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Author Topic:   Abiogenesis - Or Better Living Through Chemistry
Omega Red
Inactive Member


Message 47 of 85 (57443)
09-24-2003 6:29 AM
Reply to: Message 21 by joz
02-28-2002 10:00 AM


sadistics
quote:
joz wrote
A little article here about calculating the probability of abiogenesis......

http://www.talkorigins.org/faqs/abioprob.html#Links


quote:
From the article
Going back to our primitive ocean of 1 x 1024 litres and assuming a nucleotide concentration of 1 x 10-7 M [23], then there are roughly 1 x 1049 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 1034) could be produced in a year, let alone a million years.

I haven't had a chance to get Chyba & Sagan's Nature article, so I may be way out of line here. But what evidence is there that such a concentration of amino acids existed?

The "probabilities" article makes some very big assumptions:
1) A significant simple chemical concentration and/or number of reaction sites
2) Optimal conditions at the sites for polymer formation against "adverse" heat, acidity/alkalinity & other chemicals present, turbulence
3) All simple chemicals are reacting
4) All polymers survive for further reactions
5) See 1-4 for polymers into replicating polymers
6) See 1-4 for replicating polymers into hypercycle

As I understand it the hypercycle would be an enclosed system in which further reactions are free to take place under fairly uniform conditions. Prior to the hypercycle formation, there is the possibility of FeS membranes (Russell & Hall), which would improve some of the simple chemical/polymer reactions. Maybe I am being somewhat naive here and would appreciate someone to point me in the right direction for info.

[This message has been edited by Omega Red, 09-24-2003]


This message is a reply to:
 Message 21 by joz, posted 02-28-2002 10:00 AM joz has not yet responded

Replies to this message:
 Message 51 by DNAunion, posted 11-02-2003 8:13 PM Omega Red has not yet responded

  
Rei
Member (Idle past 4543 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 48 of 85 (57498)
09-24-2003 2:16 PM
Reply to: Message 46 by Bart007
09-15-2002 3:47 PM


quote:
I believe every experiment you refer to was intelligently designed and controlled to get the intended results

So, do you acknowledge that on a planet with an atmosphere like that in the experiments discussed, abiogenesis could occur? Because we're talking about whether it is a possible phenominon or not. These experiments seem to show that, in a variety of different atmospheres, it can happen. You can argue all you want that our particular early atmosphere (which is still largely unknown) hasn't been demonstrated yet. So?

BTW, most scientists don't believe that life developed in the exposed atmosphere; the current most likely accepted location is undersea thermal vents.

quote:
peptides may form easily in the presence of amoni acids, but none that are of any use to life

So, what type of hat did you pull that out of?

quote:
to make life, we need amino acids, sugars, bases, and phosphates.

Actually, to make life, you need a self-replicating chemical or cycle, base chemicals that can be utilized for the replication, and energy. Everything else (such as more efficient routes) can come later. There is no reason that the initial energy source must be sugars. If we're talking about a deep sea vent spewing hydrogen sulfide, we're looking at something that will react with water, but even more eagerly react with sedimentary compounds that contain a poorly bonded oxygen, or react to the water in the presence of catalysts. There's no reason why proteins in such an environment should need to follow a normal cycle, working through sugars for energy. They merely should need to, via hydrogen bonding, attract similar amino acids to themselves, and catalyze the reaction to bond them. Even if they only created a protein that is a fraction of its own chain, it has greatly increased its likelyhood of finishing a replication in the future.

------------------
"Illuminant light,
illuminate me."


This message is a reply to:
 Message 46 by Bart007, posted 09-15-2002 3:47 PM Bart007 has not yet responded

Replies to this message:
 Message 49 by DNAunion, posted 10-31-2003 11:58 PM Rei has not yet responded

    
DNAunion
Inactive Member


Message 49 of 85 (63761)
10-31-2003 11:58 PM
Reply to: Message 48 by Rei
09-24-2003 2:16 PM


quote:
Going back to our primitive ocean of 1 x 10^24 litres and assuming a nucleotide concentration of 1 x 10^-7 M [23], then there are roughly 1 x 10^49 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 10^34) could be produced in a year, let alone a million years. (from Talk Origins article)

/*DNAunion*/ But (besides other potential problems) we are no longer dealing with the complete volume of an ocean: as Rei points out.

quote:
Rei: BTW, most scientists don't believe that life developed in the exposed atmosphere; the current most likely accepted location is undersea thermal vents.

