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Author Topic:   Self-sustained Replication of an RNA Enzyme
dcarraher
Junior Member (Idle past 2448 days)
Posts: 13
From: Cols, OH
Joined: 06-05-2009


Message 16 of 52 (559992)
05-12-2010 1:07 PM
Reply to: Message 15 by RAZD
05-11-2010 8:31 PM


Re: The definition of life is ...
First, a qualifier - in my responses, I will respond to multiple previous posters in a single post. This is not an indication that I am confusing who posted what, simply brevity for the sake of brevity.

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

Fixed. Mea culpa. Congratulations, you've scorned a typo.

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.

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

This is another excellent example of premise-conflict. I'm really astonished that evolutionists would care to argue that life is indistinguishable from non-life. If there is no clear demarcation, then what is abiogenesis all about? What are scientists and universities such as Harvard wasting their time and money trying to get to? According to you both, they won't know it when they get to it.

But of course, you both know that you are speaking theoretically. You are engaged in a fairy-tale story of some non-existent form of chemical intermediary between recognizable non-life (e.g. an amino acid) and recognizable life (e.g. a single-celled organism that reproduces). And, on the basis of this (non-existent fair-tale grey) semi-organism, seen fit to ridicule creationists who have the audacity to peer into your petrie dish and say "hey, this isn't life, it's not even novel, just a chemical reaction between RNA and substrate that results in more RNA, until it runs out of substrate".

As a thought experiment, let's discuss the RNA experiment in question, shall we? Let's treat it like a high-school lab project
Project Instructions:
1) Take two RNA enzymes
2) Place in four oligonucleotide substrates
3) Observe and record

Now, there are multiple possible outcomes:
1) Stasis - nothing happens
2) Equilibrium - stuff happens, but the overall effect is negligible
3) Deterioration - stuff breaks down until it's all gone
4) Increase in RNA due to chemical combination with substrate resulting in more RNA. Based on the chemical and thermal conditions, the chemical makeup of the RNA products may vary.
5) Generation of novel organisms that have the properties of homeostasis, metabolism, growth, and reproduction (as serviceable a descriptive definition of "Life" as any)

Because results 1-3 are boring, RNA enzymes and substrates that provide these results are discarded. Result 4 (shown is this paper), is pretty much just a complex chemical reaction of reagents and products - when you run out of reagents, you're back to outcomes 1-3. If you get really interesting, the RNA might continuously break-down and re-combine, in which case you have a (random, uncontrolled) continuous reaction (thermodynamics would insist that eventually this stops).

So, at the end of the day, you have an interesting chemical reaction that is interesting not because of any relevance to abiogenesis (you haven't gone anywhere - you end up with more of what you already started with), but because it has the same qualities as a kaleidoscope - look at all the pretty colors I can get when I twist the little thingie at the end! Let's call the patterns created by our kaleidoscope "natural selection" and pat ourselves on the back for how clever we are and how stupid creationists are.

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

Back at ya. Enjoy.


This message is a reply to:
 Message 15 by RAZD, posted 05-11-2010 8:31 PM RAZD has responded

Replies to this message:
 Message 17 by Taq, posted 05-12-2010 1:34 PM dcarraher has responded
 Message 18 by dokukaeru, posted 05-12-2010 1:43 PM dcarraher has responded
 Message 19 by Blue Jay, posted 05-12-2010 2:31 PM dcarraher has responded
 Message 20 by Iblis, posted 05-12-2010 4:09 PM dcarraher has not yet responded
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Taq
Member
Posts: 6051
Joined: 03-06-2009
Member Rating: 3.7


(2)
Message 17 of 52 (559998)
05-12-2010 1:34 PM
Reply to: Message 16 by dcarraher
05-12-2010 1:07 PM


Re: The definition of life is ...
If there is no clear demarcation, then what is abiogenesis all about?

How chemistry can span the gap between non-replicating molecules and replicating molecules that give rise to life. If non-life is "black" and life is "white" then abiogenesis is the gray in between.

And, on the basis of this (non-existent fair-tale grey) semi-organism, seen fit to ridicule creationists who have the audacity to peer into your petrie dish and say "hey, this isn't life, it's not even novel, just a chemical reaction between RNA and substrate that results in more RNA, until it runs out of substrate".

