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Author Topic:   Abiogenesis
DNAunion
Inactive Member


Message 91 of 142 (96793)
04-01-2004 10:01 PM
Reply to: Message 87 by RAZD
04-01-2004 12:27 PM


Re: Details, man, details
quote:
AbbyLeever: Are you saying that we do not need DNA in a protocell construct to show behavior attributed to living matter? Would not this structure be somewhere between a virus and a (primitive) cell (the virus having lost elements of the protocell that it can replace by using elements in a current cell)?
Forget about viruses already. A virus requires a living host cell to "reproduce": if there are no living host cells, there are no viruses. Viruses are not involved in abiogenesis. A self-replicating RNA of the type proposed by OOL researchers is not a virus.

This message is a reply to:
 Message 87 by RAZD, posted 04-01-2004 12:27 PM RAZD has not replied

DNAunion
Inactive Member


Message 92 of 142 (96797)
04-01-2004 10:07 PM
Reply to: Message 87 by RAZD
04-01-2004 12:27 PM


Re: Details, man, details
quote:
Abbyleever: Is this occurring within a cell (or protocell) environment or is it occurring in a more open environment?
No. It's occuring in a lab with the researchers synthesizing all of 15-aa and 17-aa molecules, and preactivating them, with those presynthesized and preactivated halves being required for the full template - which the researchers designed - to then simply align them to help them bond - as intended - more readily.
quote:
AbbyLeever: Agreed this is not "LIFE" but it certainly looks to the development of self-replicating organic systems, definitely applicable to abiogenesis.
Definitely not applicable to abiogenesis. Unless you are suggesting that some intelligent researchers were around 3.5 - 4 billion years ago continuousaly synthesizing highly complex and specific 15-aa and 17-aa halves, preactivating them as required, and feeding them to the reaction.
Of course researcher invention would not be required if the molecules could actually self-replicate. But they can't.
[This message has been edited by DNAunion, 04-01-2004]

This message is a reply to:
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Brad McFall
Member (Idle past 5033 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 93 of 142 (97032)
04-02-2004 11:27 AM
Reply to: Message 90 by DNAunion
04-01-2004 9:50 PM


Re: Details, man, details
I see you dont need any "help" from me. Brad-oOOOOOOOOOOOOOOOOOOOOout.

This message is a reply to:
 Message 90 by DNAunion, posted 04-01-2004 9:50 PM DNAunion has not replied

RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 94 of 142 (97638)
04-04-2004 1:07 AM
Reply to: Message 86 by Black
04-01-2004 7:29 AM


peptide article
btw --
I googled on {self-replicating peptides 32-amino-acid peptide} - the information you gave and found this site:
http://www.santafe.edu/sfi/People/kauffman/sak-peptides.html
which talks about the whole procedure
thanks for the info.
{{{an open mind looks up from the hilltop to see if there are higher peaks to find}}}

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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 Message 86 by Black, posted 04-01-2004 7:29 AM Black has not replied

Muhd
Inactive Member


Message 95 of 142 (97779)
04-05-2004 12:49 AM


quote:
(1) Amino acids could form naturally
Really? I would like to see the support of this. I was under the impression that any amino acids formed naturally would be oxidized by oxygen in the atmosphere.
The probability of abiogenesis happening is NOT 100% because there are other ways we could have come to existance.
Probability only works when applied to events that are uncertain, so my existance does not count.
[This message has been edited by Muhd, 04-05-2004]

Replies to this message:
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 Message 101 by Black, posted 04-07-2004 5:26 PM Muhd has replied

RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 96 of 142 (97786)
04-05-2004 1:20 AM
Reply to: Message 95 by Muhd
04-05-2004 12:49 AM


It would help to have a little more info on which message you are replying to (If you use the little reply button with the red arrow at the end of the message it links your reply to the message).
I was under the impression that any amino acids formed naturally would be oxidized by oxygen in the atmosphere.
Remember that we are talking about a time before there was an oxygen rich atmosphere on earth
so my existance does not count
that would count as an event that has already happened.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

This message is a reply to:
 Message 95 by Muhd, posted 04-05-2004 12:49 AM Muhd has not replied

Black
Member (Idle past 5183 days)
Posts: 77
Joined: 11-28-2008


Message 97 of 142 (98251)
04-06-2004 10:10 PM
Reply to: Message 88 by DNAunion
04-01-2004 9:36 PM


Re: Details, man, details
quote:
Please don't stuff words in my mouth. I did not say that.
Oh, really? Let's see what you said before:
quote:
The only actually supported point you have is that amino acids can form naturally.
You said you only agreed with #1 (amino acids forming naturally), therefore you disagreed with the others.
Did you chance your mind?
If so, then its two down and two to go. If you don't agree, why not?
--Black
P.S. I'll get to the other posts later today...until then, cya!
[This message has been edited by Black, 04-07-2004]

This message is a reply to:
 Message 88 by DNAunion, posted 04-01-2004 9:36 PM DNAunion has replied

Replies to this message:
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wj
Inactive Member


Message 98 of 142 (98335)
04-07-2004 3:23 AM
Reply to: Message 95 by Muhd
04-05-2004 12:49 AM


Muhd writes:
(1) Amino acids could form naturally
--------------------------------------------------------------------------------
Really? I would like to see the support of this. I was under the impression that any amino acids formed naturally would be oxidized by oxygen in the atmosphere.
The Murchison meteorite shows evidence of amino acids which have formed extraterrestrially. Surely that is a natural process. And, as pointed out by Abby, there is evidence that there was only minimal oxygen in the early earth's atmosphere.