/*DNAunion*/ Under that “current most likely” scenario the Talk Origins' calculation becomes invalid.


This message is a reply to:
 Message 48 by Rei, posted 09-24-2003 2:16 PM Rei has not yet responded

  
tsjok45
Inactive Member


Message 50 of 85 (63912)
11-02-2003 7:58 AM
Reply to: Message 46 by Bart007
09-15-2002 3:47 PM


Halloliladadidads...

Quote
--------------------------------------------------------------------
I believe abiogenesis is impossible as based upon scientific considerations only
--------------------------------------------------------------------
Again some “brand- new” loads of non scientific “considerations “( ? ) then , I suppose ?

I prefer to call that kind of strategies quackery , you know ?

You will use what ?
“medicine –doctors” treatments ? ,
Voodoo , alchemy ?
some magic ?
some new age ?
you’ ll pray for me ?
what’s next
ah yes , nearly forgot it ;
___ the supernatural miracle “being(s) “ , ( blessed is THE id , I mean - )
So What ?

Well it SHALL be based on scientific “considerations “ alone

Is there something else we can accept
that is
is “understandeable” and fit enough to be “communicated “ / discussed / “revealed “ to human beings
( = non-gullible, “non-morons” ) ?
At least a common " code " " language " "agreed upon common ground "
that is installing "compatibility " between all members in a
communication network ...

Is there ?

Is this reintroduction of irrationality only "a nice try ... to “rewin” apostates ? "... or will these sinners be “punished “ and “lost for ever “ ?

How you 'll do this ?

Iow –( I summarise )
are you going to use some tricks of psychology and rhetorics or
will you stick to methodologic naturalism ?
and if not ? why not ?


This message is a reply to:
 Message 46 by Bart007, posted 09-15-2002 3:47 PM Bart007 has not yet responded

  
DNAunion
Inactive Member


Message 51 of 85 (64032)
11-02-2003 8:13 PM
Reply to: Message 47 by Omega Red
09-24-2003 6:29 AM


Re: sadistics
quote:
From the article:
"Going back to our primitive ocean of 1 x 10^24 litres and assuming a nucleotide concentration of 1 x 10^-7 M [23], then there are roughly 1 x 10^49 potential nucleotide chains, so that a fair number of efficent RNA ligases (about 1 x 10^34) could be produced in a year, let alone a million years." (from Talk Origins article)

/*DNAunion*/ I already pointed out one problem with the calculation...here's a second.

The calculation implicitly relies upon homochirality. If both enantiomeric forms of the bases (actually, the sugar moieties of the bases) were present, enantiomeric cross inhibition would hinder the formation of long polymers needed for replication or other complex function.

[This message has been edited by DNAunion, 11-02-2003]


This message is a reply to:
 Message 47 by Omega Red, posted 09-24-2003 6:29 AM Omega Red has not yet responded

Replies to this message:
 Message 52 by Rrhain, posted 11-03-2003 7:09 AM DNAunion has responded

  
Rrhain
Member
Posts: 6149
From: San Diego, CA, USA
Joined: 05-03-2003
Member Rating: 3.7


Message 52 of 85 (64105)
11-03-2003 7:09 AM
Reply to: Message 51 by DNAunion
11-02-2003 8:13 PM


Re: sadistics
DNAunion writes:

quote:
The calculation implicitly relies upon homochirality.

But achieving homochirality isn't a problem:

NAI News Article: One-Handed Life

------------------
Rrhain
WWJD? JWRTFM!


This message is a reply to:
 Message 51 by DNAunion, posted 11-02-2003 8:13 PM DNAunion has responded

Replies to this message:
 Message 53 by DNAunion, posted 11-03-2003 8:49 AM Rrhain has responded

    
DNAunion
Inactive Member


Message 53 of 85 (64118)
11-03-2003 8:49 AM
Reply to: Message 52 by Rrhain
11-03-2003 7:09 AM


Re: sadistics
quote:
/*DNAunion*/ The calculation implicitly relies upon homochirality.

quote:
Rrhain: But achieving homochirality isn't a problem:

/*DNAunion*/ Wrong. That article does not demonstrate how homochirality can originate...the "self-replicating" molecules themsevles start out chirally pure: they then select the correct enantiomeric forms. In other words, it uses preexisting homochirality to "create" homochirality.