So you are saying that a self replicating RNA molecule has nothing to do with abiogenesis? Really? Perhaps you should think about that one again. Not only that, but these replicators are competing for limited resources, a necessity for evolution. Here is a quote from the abstract, in case you missed it:

quote:
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.

These are replicating RNA enzymes. Replication is a hallmark of life.

If I start an experiment with one bacterium and come back the next day to find billions of bacteria would you claim that this is not an example of life since I just ended up with more of what I started with?

So, at the end of the day, you have an interesting chemical reaction that is interesting not because of any relevance to abiogenesis (you haven't gone anywhere - you end up with more of what you already started with)

Ending up with more of what you started with is exactly what life does. You might want to think about that for a second.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 16 by dcarraher, posted 05-12-2010 1:07 PM dcarraher has responded

Replies to this message:
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dokukaeru
Member (Idle past 1995 days)
Posts: 129
From: ohio
Joined: 06-27-2008


Message 18 of 52 (560003)
05-12-2010 1:43 PM
Reply to: Message 16 by dcarraher
05-12-2010 1:07 PM


Re: The definition of life is ...
Hello dcarraher and welcome another person from Ohio!

First, I want to say that this subject is very fascinating to me as a layperson.

This is another excellent example of premise-conflict. I'm really astonished that evolutionists would care to argue that life is indistinguishable from non-life. If there is no clear demarcation, then what is abiogenesis all about?

Why is it so astonishing? Clearly most people here can distinguish most life from most non-life, yet there are still current examples that blur this line you feel is distinct, not to mention conditions 4 BYA were much different than the present. Could you please provide a definition that distinguishes life from non-life as RAZD asked? Is it difficult for you to imagine an organism that blurs the line of life/non-life?

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.

You point out in multiple places that you feel it is clearly irrelevant, but fail to explain why. Maybe I am missing something here....why do you feel it is it not relevant?

Thanks,
Joe


This message is a reply to:
 Message 16 by dcarraher, posted 05-12-2010 1:07 PM dcarraher has responded

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Blue Jay
Member (Idle past 78 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 19 of 52 (560012)
05-12-2010 2:31 PM
Reply to: Message 16 by dcarraher
05-12-2010 1:07 PM


Re: The definition of life is ...
Hi, Dcarraher.

Welcome to EvC!

dcarraher writes:

First, a qualifier - in my responses, I will respond to multiple previous posters in a single post. This is not an indication that I am confusing who posted what, simply brevity for the sake of brevity.

You probably shouldn't do this: this board is set up so that responses can be linked to specific posts and posters, and many posters have it set up to get notification of a reply to one of their posts. It’s okay if all the messages you respond to come from the same poster (as I’m about to do here).

If you want to continue responding to multiple people in one post, you can do so by using the "Gen Reply" button at the bottom or top of the screen, rather than the "Reply" button at the bottom corner of an individual message.

Generally, it works better if you respond individually. Of course, this means you'll probably have to pick and choose which posts and points you respond to, and ignore the rest. But, it helps make the discussion more easy to follow.

-----

dcarraher writes:

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

Message 7

I’m going to add my voice to Catholic Scientist’s and say that biology is basically chemistry. I’ll alter what CS said by stating that I consider biology to be a subset of chemistry that can be studied on a different scale (i.e. organisms instead of molecules). A life form is a relatively discrete microcosm of chemical reactions, and all its characteristics ultimately derive from its constituent chemical reactions.

This little RNA experiment is a great example of the middle ground between what would classically be called “chemistry,” and what would classically be called “biology”: it is, as you say, simply a chemical reaction happening; but, its occurrence displays some of the characteristics of what we consider life (namely, growth and evolution).

Doesn’t that make you at all curious about how it fits into the puzzle of what life is and where life comes from?

-----

dcarraher writes:

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.

You’ve clearly exaggerated the point of view of evolutionists here. If a healthy, stimulating debate is what you're after, I recommend avoiding caricatures and focusing on arguments, rather than people.

From what I’ve read so far, nobody has yet claimed this to be anything more than a demonstration that the RNA World hypothesis, or something similar to it, is a feasible explanation for at least part of the process of abiogenesis. This can therefore serve as a justification for further funding and implementation of more research into the RNA World hypothesis; but it is not being taken as the silver bullet against creationism.