This message is a reply to:
 Message 95 by Muhd, posted 04-05-2004 12:49 AM Muhd has not replied

Black
Member (Idle past 5183 days)
Posts: 77
Joined: 11-28-2008


Message 99 of 142 (98490)
04-07-2004 5:24 PM
Reply to: Message 90 by DNAunion
04-01-2004 9:50 PM


Re: Details, man, details
quote:
The ribozymes that Cech discovered spliced segments out of themselves and did not have multiple turnover capabilities.
But things have happened since that time. Ever here of peptidyl transferase?
Peptidyl transferase catalyzes the synthesisof peptide bonds in vitro using substrates much smaller than the aminoacyl and peptidyl tRNAs that are the ribo-some’s normal fare.
How does it work?
The reaction that occurs when peptide bonds form on theribosome is a simple one: the aminolysis of an ester bond.The nucleophilic -amino group of the amino acid moietyof an aminoacyl tRNA bound to the so-called A site of thepeptidyl transferase center attacks the electrophilic carbonylcarbon of the ester bond linking the peptide moiety of apeptidyl tRNA bound to the so-called P site of the peptidyltransferase center. The resulting anionic, tetrahedral carbonintermediate subsequently rearranges to yield a dischargedtRNA bound to the P site, and an A-site bound tRNA joinedby an ester bond to a peptide that is one amino acid longerthan it was before the reaction occurred.
quote:
No, synthesized.
It was based on a protein found in nature, an alpha-helical coiled coil.
quote:
it absoluately requires researchers to synthesize all of its highly complex "halves" and preactivate them
[...]
No. It's occuring in a lab with the researchers synthesizing all of 15-aa and 17-aa molecules, and preactivating them, with those presynthesized and preactivated halves being required for the full template - which the researchers designed - to then simply align them to help them bond - as intended - more readily.
[...]
Definitely not applicable to abiogenesis. Unless you are suggesting that some intelligent researchers were around 3.5 - 4 billion years ago continuousaly synthesizing highly complex and specific 15-aa and 17-aa halves, preactivating them as required, and feeding them to the reaction.
No, intelligent researchers are not needed 3.5-4 billion years ago. The reason is simple: the researchers were simulating natural processes. These peptides could have been synthesised naturally.

An animated cartoon showing the self-replication process with the 32 residue peptidic template [GRAY] which binds a 15 residue nucleophilic fragment [RED] and a 17 residue electrophilic fragment [BLUE] which catalyses the thioester bond formation [YELLOW] hence catalyzing it's own formation.
A 32-residue alpha-helical peptide [GRAY; template] based on the leucine zipper motif of GCN4 is shown to act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide bond condensation of a 15-residue [RED;nucleophilic] and 17-residue [BLUE; electrophilic] constitutional peptide fragments in neutral and dilute aqueous solutions.
The self-replicating process displays parabolic growth and is goverend by square-root law kinetics in the initial period of product formation.
Self-replication.
quote:
Huh? I don't remember the GL using a single-stranded DNA hexamer? Did you misplace that paragraph?
No, its not a misplaced paragraph. Its what was published in Nature.
quote:
So? Pentium 4 CPUs exist...what do they have to do with abiogenesis?
There's no valid link between the Ghidari Ligase and abiogenesis.
You are right, Pentium 4 CPUs exist. So why aren't I bringing them up in this discussion?
Because, as you said, they have nothing to do with abiogenesis. But self-replicating peptides do because they are kind of like one of the predictions of abiogenesis theories.
Regarding RNA from peptide nucleic acids...I find that the evidence supports what I said before. PNA consists of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids.
AEG is produced directly in electric discharge reactions from CH4, N2, NH3, and H2O. Electric discharges also produce ethylenediamine, as do NH4CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH4CN polymerization in the presence of glycine leads to the adenine and guanine-N 9-acetic acids, and the cytosine and uracil-N 1-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea.
RNA may be polymerized using the PNA as template accounts for enzymatic activities including PNA replication.
So now let's review: Amino acids form naturally, as predicted by abiogenesis theories. If synthesised correctly, peptides (chains of amino acids) can self-replicate, as predicted by abiogenesis theories. The substances to create PNA (the precursor to RNA) form naturally, etc., as predicted by abiogenesis theories. RNA can do the function of DNA, as predicted by abiogenesis theories. RNA can act as a catalyst, as predicted by abiogenesis theories. RNA can do auto-catalysis, as predicted by abiogenesis theories. These things were required for abiogenesis...and now we know they are true. These are the pieces of the puzzel. I put them together....and come to the conclusion that abiogensis is possible....and is probably what happened!
--Black