Also, the calculation I was referencing dealt with polynucleotides, not peptides.

By the way, there are other problems with using that paper to support origin of life, as in, "See, this is how life arose". For example, despite the misleading term used by the authors and others, the peptides do not self-replicate.

[This message has been edited by DNAunion, 11-03-2003]


This message is a reply to:
 Message 52 by Rrhain, posted 11-03-2003 7:09 AM Rrhain has responded

Replies to this message:
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DNAunion
Inactive Member


Message 54 of 85 (64156)
11-03-2003 12:19 PM
Reply to: Message 53 by DNAunion
11-03-2003 8:49 AM


Re: sadistics
/*DNAunion*/ My internet playtime will be short for a few days, so I figured I'd go ahead and follow up what I said in my last post. The following is from my personal notes.

Ghadiri Ligase is not a True Self-Replicator

First, I will use an analogy that employs the letters of the English alphabet and a short sentence in order to demonstrate why the Ghadiri ligase is not a true self-replicator.

For this analogy, I will equate the 23-character “sentence” METHINKSITISLIKEAWEASEL with the 32-amino-acid Ghadiri ligase. Each of the letters represents an amino acid residue along the length of the GL (my abbreviation for the Ghadiri ligase) where each of the individual “letters” is covalently bonded to its nearest neighbor(s) on the same strand (analogous to the same physical sentence, when there are two). The covalent bonds between the units will be represented with dashes (-) between the “letters” (M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L).

A true self-replicator can extract its individual building blocks (monomers/letters) one at a time from its surroundings (a pool of monomers/letters) and construct a functional copy of itself using itself as a template for the sequencing of the units, followed by release of the copy. In order to allow them to separate from each other but to not decompose, the template and the copy should not be covalently bonded together but both the template and the copy should be covalently bonded internally. Note that the letters can’t simply line up according to the template’s sequence and be done with it; they also have to be covalently linked to their nearest neighbors in the growing copy after being non-covalently attached to the template. Forming this bond between units within the same strand requires either a catalyst or the pre-activation of each of the building blocks. And since we are looking for a true self-replicator, the sequence itself should be performing the function, whether it is catalyzing the bond directly or pre-activating incoming monomers. The process we will look at (the less involved of the two) involves two basic steps for each monomer added: first, the correct monomer is “chosen” from the stocked pool of monomers and lines up along the template, then the template sequence covalently bonds the new monomer to the elongating string.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M (correct monomer lines up non-covalently with template)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M E (correct monomer lines up non-covalently with template)
M-E (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E T (correct monomer lines up non-covalently with template)
M-E-T (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T H (correct monomer lines up non-covalently with template)
M-E-T-H (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H I (correct monomer lines up non-covalently with template)
M-E-T-H-I (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I N (correct monomer lines up non-covalently with template)
M-E-T-H-I-N (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N K (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K S (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S I (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S-I (template sequence covalently bonds new monomer to growing string)

[next 26 steps omitted to save space]

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E L (monomer lines up with template)
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L (final monomer covalently bonded to others)

So how does the actual Ghadiri ligase measure up (in a prebiotic context)? Not very well. Using the same analogy, here is how the GL functions.

The first PREEXISTING half of the sequence -- M-E-T-H-I-N-K-S-I-T, which for some unknown reason just happens to be floating around nearby, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T

The second PREEXISTING half of the sequence -- I-S-L-I-K-E-A-W-E-A-S-E-L, which is also just floating around nearby for some unknown reason, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T I-S-L-I-K-E-A-W-E-A-S-E-L

The two halves are covalently bonded together – BUT NOT BY ANY EXTRA ACTION PERFORMED BY THE TEMPLATE SEQUENCE ITSELF, BUT BY THE SEPARATE TWO HALVES THEMSELVES, BECAUSE ONE OF THEM WAS PRE-ACTIVATED BY SOME OTHER PROCESS.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L

How is it that the needed halves just happen to be floating around? Because the researchers intentionally synthesize those exact two sequences, preactivate the copies of one of the sequences, and then supply both for reaction.

This analogy points out some conceptual reasons why the Ghadiri ligase is not a true self-replicator: it absolutely requires (1) the correct 15- and 17-aa sequences already be available in the surroundings, (2) both halves to already be held together by covalent bonds, and (3) one of the two halves to already be activated. The Ghadiri ligages is powerless to recreate itself from the individual building blocks that make it up.

