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Author Topic:   Abiogenesis
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 76 of 142 (96059)
03-30-2004 4:59 PM
Reply to: Message 59 by RAZD
03-26-2004 12:20 PM


Re: Viruses, prions and curious implications
I think the standard difference of metabolism and replication has lulled you into a vision of a cell that can indeed be narrower than you represented so far but that really is my opnion and is not something I have ever yet tried to depose on anyone on this board. Best Brad. I heard what DNAUNION said, mind you.

This message is a reply to:
 Message 59 by RAZD, posted 03-26-2004 12:20 PM RAZD has replied

Replies to this message:
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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 77 of 142 (96060)
03-30-2004 5:02 PM
Reply to: Message 58 by Darwin Storm
03-26-2004 11:15 AM


Re: Viruses, prions and curious implications
I have started to discuss this under "incidence vs co-incidence" in another thread. Do you want me to comment to computation directly on what has been going back and forth between DNAu and AL?

This message is a reply to:
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 78 of 142 (96076)
03-30-2004 5:56 PM
Reply to: Message 76 by Brad McFall
03-30-2004 4:59 PM


Re: Viruses, prions and curious implications
Sometimes the envelope needs to be pushed across the table before it is opened.

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 76 by Brad McFall, posted 03-30-2004 4:59 PM Brad McFall has not replied

Replies to this message:
 Message 80 by secondlaw, posted 03-31-2004 7:42 AM RAZD has replied

DNAunion
Inactive Member


Message 79 of 142 (96195)
03-30-2004 10:53 PM
Reply to: Message 75 by RAZD
03-30-2004 1:53 PM


Re: jump in the mix
Just to make sure we're all on the same page....
The probability that event E occurred given that we already know that E in fact did occur is 1 (100% certainty). However, if we only strongly believe that event E occurred, then it's probability doesn't have to be 1.
For example, what is the probability that life arose on Earth? We can't say "It's 100% because we know it happened". We DON'T know it happened: life may have arisen on Mars or elsewhere and then been transferred here, for example.
So to restate it, we can't simply say that the probability of a "past event" is 100% unless we know for sure that it actually did occur.

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Replies to this message:
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secondlaw
Inactive Member


Message 80 of 142 (96269)
03-31-2004 7:42 AM
Reply to: Message 78 by RAZD
03-30-2004 5:56 PM


for those interested
I have posted under Lam's "Why do people believe what they believe forum?"
This post has one documentation of mathematical probability and the 'development' of the first cell by chance.

This message is a reply to:
 Message 78 by RAZD, posted 03-30-2004 5:56 PM RAZD has replied

Replies to this message:
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Admin
Director
Posts: 12998
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.2


Message 81 of 142 (96289)
03-31-2004 9:32 AM
Reply to: Message 72 by secondlaw
03-30-2004 12:42 PM


Re: jump in the mix
Erroneous message deleted. --Admin
[This message has been edited by Admin, 03-31-2004]

--Percy
EvC Forum Administrator

This message is a reply to:
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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 82 of 142 (96290)
03-31-2004 9:34 AM
Reply to: Message 72 by secondlaw
03-30-2004 12:42 PM


Re: jump in the mix
secondlaw writes:
If asked, I have documentation showing statistical evidence that the chance of life from non-life is nil (10 to the power of 1.4 million).
Consider yourself asked.
--Percy

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Replies to this message:
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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 83 of 142 (96292)
03-31-2004 9:37 AM
Reply to: Message 79 by DNAunion
03-30-2004 10:53 PM


Re: jump in the mix
DNAunion writes:
For example, what is the probability that life arose on Earth?
Is this the question this thread is currently addressing? Or is it whether life arose naturally?
--Percy

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 Message 79 by DNAunion, posted 03-30-2004 10:53 PM DNAunion has not replied

secondlaw
Inactive Member


Message 84 of 142 (96294)
03-31-2004 9:43 AM
Reply to: Message 82 by Percy
03-31-2004 9:34 AM


Re: jump in the mix
I have placed that information in Lam's post of "Why do people believe that they believe?"

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 Message 82 by Percy, posted 03-31-2004 9:34 AM Percy has not replied

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


Message 85 of 142 (96382)
03-31-2004 2:59 PM
Reply to: Message 80 by secondlaw
03-31-2004 7:42 AM


Re: for those interested
why there and not here? I will find it.

