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Author Topic:   Abiogenesis
Black
Member (Idle past 3527 days)
Posts: 77
Joined: 11-28-2008


Message 61 of 142 (95196)
03-27-2004 7:35 PM
Reply to: Message 45 by DNAunion
03-23-2004 11:33 PM


OK, DNAunion, you asked me to back up my statements, well here we go!

quote:
(2) Amino acids could link together (as peptides) and reproduce naturally

Amino acid chains have been observed that can reproduce naturally:

David H. Lee, Juan R. Granja, Jose A. Martinez, Kay Severin & M. Reza Ghadiri; "A self-replicating peptide" Nature 382, 525 - 528 (1996).

Natural selection also happens:

Yao, S.; Ghosh, I.; Chmielewski, J.; "Natural Selection in Self-Replicating Peptides", Peptides: Chemistry, Structure and Biology, 1998, 15, 0000.

More about this:

Yao, S.; Ghosh, I.; Zutshi, R.; Chmielewski, J.; "Self-replicating Peptide under Ionic Control", Angew. Chem. Int. Ed. Eng., 1998, 37, 478-481.

Yao, S.; Ghosh I.; Zutshi, R.; Chmielewski, J.; "A pH-Modulated Self-Replicating Peptide", J. Am. Chem. Soc., 1997, 119, 10559-10560.

quote:
(3) RNA could form from amino acid chains (peptides)

What I meant was RNA could come from peptide nucleic acids:

Böhler, C., P. E. Nielsen, and L. E. Orgel, 1995. Template switching between PNA and RNA oligonucleotides. Nature 376: 578-581. See also: Piccirilli, J. A., 1995. RNA seeks its maker. Nature 376: 548-549.

Also interesting, formamide has been found to catalyze the formation of nucleobases:

Saladino R., C. Crestini, G. Costanzo, R. Negri, and E. Di Mauro, 2001. A possible prebiotic synthesis of purine, adenine, cytosine, and 4(3H)-pyrimidinone from formamide: Implications for the origin of life. Bioorganic and Medicinal Chemistry 9(5): 1249-1253.

quote:
(4) RNA would need neither DNA nor protein to catalyze its own replication

Yes, this is true:

Jeffares, D. C., A. M. Poole and D. Penny, 1998. Relics from the RNA world. Journal of Molecular Evolution 46: 18-36.

Poole, A. M., D. C. Jeffares, and D. Penny, 1998. The path from the RNA world. Journal of Molecular Evolution 46: 1-17.

Leipe, D. D., L. Aravind, and E. V. Koonin, 1999. Did DNA replication evolve twice independently. Nucleic Acids Research 27: 3389-3401.

Also, a deoxyribozyme can both catalyze its own replication and function to cleave RNA -- all without any protein enzymes:

Levy, Matthew and Andrew D. Ellington, 2003. Exponential growth by cross-catalytic cleavage of deoxyribozymogens. Proceedings of the National Academy of Science USA 100(11): 6416-6421.

Thus, the conclusion I come to is that abiogenesis is possible.

BTW, I am sure I can find more references. If it interests you, let me know and I will...

[This message has been edited by Black, 03-27-2004]


This message is a reply to:
 Message 45 by DNAunion, posted 03-23-2004 11:33 PM DNAunion has responded

Replies to this message:
 Message 63 by DNAunion, posted 03-27-2004 7:55 PM Black has responded
 Message 64 by DNAunion, posted 03-27-2004 8:04 PM Black has not yet responded

RAZD
Member
Posts: 20332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.7


Message 62 of 142 (95199)
03-27-2004 7:52 PM
Reply to: Message 60 by DNAunion
03-27-2004 2:07 PM


Re: Viruses, prions and curious implications
Against my better judgement about getting into an one-upmanship contest, I will answer this one simply:

You still have not shown where I say that viruses or prions are living.

Until you do that your argument is all based on a false assumption of what I said. Your quotes do not show that. My posts do not show that.

You are in error. Again.

I have no need to converse with fools who repeat their mistakes. Especially after being corrected.