Let’s try looking at it with a second analogy.

What do we know that truly self-replicates? The most obvious answer is, life. To make sure that we are not throwing in excess complexity, what is the simplest form of life known? A bacterium (or to be a bit more precise, the bacterium Mycoplasma genitalium). Let’s double check…does a bacterium self-replicate? Yes. Okay, how?

In very simple terms, a bacterium takes in simple, raw materials from its surroundings and then the bacterium uses those simpler precursors to construct extra copies of its own constituents – such as DNA, proteins, mRNA, etc. – and then divides to form two bacteria, each like the original.

Now, is this similar to the way the GL “self-replicates”? No, not at all. If the GL were a bacterium, it would require two preexisting halves of another bacterium that would then simply line up with it and join together to form a whole bacterium. In the real world, a bacterium is given only simple raw materials such as inorganic substances and sugars, that it uses to build a complete copy of itself from scratch; whereas in the “GL world” the bacterium has to be handed EVERYTHING already setup, for free, and just joins the two preexisting halves together.

Okay, let’s try looking at this from an informational point of view.

A true self-replicating protein would not need any help by being supplied large amounts of very specific, external information; the needed information for self-replication would be contained in the self-replicator itself. But for the GL, it requires being handed approximately 130 bits of information*. How much is that? Suppose a random process were used to select a single number between 1 and 429,000,000,000,000,000,000,000,000,000,000,000,000,000, and that you know nothing other than the range and that the integer was chosen randomly, with each integer in that range being just as likely to have been selected as any other. Would you be willing to bet your life that you could guess the single number selected given just a single try? Of course not – that would be suicide. But, handed 130 bits of information, you’d be able to correctly pick that one integer in one try. And even if the rough calculation is too high by 10 orders of magnitude, or even 20 orders of magnitude, the fact still remains that the GL requires an enormous amount of preexisting information to be handed to it, for free, in order for it to “self-replicate”.

Where does that information come from? Some other process, which is doing “99.99…%” of the work. The GL absolutely relies upon some unknown, informationally rich, external process to build the parts of the GL. Just as a printed page cannot self-replicate – it requires a vastly more complex, external object (a photocopier) to do nearly all of the work – neither can the GL.

And here’s the kicker. The GL would need to be handed that much information for free to create just ONE copy of itself. In order to create a second copy, it would need to be handed, for free, ANOTHER 130* bits of information! Need a third copy? That requires yet ANOTHER 130* bits of information, and so on, and so on, and so on.

However you slice it, the GL is not a true self-replicator. And others have pointed this out.

quote:
”David Lee and his colleagues at the Scripps Research Institute in La Jolla, California, have now shown that autocatalytic capabilities are not confined to RNA or DNA or even PNA. They isolated a small peptide, part of a protein made by yeast, and showed that it could catalyze the joining together of two fragments of itself to make more copies of the complete peptide.

Here again, of course, the result is far from a completely self-replicating molecule. Such a molecule would have to start not with two pieces of itself but with a set of building blocks – in this
case amino acids – and make a copy of itself from scratch.” (Christopher Wills & Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p136)


So is the GL a catalyst? Yes – it accelerates the rate of the two halves joining without itself being altered in the process. It has been shown that even in the absence of the GL, the preexisting, pre-activated 15-aa and 17-aa fragments will bond together to form the full 32-aa GL. In the presence of the full GL, this rate of combination of the halves to form the full template is increased, and after doing so, the original template is ready to align another set of two halves so that they too will bond together. What the GL does is to orient two preexisting, pre-activated, specific sequences in the correct manner so that they can interact more readily (of course the probability of two halves finding each other and being properly oriented in order to link up is much greater when they are aligned linearly in tandem on a template than when colliding randomly in a solution). So yes, the GL is a true catalyst.

So does the term autocatalytic fit the GL? Yes – it is a catalyst whose product is itself.

Is the GL a true self-replicator? No.

