evolution in RNA chemicals" from various places I read RSS feeds from - in short, scientists have observed evolutionary traits in non-living chemicals.

quote:

The abstract is from http://www.cosmosmagazine.com/.../life-evolution-a-test-tube

An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.


so, in short, they had these RNA molecules (which replicate imperfectly, such that random mutation would take place) compete for food (the substrate in the testtube) - those which were "more fit" would become more numerous by "eating" more of the substrate. When the substrate was exhausted, samples were taken and the experiment started again with a new substrate.

From the beginning until the end, the RNA molecules "evolved" through "natural selection" as natural mutations and the pressure to "survive" did pretty much exactly the same as has been theorized by Darwin and many others.

It's not quite abiogenesis and it's definitely not life, but it is showing something that looks a lot like it and is taken as pretty good proof of how it works as well as giving us a glimpse of how things could have been before chemistry became life.

This topic then is two-fold, as I'd like to know what everyone thinks of this article (and the actual paper!) from http://www.cosmosmagazine.com/.../life-evolution-a-test-tube AND what they think of the very first comment:

quote:
Hype+Buzz Words != Science

Hmmm... sounds fascinating, but reading between the lines, its not really clear what these scientists observed or accomplished beyond a specific type of chemical reaction.

What was the mechanism that allowed these molecules to grow in complexity? What "problems" are they solving? What is meant by complexity? These words are so incredibly ambiguous and overloaded that without very clear definitions and specifics, I remain skeptical.
Submitted by Visitor on 21 February 2010 - 12:18pm.


because I think the very first comment is a religious nut. Why? Several reasons:

1) the first sentence makes out that the experiment didn't do anything (denial)
2) it talks about "a mechanism" for the chemicals to "grow in complexity" (sounds like "designer" to me)
3) it brings in the word "complexity", and then acts as if it's actually brought in by the article, and because it's "not defined" can be used to further denigrate the work
4) it calls the words "complexity" and "problems" as "ambiguous" and "overloaded" when these words weren't in the original article, yet still attempts to make it stick
5) it's quite obvious the reader didn't actually read the article because the commenter doesn't understand what happened (because point #4 is irrelevant)

All these add up to textbooks ignorant/conniving creationists (now, not all creationists are like this, but some most certainly are).

Am I wrong? why?

Edited by greyseal, : the extra abstract was added in explaining what was done, how and why.

Edited by Adminnemooseus, : Topic title changed from pretty worthless "To catch a creationist..." to "Self-sustained Replication of an RNA Enzyme", which is the title of the paper cited in message 4.


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Admin
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Message 2 of 52 (547760)
02-22-2010 11:17 AM
Reply to: Message 1 by greyseal
02-22-2010 9:52 AM


Could you add a paragraph of summary of how the article describes this evolution-in--test-tube working? Post a note or send me a PM when you're done and I'll take another look.


--Percy
EvC Forum Director

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Admin
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Message 3 of 52 (548097)
02-25-2010 1:54 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the To catch a creationist... thread in the Proposed New Topics forum.
    
Taq
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Joined: 03-06-2009
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Message 4 of 52 (548100)
02-25-2010 3:05 PM


For those interested, you can read the peer reviewed paper (author's manuscript) here:

Link


  
AnswersInGenitals
Member
Posts: 488
Joined: 07-20-2006


Message 5 of 52 (548142)
02-25-2010 7:20 PM
Reply to: Message 1 by greyseal
02-22-2010 9:52 AM


It has recently been discovered that Prions, which are proteins, can also evolve without the intercession of nucleic acid intermediaries. See, for example, Darwinian Evolution of Prions in Cell Culture.

It is becoming evident that the Darwinian evolutionary process (random variation followed by selection to some criterion) is a very general one and is not restricted to biological species evolution. It has long been known to be an important component, and perhaps the most important component, of technological evolution. It is also an important part of intelligent design, as any engineer who has participated in "brainstorming" sessions can attest. In fact, subconscious brainstorming might well be the basis of all (human) intelligent design.

I'm sorry that I don't have an answer to your specific question about creationists connivances. I really don't give a dying duck what ignoramuses think. Science marches on and reveals all.


This message is a reply to:
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greyseal
Member (Idle past 1363 days)
Posts: 464
Joined: 08-11-2009


Message 6 of 52 (548180)
02-26-2010 2:01 AM
Reply to: Message 5 by AnswersInGenitals
02-25-2010 7:20 PM


so IDiots ignore this too?
It is becoming evident that the Darwinian evolutionary process (random variation followed by selection to some criterion) is a very general one and is not restricted to biological species evolution.