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


Message 86 of 142 (96583)
04-01-2004 7:29 AM
Reply to: Message 63 by DNAunion
03-27-2004 7:55 PM


Details, man, details
OK, DNAUnion, you asked for details, well here we go:
quote:
Where? You don't support ANYTHING. Simply posting article titles is not supporting one's position, neither is posting mere abstracts. Science is in the details. Now, if you have actual evidence that supports for your position, then you should present it.
Wow. Chill, man! Don't get mad here. I am not just a reference babbler and I'll try to prove it!
Let's start with autocatalyzing RNA. You say this don't exist. Let's find out. First let's make sure we have our terms defined.

autocatalysis: Self-catalysis; catalysis of a substance by one of its own products, as of silver oxide by the silver formed by reduction of a small portion of it.
RNA (ribonucleic acid): A polymeric constituent of all living cells and many viruses, consisting of a long, usually single-stranded chain of alternating phosphate and ribose units with the bases adenine, guanine, cytosine, and uracil bonded to the ribose. The structure and base sequence of RNA are determinants of protein synthesis and the transmission of genetic information.

OK, what was originally thought was that "DNA makes RNA makes protein." Obviously, if all three of these are needed at the same time for life, it causes problems for abiogenesis. However, we now know that certain things do not need DNA but instead reverse transcribe their RNA. So we can illiminate DNA from that formula. Can we also illiminate proteins? Well, we also now know that RNA can do the function of proteins and act as an enzyme (this was proved by Nobel Prize-winning researcher Thomas R. Cech). Enter the term ribozyme.
ribozyme: An RNA segment that has the ability to catalyze the cleavage and formation of covalent bonds in RNA strands at specific sites.
Back to autoctalysing RNA: autocatalyzing ribozymes DO exist. Let me give an example (and I'll give the details): the hammerhead ribozyme.
Hammerhead ribozymes are small, catalytic RNAs that undergo self-cleavage of their own backbone to produce two RNA products. All hammerhead ribozymes contain three base-paired stems and a highly conserved core of residues required for cleavage. The cleavage reaction proceeds by an attack of a 2' hydroxyl oxygen of a catalytic site cytosine on the phosphorus atom attached to the 3' carbon of the same residue, breaking the sugar phosphate backbone and producing a 2', 3' cyclic phosphate. As for protein ribonucleases, a metal ion bound in the active site (Mg++) stabilizes the ionized form of the 2' hydroxyl oxygen, promoting the catalytic attack.
The hammerhead ribozyme coordinates Mg++ in the proper geometry to stabilize the trigonal bipyramid intermediate formed by attack of the 2-OH on the phosphate. The end products are a 2,3 cyclic phosphate and a 5-OH.
Now regarding self replicating peptides, uh, well first the details :
There have been several self-replicating peptides discovered. The one I referenced was a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4, can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution.
It uses a single-stranded DNA hexamer and its two trimer fragments) are based on a polymer catalysing its own formation from two fragments.
Now you say this does not have any application for abiogenisis. I say it does. Self replicating peptides DO exist. I admit that they were not *formed* by some abiogenesis expirement, but they *exist* which is what I was saying. Currently, our knowledge of abiogenesis is like a puzzel. We have most of the pieces, we just have not put them together (and made life). Self replicating peptides ARE one of the pieces. Before we discovered self replicating peptides, we needed some way for amino acids to reproduce....and we did not have a way. The discovery of self-replicating peptides was in a way confirmation of a prediction that abiogensis theories made. If you think not, you should explain why not.
Regarding RNA comING from peptide nucleic acids. I have not looked into that yet, but that will be the next thing I do, I will post the details that I find.
BTW, DNAUnion, thanks for challenging me on this. You forced me to look things up and I learned alot. Unfortunately for you, even after doing the research, my conclusion remains the same. Note that if I had done the research and not found things to support my statements, I would have withdrawn them.
I will post on peptide nucleic acids soon. I have not tryed to find anything about it yet.....Till then
--Black
P.S. I didn't get all the details. Want more? Ask me....or do the research yourself
[This message has been edited by Black, 04-01-2004]

This message is a reply to:
 Message 63 by DNAunion, posted 03-27-2004 7:55 PM DNAunion has replied

Replies to this message:
 Message 87 by RAZD, posted 04-01-2004 12:27 PM Black has replied
 Message 88 by DNAunion, posted 04-01-2004 9:36 PM Black has replied
 Message 89 by DNAunion, posted 04-01-2004 9:40 PM Black has not replied
 Message 90 by DNAunion, posted 04-01-2004 9:50 PM Black has replied
 Message 94 by RAZD, posted 04-04-2004 1:07 AM Black has not replied

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


Message 87 of 142 (96627)
04-01-2004 12:27 PM
Reply to: Message 86 by Black
04-01-2004 7:29 AM