*******************************************
* The information calculation was done very quickly in “back-of-the-napkin” fashion. The complete peptide is 32 amino acids long, and the rule is that living cells use 20 amino acids in the production of peptides. Since we are not looking at preexisting life or evolution in order to generate the correct sequence, and since intelligent direction is not involved either, the sequence of monomers would be generated by undirected, non-biological process alone. So, using the simplifying assumption that each amino acid is just as likely as any other to be incorporated at position X, we have 20 equally likely possibilities for each of 32 positions. That gives a total of 20^32, or about 4.29 x 10^41, possible unique sequences. On a piece of paper, in just four lines of “code”, I calculated 4.29 x 10^41 to be about 2^130 (the first number is actually almost 1,000 times greater than the second, but I was trying to avoid doing a complicated calculation and also didn’t want to overestimate). With 2^130 equally likely possibilities, you need, on average, 130 bits of information to find the one correct outcome in one shot. Also, note that I mention above in the actual discussion that the information calculation’s being too high by even 20 orders of magnitude would not alleviate the problem with the GL. That is, if a more detailed calculation came out to 10^21, it would still require about 70 bits of information be handed to it for free, which is still probably enough to win a state lottery, twice in a row. And the GL would need that huge amount of information for each copy of itself it was to make.

[This message has been edited by DNAunion, 11-03-2003]


This message is a reply to:
 Message 53 by DNAunion, posted 11-03-2003 8:49 AM DNAunion has not yet responded

Replies to this message:
 Message 55 by Rei, posted 11-03-2003 12:51 PM DNAunion has responded

  
Rei
Member (Idle past 4543 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 55 of 85 (64168)
11-03-2003 12:51 PM
Reply to: Message 54 by DNAunion
11-03-2003 12:19 PM


Re: sadistics
First off, the Ghadiri self-replicator is just a single example; there are countless possibilities (I could equally, say, go into the SunY self-replicator, the hexanucleotide self-replicator, Eckland's RNA polymerase self replicator, etc). In reality, there are going to be millions of possible simple self-replicators, and many times more self-catylizing cycles (i.e., where no single chemical is a self-replicator, but together they encourage the creation of more of their components). However, let's just use the Ghadiri self-replicator:

RMKQLEEKVYELLSKVACLEYEVARLKKVGE (sp? I think I'm missing one...)

Just assuming that the Ghadiri peptide is randomly pieced together (just coincidentally, it is of a form that is ideally suited to be formed by abiotic peptide synthesis, but we'll ignore that), you would have odds of 4.29e41 for producing it. However, its subunits 6.655e20 - 6.655e20 times as common as the original self-replicating peptide. If the Ghadiri ligase was formed in an environment that tends to form peptides like itself, then its subunits are quite likely to occur there as well.

Furthermore, I might ask: when given partial subunits, will the replicator assemble a partial copy of itself? If so, then its odds of survival just vastly increased, because the partial copy is well on its way to becoming a full copy, or even a deformed copy that itself makes partial copies. Anything that turns the pool of amino acids more toward a self-replicating form is a "good thing", and a positive step on the way to creating life. I'm unable to find an article on this subject either confirming or denying this possibility in respect to the Ghadiri replicator, but it seems realistic. Catalyzation to produce chemicals similar to but not exactly like the original, is likely the first step in abiogenesis, because it would be far more common than forming a complete self-replicator. This catalyzation progresses into a full hypercycle, which progresses into an ur-cell.

------------------
"Illuminant light,
illuminate me."


This message is a reply to:
 Message 54 by DNAunion, posted 11-03-2003 12:19 PM DNAunion has responded

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Rrhain
Member
Posts: 6149
From: San Diego, CA, USA
Joined: 05-03-2003
Member Rating: 3.7


Message 56 of 85 (64218)
11-03-2003 6:20 PM
Reply to: Message 53 by DNAunion
11-03-2003 8:49 AM


Re: sadistics
DNAunion responds to me:

quote:
quote:
But achieving homochirality isn't a problem:

/*DNAunion*/ Wrong. That article does not demonstrate how homochirality can originate...the "self-replicating" molecules themsevles start out chirally pure: they then select the correct enantiomeric forms.


First, it was a start to more research. Not the sole piece of information.

Second, you're ignoring an important point in the paper: Mutations get corrected:

They further discovered that if they added "mutant" peptide templates with a single incorrectly handed molecule, these would not make more mutant templates. They would instead correct the mistake and catalyze the formation of new molecules with the correct composition.

It seems you're simplifying.