I think that's fascinating! For years I'd been hearing "you don't know X so you must be wrong" from creationists, and all along it's been "now we know this" and "now we know that" and it seems people opposed to this viewpoint (and opposed to the very examination of the facts) will wholesale ignore this research.

I think that first comment is a great giveaway of the mindset. Reading between the lines, the comment was "it's still not abiogenesis, so you're still wrong".


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dcarraher
Junior Member (Idle past 2569 days)
Posts: 13
From: Cols, OH
Joined: 06-05-2009


(1)
Message 7 of 52 (559776)
05-11-2010 2:28 PM
Reply to: Message 5 by AnswersInGenitals
02-25-2010 7:20 PM


...find a creationist as ignorant as an evolutionist
I hate to interrupt all the self-congratulatory back-slapping and name-calling (ignoramouses? really?), but you can't seriously think that the article has anything to do with abiogenesis, can you?

What you have here is a purely chemical reaction, in which you take chemicals (RNA) that are known to react, put them in a solution of chemicals that they react with, and watch as the concentration levels of various combinations of the chemicals change. Color me bored.

What you don't have is:
1) Information - the RNA is merely undergoing chemical reactions, it is not following "instructions" (e.g. DNA) to regenerate.
2) Translation - there is no mechanism for "interpreting" the information (non-existent) of the RNA and utilizing to build a product (e.g. Protein).
3) Control - there isn't any control to the system - like all unguided chemical reactions, its a mere matter of what comes in contact with what under what environmental conditions.
In other words, there isn't a single element of what distinguishes biology from chemistry.

As a chemical analogy to "natural selection", it is an interesting(?) experiment, that may or may not (I'm guessing not) provide insight into population density changes in biological environments.

As far as "abiogenesis" is concerned, this experiment is about as relevant as dropping alka-seltzer in a glass of water, and noticing that the chemical composition of the solution changes.

This, btw, is a good example of why most conversations between evolutionists and creationists are pointless. To an educated creationist, this article is so clearly irrelevant to the entire argument of abiogenesis, it shouldn't even need refuted. To an evolutionist, apparently, this is practically first life, and a clear refutation of any creationist concerns over the impracticability of abiogenesis. Ah, well.

Whether or not "Darwinian Processes" as defined in the post above are common, is irrelevant to the validity of Evolution or Creation as an explanation of the origin of life. Support for natural selection as a generic process <> support for Evolution/refutation of Creation.

Just out of curiosity - any evolutionists willing to stand up and admit that recombinant RNA concentrations in a pool of RNA is kinda irrelevant to the idea of abiogenesis? Or is ceding a point to the other side, even a valid one, still verbotten?


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New Cat's Eye
Member
Posts: 11683
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.6


Message 8 of 52 (559779)
05-11-2010 2:54 PM
Reply to: Message 7 by dcarraher
05-11-2010 2:28 PM


Re: ...find a creationist as ignorant as an evolutionist
but you can't seriously think that the article has anything to do with abiogenesis, can you?

What you have here is a purely chemical reaction,

Abiogenesis was purely chemical reactions too.

In other words, there isn't a single element of what distinguishes biology from chemistry.

I know, right! Well, biology IS chemistry (and chemistry is physics). There is no distinction.

What do YOU think distinguishes biology from chemistry?

Information - the RNA is merely undergoing chemical reactions, it is not following "instructions" (e.g. DNA) to regenerate.

DNA merely undergoes chemical reactions and does not rely on following instruction in the sense of containing actual information.

As far as "abiogenesis" is concerned, this experiment is about as relevant as dropping alka-seltzer in a glass of water, and noticing that the chemical composition of the solution changes.

Maybe if the creationists were saying that god is required for making an effervescent liquid...

Whether or not "Darwinian Processes" as defined in the post above are common, is irrelevant to the validity of Evolution or Creation as an explanation of the origin of life. Support for natural selection as a generic process <> support for Evolution/refutation of Creation.

Just out of curiosity - any evolutionists willing to stand up and admit that recombinant RNA concentrations in a pool of RNA is kinda irrelevant to the idea of abiogenesis?

Its just another baby-step in the right direction. Not some nail in the coffin.