Re: Details, man, details
Black --
Welcome to the fray from another newbie. Nice post.
Chill, man! Don't get mad here
Don't worry, I think this is DNU's modus operandi with new people.
... originally thought was that "DNA makes RNA makes protein." ... we now know that certain things do not need DNA but instead reverse transcribe their RNA. So we can illiminate DNA ...
Hammerhead ribozymes are small, catalytic RNAs that undergo self-cleavage of their own backbone to produce two RNA products
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)?
There have been several self-replicating peptides discovered. The one I referenced was a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4, can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution.
Is this occurring within a cell (or protocell) environment or is it occurring in a more open environment? Agreed this is not "LIFE" but it certainly looks to the development of self-replicating organic systems, definitely applicable to abiogenesis.
Currently, our knowledge of abiogenesis is like a puzzel.
Another analogy is a bridge - one shore is non-life, the other is life. From one shore we can build an abutment extending into the river based on known organic molecules that existed and can be easily created (amino acids would be in this group). From the other shore we can build an abutment extending into the river based on minimizing the elements needed for a living cell (LUCA would fall in this category, self replicating RNA would fall in this category). The river is swift and filled with rocks -- some rocks can be used as stepping stones to build a temporary guide for the bridge, some rocks are eroded (viruses and prions) and some are fairly robust (replicating peptides), but all are useful.
I look forward to your next post on this topic.
AL.

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 86 by Black, posted 04-01-2004 7:29 AM Black has replied

Replies to this message:
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 Message 92 by DNAunion, posted 04-01-2004 10:07 PM RAZD has not replied
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DNAunion
Inactive Member


Message 88 of 142 (96775)
04-01-2004 9:36 PM
Reply to: Message 86 by Black
04-01-2004 7:29 AM


Re: Details, man, details
quote:
Black: Let's start with autocatalyzing RNA. You say this don't exist.
Please don't stuff words in my mouth. I did not say that.

This message is a reply to:
 Message 86 by Black, posted 04-01-2004 7:29 AM Black has replied

Replies to this message:
 Message 97 by Black, posted 04-06-2004 10:10 PM DNAunion has replied

DNAunion
Inactive Member


Message 89 of 142 (96777)
04-01-2004 9:40 PM
Reply to: Message 86 by Black
04-01-2004 7:29 AM


Re: Details, man, details
quote:
Black: Well, we also now know that RNA can do the function of proteins and act as an enzyme (this was proved by Nobel Prize-winning researcher Thomas R. Cech).
Technically, that is incorrect. Enzymes are (biological) catalysts and catalysts are not permanentaly altered when they catalyze a reaction. The ribozymes that Cech discovered spliced segments out of themselves and did not have multiple turnover capabilities.

This message is a reply to:
 Message 86 by Black, posted 04-01-2004 7:29 AM Black has not replied

DNAunion
Inactive Member


Message 90 of 142 (96784)
04-01-2004 9:50 PM
Reply to: Message 86 by Black
04-01-2004 7:29 AM


Re: Details, man, details
quote:
Black: There have been several self-replicating peptides discovered.
No, synthesized.
quote:
Black: The one I referenced was a 32-amino-acid peptide, folded into an alpha-helix and having a structure based on a region of the yeast transcription factor GCN4,
Yeah, I know: the scientists designed that molecule to "self-replicate": it wasn't discovered.
It also cannot self-replicate: it absoluately requires researchers to synthesize all of its highly complex "halves" and preactivate them. Using the term self-replicating for the simple activity this molecule performs and then trying to use this molecule's self-replication when talking about abiogenesis is equivocation.
quote:
Black: It uses a single-stranded DNA hexamer and its two trimer fragments) are based on a polymer catalysing its own formation from two fragments.
Huh? I don't remember the GL using a single-stranded DNA hexamer? Did you misplace that paragraph?
quote:
Now you say this does not have any application for abiogenisis. I say it does. Self replicating peptides DO exist.
Equivocation at a minimum.
quote:
Black: I admit that they were not *formed* by some abiogenesis expirement, but they *exist* which is what I was saying.
So? Pentium 4 CPUs exist...what do they have to do with abiogenesis?
There's no valid link between the Ghidari Ligase and abiogenesis.
quote:
Black: Self replicating peptides ARE one of the pieces. Before we discovered self replicating peptides, we needed some way for amino acids to reproduce....and we did not have a way. The discovery of self-replicating peptides was in a way confirmation of a prediction that abiogensis theories made. If you think not, you should explain why not.
Because that peptide can't actually self-replicate, despite the misleading term so many scientists use.
[This message has been edited by DNAunion, 04-01-2004]

This message is a reply to:
 Message 86 by Black, posted 04-01-2004 7:29 AM Black has replied

Replies to this message:
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