Here's some more analysis of that paper:

Biochemistry: Single-handed cooperation

Synthetic polymers are simpler than biological systems and provide a model for understanding the origin of homochirality in biomolecules. One proposal stems from observations that polymers made from building blocks of random handedness will contain mixtures of right- and left-handed blocks so complex that no two polymers will have identical stereochemistry. All the polymers will be chiral, but if one exists, it is unlikely that its mirror image will too. For small polymers consisting of only a few building blocks, the number of possible combinations of right- and left-handed blocks is small, and the mirror images are easily formed. However, for a polymer comprising 20 building blocks there are almost a million possibilities, and an enormous number of blocks would be required to build all the possible mirror images. Biological molecules often have over 100 building blocks, pushing the limits of available materials and making it extremely unlikely that a molecule and its mirror image can be prepared in the same batch. If the sample of polymers contained some that were self-replicating, it is reasonable that the most efficient one will emerge, and only this homochiral polymer will exist.

quote:
Also, the calculation I was referencing dealt with polynucleotides, not peptides.

Is there some reason to assume that chirality in polynucleotides would not have similar methods of establishment compared to peptides?

quote:
By the way, there are other problems with using that paper to support origin of life, as in, "See, this is how life arose".

Nobody is saying that. Is there a particular reason why you are assuming that the work into how life could have arisen necessarily means that what is found is the precise method about how it actually did? As the second link I just provided states, "The origin of one-handedness in biological molecules is not yet clear."

The point is that there are ways to achieve homochirality. We should not simply claim that because something is difficult for us right now means that it will never be possible to figure out. Too many times we have claimed something to be impossible (like the synthesis of organic compounds from inorganic reagents) only to find out that it is quite possible.

quote:
For example, despite the misleading term used by the authors and others, the peptides do not self-replicate.

Incorrect. Did you read the article?

For the "template" peptides to replicate, the correctly-handed components in the mixture would have to stick to the correct location on the peptides and then link up, forming exact copies of the template molecules, and this is exactly what they observed.

What do you think "For the 'template' peptides to replicate" means?

Not only did the results show that the peptides favored the synthesis of correct duplicates, but the duplicates auto-catalyzed the reaction, speeding it up.

What do you think "the peptides favored the synthesis of correct duplicates" means?

------------------
Rrhain
WWJD? JWRTFM!


This message is a reply to:
 Message 53 by DNAunion, posted 11-03-2003 8:49 AM DNAunion has responded

Replies to this message:
 Message 59 by NosyNed, posted 11-04-2003 12:38 AM Rrhain has not yet responded
 Message 60 by DNAunion, posted 11-04-2003 12:46 AM Rrhain has responded
 Message 61 by DNAunion, posted 11-04-2003 12:57 AM Rrhain has not yet responded
 Message 62 by DNAunion, posted 11-04-2003 1:05 AM Rrhain has not yet responded
 Message 63 by DNAunion, posted 11-04-2003 1:32 AM Rrhain has not yet responded

    
DNAunion
Inactive Member


Message 57 of 85 (64294)
11-04-2003 12:22 AM
Reply to: Message 55 by Rei
11-03-2003 12:51 PM


Re: sadistics
quote:
Rei: First off, the Ghadiri self-replicator is just a single example;

/*DNAunion*/ It was THE ONE example that was offered, and I showed it didn't work. I did my job, now its your turn (see below).

quote:
Rei: there are countless possibilities (I could equally, say, go into the SunY self-replicator, the hexanucleotide self-replicator, Eckland's RNA polymerase self replicator, etc).

/*DNAunion*/ But since you have asserted as fact that the SunY ribozyme and Eckland's RNA polymerase are self-replicators, you have a position to back up. So you now need to post quotes from the papers for the experiments that show those molecules actually self-replicate.

quote:
Rei: In reality, there are going to be millions of possible simple self-replicators,

/*DNAunion*/ Gee, then why in the world are OOL researchers still looking, considering that they've conducted numerous experiments that start with pools consisting of trillions of random sequences? And why is the closest thing to a self-replicating RNA designed so far around 180 nucleotides long?