But, sometimes when we talk about abiogenesis, and we get into pre-biotic or non-life chemical reactions, creationists will sometimes argue that the thing has to actually be alive for evolution to work on it. Apparently they are wrong (again).


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Iblis
Member (Idle past 1397 days)
Posts: 663
Joined: 11-17-2005


Message 9 of 52 (559781)
05-11-2010 3:24 PM
Reply to: Message 7 by dcarraher
05-11-2010 2:28 PM


Of course it's chemical
In other words, there isn't a single element of what distinguishes biology from chemistry.

That's rather the point. The "RNA World" is normally classified as part of the abiogenesis question, because it is an attempt to describe what pre-cellular pre-"biological" processes would be necessary to get from the numerous examples of self-constructing complex "organic" molecules we have been studying since Miller-Urey to the real primitive life forms we can observe now such as archaea, bacteria and protozoa.

What this experiment shows is one way in which these theoretical RNA organisms themselves might have undergone the natural selection necessary for beneficial increases in complexity and information. All it proves is that these processes can happen, not that that is the way that they did happen.


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dcarraher
Junior Member (Idle past 2569 days)
Posts: 13
From: Cols, OH
Joined: 06-05-2009


Message 10 of 52 (559787)
05-11-2010 4:31 PM
Reply to: Message 9 by Iblis
05-11-2010 3:24 PM


Re: Of course it's chemical
Well, biology IS chemistry (and chemistry is physics). There is no distinction.

This explains alot, really. If you see no distinction between chemistry and biology, no line of demarcation that says "this is life" and "this is not", then abiogenesis is not an issue because the very word has no meaning - life is non-life, so no need to explain life from non-life.

Disqualified.

All it proves is that these processes can happen, not that that is the way that they did happen.

Ah. So, taking existing RNA, mixing it with chemicals, and ending up with different RNA that cannot be qualitatively shown to be more "complex" or contain more information (or really any - if the RNA has more "information", what "information" does it have? how to build a protein? how is the resultant RNA any different than chemical "noise"?), somehow proves that you can get something other than random RNA?

Now, maybe if the experiment had started with amino acids, and ended with RNA, you might have something...

If nothing else, thank you for demonstrating that these types of conversations are indeed pointless. Simply because creationists and evolutionists refuse to accept each other's premises (e.g. "Life is different than Chemistry", "Specified Complexity has meaning and is measurable", "Any type of change is qualitatively equal to the type of change desired"), and without agreement on premises, arguing specifics (this type of change doesn't help evolution) is pointless.

One last try - Creationists don't AGREE with you on whether this experiment has value - that does NOT mean that they don't UNDERSTAND you, or are STUPID. I'm not certain the converse is true, but I'll cut you some slack.


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New Cat's Eye
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Posts: 11683
From: near St. Louis
Joined: 01-27-2005
Member Rating: 2.6


(1)
Message 11 of 52 (559788)
05-11-2010 4:43 PM
Reply to: Message 10 by dcarraher
05-11-2010 4:31 PM


Re: Of course it's chemical
Well, biology IS chemistry (and chemistry is physics). There is no distinction.

This explains alot, really. If you see no distinction between chemistry and biology, no line of demarcation that says "this is life" and "this is not", then abiogenesis is not an issue because the very word has no meaning - life is non-life, so no need to explain life from non-life.

I'll take this line by line...

If you see no distinction between chemistry and biology,

Care to point it out, specifically?

Biology is essentially macro-chemistry. Everything going on inside your body is the result of chemical reactions. Show me the difference.

no line of demarcation that says "this is life" and "this is not",

Sure, I can look at a rock and rhino and say that the one is not alive but the other is... but that's beside the point. If we zoom in to the atomic scale, we cannot distinguish between the calcium in the rock and the calcium in the rhino's horn. There is nothing special about either one. They will both react chemically according to the physical and chemical laws.

And even at the cellular level, what we see is just a bunch of chemical reactions going on. Same reactions as if they were in a beaker.

then abiogenesis is not an issue because the very word has no meaning - life is non-life, so no need to explain life from non-life.

When you get down to the nitty-gritty of abiogenesis, at the point where non-life is emerging into life, there is not going to be a "line" dividing the two. We're gonna have a big grey blur of things that are something in between... and its still going to be chemical reactions.

Disqualified.

Non-sequitor.

Edited by Catholic Scientist, : No reason given.