Science is never specifically about what one is showing now, but always about how our current and future picture of the world is changed by what one is showing now. Iblis has provided a great demonstration of this in his brief discussion. The whole point of science is to get people like Iblis to start thinking critically about what needs to be done next to fill in the remaining gaps in our understanding.

Abiogenesis is a very tough thing to show, and I’m confident that it is a vanishingly small minority of biologists and other scientists who believe that one experiment is the final word on any given topic. Most of us reach our air of finality when we connect the dots between this little experiment and the hundreds of other, similar little experiments that have been done before it.

-----

dcarraher writes:

dcarraher writes:

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

Fixed. Mea culpa. Congratulations, you've scorned a typo.

DNA also isn’t made of amino acids.
DNA and RNA are both nucleic acids (that’s what the “NA” stands for).
I repeat Cavediver’s sentiment: either way (RNA or DNA), it would have been a very remarkable experiment, indeed.

-----

dcarraher writes:

If there is no clear demarcation [between life and non-life], then what is abiogenesis all about?

Is it your view that we should only study things that are clearly demarcated?
Is the emergence of life any less intriguing if we can’t easily delimit what “life” is? I don’t see how that could be: it seems to make it more intriguing, at least to me.
Part of the reason for exploring the emergence of life is to fuel the quest to understand what life actually is.

-----

dcarraher writes:

So, at the end of the day, you have an interesting chemical reaction that is interesting not because of any relevance to abiogenesis (you haven't gone anywhere - you end up with more of what you already started with)...

That’s the whole point! Life is just “more of what it started with”: chemistry, building on top of chemistry. We don’t need to “go anywhere,” we just need “more of what we already started with.” This experiment is just one tiny piece of a large puzzle that shows that life is a case of more chemistry than what it originally had! This is precisely why this experiment is interesting!

Edited by Bluejay, : "against" and "fits into"


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 16 by dcarraher, posted 05-12-2010 1:07 PM dcarraher has responded

Replies to this message:
 Message 31 by dcarraher, posted 05-13-2010 1:48 PM Blue Jay has acknowledged this reply

  
Iblis
Member (Idle past 1276 days)
Posts: 663
Joined: 11-17-2005


Message 20 of 52 (560024)
05-12-2010 4:09 PM
Reply to: Message 16 by dcarraher
05-12-2010 1:07 PM


Re: The definition of life is ...
First, a qualifier - in my responses, I will respond to multiple previous posters in a single post. This is not an indication that I am confusing who posted what, simply brevity for the sake of brevity.

Right, but I specifically am the last quote before your rant about life and non-life and I conceded a clear distinction, the cell. Bad form, basically what you want to do is rant at the evil atheist / evolutionist / commie / fag / junkie / devil worshipper / internet community, and there's no such faceless whole. I can argue for hours (in a non-aggressive non-stupid way) with scientists who disagree with me about the most basic things like which came first or what math really represents.

Fixed. Mea culpa. Congratulations, you've scorned a typo.

Nope, we've scorned a person who doesn't understand basic biochemistry yet feels qualified to speak on abiogenesis. Nucleic acids aren't amino acids, chromosomes aren't protein, the processes which create amino acids in nature leave a lot of leftover unused crud which develop, by other processes, into the building-blocks of nucleic acids and lipids and so on. It's like saying if someone had made lead by starting with unleaded gasoline, that would be impressive. Yes, yes it would.

And, on the basis of this (non-existent fair-tale grey) semi-organism, seen fit to ridicule creationists who have the audacity to peer into your petrie dish and say "hey, this isn't life, it's not even novel, just a chemical reaction between RNA and substrate that results in more RNA, until it runs out of substrate".

Are you seriously not getting this? They have found conditions in which extra-cellular RNA can reproduce successfully for unlimited periods of time! I have to pay serious attention now to the "RNA World" theory again for the first time since the late 90s.

Something similar happened with Miller-Urey. The amino acids produced were objectionable for several different reasons, in terms of what we expected to need to make real proteins out of, never mind cells and life. Then Sidney Fox showed that under plausible tidal conditions even these inferior weird racemic aminos could form into proteinoids (polypeptide microspheres) which could grow and reproduce imperfectly, engaging in chemical evolution at the very simple "bubble" level.

http://en.wikipedia.org/...icrospheres#Biological_Protocells

I'm really astonished that evolutionists would care to argue that life is indistinguishable from non-life. If there is no clear demarcation, then what is abiogenesis all about?