This message is a reply to:
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Replies to this message:
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Black
Member (Idle past 5183 days)
Posts: 77
Joined: 11-28-2008


Message 100 of 142 (98491)
04-07-2004 5:25 PM
Reply to: Message 87 by RAZD
04-01-2004 12:27 PM


Re: Details, man, details
quote:
Are you saying that we do not need DNA in a protocell construct to show behavior attributed to living matter? Would not this structure be somewhere between a virus and a (primitive) cell (the virus having lost elements of the protocell that it can replace by using elements in a current cell)?
RNA can do the function of DNA. So the answer is, yes, we do not need DNA to show behavior attributed to living matter.

This message is a reply to:
 Message 87 by RAZD, posted 04-01-2004 12:27 PM RAZD has not replied

Black
Member (Idle past 5183 days)
Posts: 77
Joined: 11-28-2008


Message 101 of 142 (98493)
04-07-2004 5:26 PM
Reply to: Message 95 by Muhd
04-05-2004 12:49 AM


quote:
I was under the impression that any amino acids formed naturally would be oxidized by oxygen in the atmosphere.
Most of the Oxygen in our atmosphere comes from processes like photosynthesis which release Oxygen into the atmosphere as one of there waste products. So, of course when life was forming there would not have been any photosynthesis going on (and therefore, very little Oxygen)!
We can also, through different methods, detect how much Oxygen was in the atmosphere back then...and what we find matches our predictions.

This message is a reply to:
 Message 95 by Muhd, posted 04-05-2004 12:49 AM Muhd has replied

Replies to this message:
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Muhd
Inactive Member


Message 102 of 142 (98534)
04-07-2004 7:23 PM
Reply to: Message 101 by Black
04-07-2004 5:26 PM


Okay...
I would like to know your sources of this information.
Also,
If there was no or little oxygen in the early Earth atmosphere, then what would protect the amino acids and the potential proteins from UV light (oxygen produces ozone)?
[This message has been edited by Muhd, 04-07-2004]

This message is a reply to:
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Replies to this message:
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DNAunion
Inactive Member


Message 103 of 142 (98579)
04-07-2004 11:46 PM
Reply to: Message 97 by Black
04-06-2004 10:10 PM


Re: Details, man, details
quote:
Black: Let's start with autocatalyzing RNA. You say this don't exist.
quote:
DNAunion: Please don't stuff words in my mouth. I did not say that.
quote:
Black: Oh, really?
Yes really. And anyone who made it past elementary school can see that I didn't say it.
Your following support falls flat on its face. But since you seem incapable of grasping something so simple, let me explain it to you.
quote:
Black: Let's see what you said before:
----------------------------------------------------------------------
DNAunion: The only actually supported point you have is that amino acids can form naturally.
----------------------------------------------------------------------
You said you only agreed with #1 (amino acids forming naturally), therefore you disagreed with the others.
Did you chance your mind?
Nope. Did you lose your mind? Yep.
If you had half a brain and were honest you wouldn't be able to try to claim that two very different things you said were the same. Here, look again at your original list of 4, for which only (1) has been demonstrated.
quote:
(1) Amino acids could form naturally
(2) Amino acids could link together (as peptides) and reproduce naturally
(3) RNA could form from amino acid chains (peptides)
(4) RNA would need neither DNA nor protein to catalyze its own replication
Now, Black, which one of those says just that autocatalyzing RNA exists? Not one of them! And no, (4) doesn't say that: it says something COMPLETELY different.
quote:
Black: If so, then its two down and two to go.
Sorry, but you still have only 1 out of 4.
[This message has been edited by DNAunion, 04-07-2004]

This message is a reply to:
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Replies to this message:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 104 of 142 (98581)
04-07-2004 11:51 PM
Reply to: Message 103 by DNAunion
04-07-2004 11:46 PM


If you had half a brain and were honest
Naturally, one can't disagree with DNA unless they're an idiot and a liar.
What I love most is how DNA's contributions consistently raise the bar of tact and maturity at the ol' EvC forum.

This message is a reply to:
 Message 103 by DNAunion, posted 04-07-2004 11:46 PM DNAunion has not replied

AdminAsgara
Administrator (Idle past 2302 days)
Posts: 2073
From: The Universe
Joined: 10-11-2003


Message 105 of 142 (98591)
04-08-2004 12:29 AM
Reply to: Message 103 by DNAunion
04-07-2004 11:46 PM


Re: Details, man, details
DNA, is there really a need for the ad hominems? Tone it down please.
The attitude seems to be your modus operandi around here and if it is going to continue you'll be taking an extended break.
And anyone who made it past elementary school can see that I didn't say it
But since you seem incapable of grasping something so simple, let me explain it to you
Did you lose your mind? Yep
If you had half a brain and were honest you wouldn't be able to try to claim that two very different things you said were the same

AdminAsgara
Queen of the Universe

This message is a reply to:
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