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Iblis
Member (Idle past 1397 days)
Posts: 663
Joined: 11-17-2005


(2)
Message 12 of 52 (559797)
05-11-2010 5:31 PM
Reply to: Message 10 by dcarraher
05-11-2010 4:31 PM


Re: Of course it's chemical
You don't seem to be able to keep track of who you are responding to, and that's not a particularly good boost to your creationists-not-necessarily-stupid premise.

If you see no distinction between chemistry and biology

Not my problem really, not in this thread at least, I already conceded the normal creationist position on this, cells are life, raw RNA isn't. In more intelligent arguments I would tend to argue that anything that can reproduce imperfectly and is subject to natural selection might be considered life, but it's not worth arguing here. But that still leaves RNA open to thorough debate.

somehow proves that you can get something other than random RNA?

Demonstrates that the sort of processes demonstrated to increase fitness over time for entities which survive them, can exist at the RNA level.

I'm not actually a very big supporter of the strong RNA World position, my studies lead me to believe that simple cells (liposomes) appeared long before any such complex nucleic acids.

Now, maybe if the experiment had started with amino acids, and ended with RNA, you might have something...

RNA isn't made of amino acids, they are where proteins come from. Nucleic acids are made of bases and chaining elements. Bases are easily produced by trapping the by-products of amino acid production near a chemical power-source, as in the Iron-Sulphur World for example. This is part of the reason I favor liposomes before nucleic acids proper, as these are produced in the same processes and useful in preventing diffusion of the chemicals in question.

One last try - Creationists don't AGREE with you on whether this experiment has value - that does NOT mean that they don't UNDERSTAND you, or are STUPID.

But being aggressively wrong, is somehow different from being stupidly wrong? Do some more reading, read for comprehension instead of ammunition, and your lack of social skills might not hurt you Quite so bad in this sort of debate.


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Taq
Member
Posts: 7043
Joined: 03-06-2009
Member Rating: 3.8


(1)
Message 13 of 52 (559802)
05-11-2010 5:48 PM
Reply to: Message 10 by dcarraher
05-11-2010 4:31 PM


Re: Of course it's chemical
One last try - Creationists don't AGREE with you on whether this experiment has value - that does NOT mean that they don't UNDERSTAND you, or are STUPID. I'm not certain the converse is true, but I'll cut you some slack.

You destroyed your own argument when you stated:

"Now, maybe if the experiment had started with amino acids, and ended with RNA, you might have something..."

The whole point is that you may not need amino acids at all. RNA is capable of dual roles as both a genetic molecule (like DNA) and as an enzyme (like proteins). If you understood this then you wouldn't have put forth the above requirements.


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cavediver
Member (Idle past 1144 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 14 of 52 (559834)
05-11-2010 7:28 PM
Reply to: Message 10 by dcarraher
05-11-2010 4:31 PM


Re: Of course it's chemical
Now, maybe if the experiment had started with amino acids, and ended with RNA, you might have something...

Given that RNA is not made up of amino acids, that would be a remarkable experiment

One last try - Creationists don't AGREE with you on whether this experiment has value - that does NOT mean that they don't UNDERSTAND you, or are STUPID.

Quite true. The facts that they are stupid and do not understand are quite independent of their agreement or otherwise...


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RAZD
Member
Posts: 18868
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.6


Message 15 of 52 (559848)
05-11-2010 8:31 PM
Reply to: Message 10 by dcarraher
05-11-2010 4:31 PM


The definition of life is ...
Hi dcarraher, and welcome to the fray.

This explains alot, really. If you see no distinction between chemistry and biology, no line of demarcation that says "this is life" and "this is not", then abiogenesis is not an issue because the very word has no meaning - life is non-life, so no need to explain life from non-life.

Disqualified.

Ah, so then you have a definition of life that can always distinguish life from non-life ... what is it?

... or contain more information (or really any - if the RNA has more "information", what "information" does it have? ...

Now you can define how information can be measured and then we can see. Interestingly, without some mechanism or method for actually measuring the information content, your comment is absolutely useless.

One last try - Creationists don't AGREE with you on whether this experiment has value - that does NOT mean that they don't UNDERSTAND you, or are STUPID. I'm not certain the converse is true, but I'll cut you some slack.

Curiously, it does not matter one piece of ant frass in antarctica what you (or any other creationist) agrees with, it only matters what the evidence shows, and whether the evidence conforms with theory or invalidates it.

You are welcome to your opinion, however opinion has been found to be rather amusingly inept at changing or altering reality in any way.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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