I guess all the OOL researchers just don't know what they're doing. Tell you what...why don't you become one and solve the riddles for them. You just might get a Nobel Prize.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 55 by Rei, posted 11-03-2003 12:51 PM Rei has not yet responded

Replies to this message:
 Message 78 by DNAunion, posted 11-29-2003 3:10 PM DNAunion has responded

  
DNAunion
Inactive Member


Message 58 of 85 (64296)
11-04-2003 12:32 AM
Reply to: Message 55 by Rei
11-03-2003 12:51 PM


Re: sadistics
quote:
Rei: Just assuming that the Ghadiri peptide is randomly pieced together (just coincidentally, it is of a form that is ideally suited to be formed by abiotic peptide synthesis, but we'll ignore that)

/*DNAunion*/ Uhm, no we won't. You've asserted that as fact...you have an obligation to support your claim or withdraw it.

quote:
Rei: ... you would have odds of 4.29e41 for producing it. However, its subunits 6.655e20 - 6.655e20 times as common as the original self-replicating peptide. If the Ghadiri ligase was formed in an environment that tends to form peptides like itself, then its subunits are quite likely to occur there as well.

/*DNAunion*/ So show that such is the case: show us an experiment where the Ghadiri ligase halves were formed under prebiotically plausible conditions. Of course, you can't. More of your unsupported speculation.

quote:
Rei: Furthermore, I might ask: when given partial subunits, will the replicator assemble a partial copy of itself? If so, then its odds of survival just vastly increased, because the partial copy is well on its way to becoming a full copy, or even a deformed copy that itself makes partial copies.

/*DNAunion*/ Actually, under the conditions used in the experiment, if some partial subunits were added and they ended up binding to the template or the "halves", they would hinder "self-replication".

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 55 by Rei, posted 11-03-2003 12:51 PM Rei has not yet responded

  
NosyNed
Member
Posts: 8799
From: Canada
Joined: 04-04-2003
Member Rating: 8.7


Message 59 of 85 (64298)
11-04-2003 12:38 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
Rrhain, I think that DNA has a more restricted definition of "self replicator" than you do.

I see some value in both sides.

Your's is saying that there are things which can catalyze their own production given the right initial environment. That is a resonable step in unraveling the complex questions at the origin of life.

However, I think DNA is going the whole way and saying that something isn't a useful sort of self replicator if it can't build itself out of rather simple building blocks that we can demonstrate are reasonably likely in a pre-biotic earth. The partial polymers of the GL don't count with that view.

I think he has a point.


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has not yet responded

  
DNAunion
Inactive Member


Message 60 of 85 (64299)
11-04-2003 12:46 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
Rrhain: First, it was a start to more research. Not the sole piece of information.

/*DNAunion*/ First, it was THE ONLY paper you gave as support.

quote:
Rrhain: Second, you're ignoring an important point in the paper: [“enantiomeric”] Mutations get corrected:

/*DNAunion*/ Ignoring something completely irrelevant to the discussion does not make one guilty of “ignoring” something, despite your insinuation.

That such “mutations” are corrected is completely irrelevant as to the ORIGIN of homochirality (which was your point, wasn’t it), and also completely irrelevant to whether or not the GL is a self-replicator (which was my point). So why should I need to address such an irrelevant point? Fact is, there is no reason.


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has responded

Replies to this message:
 Message 64 by Rrhain, posted 11-07-2003 5:59 AM DNAunion has responded

  
DNAunion
Inactive Member


Message 61 of 85 (64301)
11-04-2003 12:57 AM
Reply to: Message 56 by Rrhain
11-03-2003 6:20 PM


Re: sadistics
quote:
Rrhain: The point is that there are ways to achieve homochirality.

/*DNAunion*/ So show us the experiment that started with racemic mixtures of ribonucleotides and produced homochirality in polynucleotides under prebiotically plausible conditions. “In principle” is one thing, experimental support is another.

quote:
Rrhain: We should not simply claim that because something is difficult for us right now means that it will never be possible to figure out.

/*DNAunion*/ So who’s doing that?

quote:
Rrhain: Too many times we have claimed something to be impossible (like the synthesis of organic compounds from inorganic reagents) only to find out that it is quite possible.

/*DNAunion*/ Not the most parallel analogy. What you bring up was stated to be literally impossible and was based on a philosophical world view. What I am pointing out is very different.

[This message has been edited by DNAunion, 11-04-2003]


This message is a reply to:
 Message 56 by Rrhain, posted 11-03-2003 6:20 PM Rrhain has not yet responded

Replies to this message:
 Message 69 by MarkAustin, posted 11-14-2003 8:28 AM DNAunion has responded

  
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