Here, show the line. Pick the last thing you consider life or the first thing you consider non-life.

People, monkeys, frogs, fish, protozoa, ricketsia, archaea, DNA viruses, RNA viruses, prions, liposomes, proteinoids

This way all we have to do to satisfy your profoundly simplistic idea of what abiogenesis "ought to mean" is show how to get from one side of the line to the other.

In real life though, we need to understand every link in the chain from elements to eukaryotes.

Edited by Iblis, : Said I wouldn't so of course I will


This message is a reply to:
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RAZD
Member
Posts: 18251
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.2


Message 21 of 52 (560032)
05-12-2010 6:59 PM
Reply to: Message 16 by dcarraher
05-12-2010 1:07 PM


Re: The definition of life is ... try again ...
Hi dcarraher, thanks.

First some formatting tips:

First, a qualifier - in my responses, I will respond to multiple previous posters in a single post. This is not an indication that I am confusing who posted what, simply brevity for the sake of brevity.

No problem. for clarity you can use [qs=RAZD]quotes are easy[/qs] and it becomes:

RAZD writes:

quotes are easy

Then we at least know who the comment comes from.

You can further provide clarity by using the message ID number to link to the specific post -- it's the gray number in parenthesis at the top of the post. For example at the top of your post is:

Message 16 of 20 (559986)

So I can use [qs]dcarraher [mid=559986]: First, a qualifier[/qs] and it becomes:

dcarraher Message 16: First, a qualifier



Now that the formating issue has been addressed we can deal with the issue (or watch you continue to avoid it) of the definition of life ...

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

This is another excellent example of premise-conflict. I'm really astonished that evolutionists would care to argue that life is indistinguishable from non-life.

Amusingly, you have failed to provide a simple definition to distinguish life from non-life.

If you are really truly astonished, then it should be a simple matter to set us on the right path, and provide a definition that can be used that will always distinguish life from non-life: you must know one if you are really truly astonished.

If you cannot provide such a definition, then your astonishment is nothing more than your personal incredulity and opinion, both of which are useless in discussing this simple little issue.

So, dcarraher, what is your definition of life?

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 16 by dcarraher, posted 05-12-2010 1:07 PM dcarraher has not yet responded

Replies to this message:
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Straggler
Member
Posts: 10192
From: London England
Joined: 09-30-2006


Message 22 of 52 (560035)
05-12-2010 7:14 PM
Reply to: Message 21 by RAZD
05-12-2010 6:59 PM


Re: The definition of life is ... try again ...
So, dcarraher, what is your definition of life?

He is obviously not going to have one. The question is do we?

We all agree that abiogenesis is an unsolved scientific mystery. Yes? So where are we drawing the line as to the life/non-life boundary?

There are things we can point to and all agree as being "life". There are things we can point to as not being life.

So (I ask for the sake of education - not to make a point) where is the "missing link" in all of this? What is the step we are yet to observe between "mere" chemistry and that which we all consider to be "life"?


This message is a reply to:
 Message 21 by RAZD, posted 05-12-2010 6:59 PM RAZD has responded

Replies to this message:
 Message 23 by Wounded King, posted 05-12-2010 7:51 PM Straggler has not yet responded
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Wounded King
Member (Idle past 1475 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 23 of 52 (560039)
05-12-2010 7:51 PM
Reply to: Message 22 by Straggler
05-12-2010 7:14 PM


Re: The definition of life is ... try again ...
Viruses are often suggested as a borderline case given their reliance on host cells to provide the machinery of replication for them. But viruses don't provide a viable intermediate in a situation where such replicative machinery does not already exist.

TTFN,

WK


This message is a reply to:
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RAZD
Member
Posts: 18251
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.2


Message 24 of 52 (560045)
05-12-2010 8:17 PM
Reply to: Message 22 by Straggler
05-12-2010 7:14 PM


Re: The definition of life is ... try again ... (paging dcarraher ... )
Hi Straggler,

He is obviously not going to have one. The question is do we?

Maybe I'm an optimist, but I'll cut him some slack, (seeing as he is a noob to this forum) and give him another round to produce one .

There are things we can point to and all agree as being "life". There are things we can point to as not being life.

Which is what makes it so much fun to delve into an actual definition, because this seems to be such an easy question to answer at first.

And yes, I do have an answer, a fairly simple one.

Enjoy.

Edited by RAZD, : hidden


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
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Dr Jack
Member
Posts: 3500
From: Leicester, England
Joined: 07-14-2003


Message 25 of 52 (560100)
05-13-2010 8:17 AM
Reply to: Message 7 by dcarraher
05-11-2010 2:28 PM


Re: ...find a creationist as ignorant as an evolutionist
Hi Dcarraher, and welcome to EvC. I hope you'll stick around

Others have picked up most of your points, but I want to pick up a few points:

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

What is information? Why is the ability of the RNA in this experiment to catalyse it's own replication not to be considered information? What property of this replication is there that distinguishes it from DNA replication in such a way that this is not information but DNA replication is?

2) Translation - there is no mechanism for "interpreting" the information (non-existent) of the RNA and utilizing to build a product (e.g. Protein)

Ribozymes (that is, RNA with catalytic properties) are a key part of the DNA replication and translation processes, these RNAs are not translated from DNA but rather simply transcribed. Why is it such a problem that the same occurs here? Particularly as the whole point of the experiment is to demonstrate the possibility of simpler systems?


This message is a reply to:
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Dr Jack
Member
Posts: 3500
From: Leicester, England
Joined: 07-14-2003


Message 26 of 52 (560101)
05-13-2010 8:18 AM
Reply to: Message 22 by Straggler
05-12-2010 7:14 PM


Re: The definition of life is ... try again ...
He is obviously not going to have one. The question is do we?

No. For the same reason that we don't have a good definition of species: the reality is fuzzier than our abstractions.


This message is a reply to:
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Straggler
Member
Posts: 10192
From: London England
Joined: 09-30-2006


Message 27 of 52 (560107)
05-13-2010 8:51 AM
Reply to: Message 26 by Dr Jack
05-13-2010 8:18 AM


Re: The definition of life is ... try again ...
Straggler on the definition of life writes:

He is obviously not going to have one. The question is do we?

Mr Jack writes:

No. For the same reason that we don't have a good definition of species: the reality is fuzzier than our abstractions.

That is my instinctive answer too. But RAZ says he does have a definition.

RAZD writes:

And yes, I do have an answer, a fairly simple one.

So I guess we'll see where this thread goes once that is revealed.


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slevesque
Member (Idle past 2021 days)
Posts: 1456
Joined: 05-14-2009


Message 28 of 52 (560119)
05-13-2010 11:56 AM
Reply to: Message 27 by Straggler
05-13-2010 8:51 AM


Re: The definition of life is ... try again ...
Yeah I too am in the forever mental search for a good definition of what is life. Just waiting after RAZD ...
This message is a reply to:
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dcarraher
Junior Member (Idle past 2448 days)
Posts: 13
From: Cols, OH
Joined: 06-05-2009


Message 29 of 52 (560132)
05-13-2010 1:38 PM
Reply to: Message 17 by Taq
05-12-2010 1:34 PM


Re: The definition of life is ...
If I start an experiment with one bacterium and come back the next day to find billions of bacteria would you claim that this is not an example of life since I just ended up with more of what I started with?

No - because you started with something that is unarguably "Life", and ended with more. In the RNA experiment, you started with RNA, which is unarguably "Not Life", and ended up with more "Not Life". QED - Experiments that start with non-life and end up with more non-life = irrelevant to abiogenesis.


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dcarraher
Junior Member (Idle past 2448 days)
Posts: 13
From: Cols, OH
Joined: 06-05-2009


Message 30 of 52 (560135)
05-13-2010 1:45 PM
Reply to: Message 18 by dokukaeru
05-12-2010 1:43 PM


Re: The definition of life is ...
You point out in multiple places that you feel it is clearly irrelevant, but fail to explain why. Maybe I am missing something here....why do you feel it is it not relevant?

Because the experiment starts with something that is clearly non-life, and ends with more of something that is not significantly different. You started with the ability to replicate, and ended with the ability to replicate - you did not add the ability to replicate, nor did you add any other "life-like" characteristics. Ergo, irrelevant to the question of abiogenesis.


This message is a reply to:
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