Enjoy yourself.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist


This message is a reply to:
 Message 60 by DNAunion, posted 03-27-2004 2:07 PM DNAunion has responded

Replies to this message:
 Message 66 by DNAunion, posted 03-27-2004 8:22 PM RAZD has responded
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DNAunion
Inactive Member


Message 63 of 142 (95201)
03-27-2004 7:55 PM
Reply to: Message 61 by Black
03-27-2004 7:35 PM


quote:
OK, DNAunion, you asked me to back up my statements, well here we go!

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.

quote:

-----------------------------------------------------------------
(2) Amino acids could link together (as peptides) and reproduce naturally
-----------------------------------------------------------------

Amino acid chains have been observed that can reproduce naturally:


I figured you were referring to the “GL” (Ghadiri ligase), and now I see that you were here.

quote:
David H. Lee, Juan R. Granja, Jose A. Martinez, Kay Severin & M. Reza Ghadiri; "A self-replicating peptide" Nature 382, 525 - 528 (1996).

That peptide was NOT formed naturally, nor can it replicate in any way relevant to abiogenesis (which was the context in which you made your assertions).

quote:

-----------------------------------------------------------------
(3) RNA could form from amino acid chains (peptides)
-----------------------------------------------------------------

What I meant was RNA could come from peptide nucleic acids:


If you have support, please provide it.

quote:

-----------------------------------------------------------------
(4) RNA would need neither DNA nor protein to catalyze its own replication
-----------------------------------------------------------------

Yes, this is true:


Then present the evidence that shows this.

There has been no experiment carried out under prebiotically plausible conditions that has produced RNA capable of replicating itself in an abiogenesis relevant manner.

quote:
Thus, the conclusion I come to is that abiogenesis is possible.

Now if you could just support that conclusion.

[This message has been edited by DNAunion, 03-27-2004]


This message is a reply to:
 Message 61 by Black, posted 03-27-2004 7:35 PM Black has responded

Replies to this message:
 Message 86 by Black, posted 04-01-2004 7:29 AM DNAunion has responded

DNAunion
Inactive Member


Message 64 of 142 (95203)
03-27-2004 8:04 PM
Reply to: Message 61 by Black
03-27-2004 7:35 PM


A note on why article titles are not sufficient to support one's position. Here is an article title from Origins of Life and Evolution of the Biosphere (vol 30, No 1, Feb 2000): Self-Programmable, Self-Assembling Two-Dimensional Genetic Matter.

What an impressive sounding paper! If the experiment accomplished what the title leads one to believe, then the origin of life would basically be solved. Genetic matter self-assembling and self-programming! Wow!

But when one reads the actual paper, one sees a completely different picture. Basically, they dumped some nucleotides on a surface and since their were some irregularities in the arragenment that resulted....bingo, self-programmable, self-assembling, two-dimensional genetic matter.

The actual science is not to be found in the title - it's in the details of the experiment. Maybe if some scientists were sued for false advertisement - which is about what their very misleading titles basically amount to - then we'd see more honesty.

[This message has been edited by DNAunion, 03-27-2004]


This message is a reply to:
 Message 61 by Black, posted 03-27-2004 7:35 PM Black has not yet responded

Replies to this message:
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crashfrog
Inactive Member


Message 65 of 142 (95205)
03-27-2004 8:12 PM
Reply to: Message 64 by DNAunion
03-27-2004 8:04 PM


A note on why article titles are not sufficient to support one's position.

I agree that titles or even abstracts alone aren't really sufficient to support an argument, but often times the problem is that copyright issues prevent the article from being posted. Most scientific papers of any relevance simply aren't avaliable publicly without an academic site license or a fee.

Sometimes we post abstracts because that's all the we can. In such situation I think a precis of the article in question is appropriate.


This message is a reply to:
 Message 64 by DNAunion, posted 03-27-2004 8:04 PM DNAunion has not yet responded

DNAunion
Inactive Member


Message 66 of 142 (95207)
03-27-2004 8:22 PM
Reply to: Message 62 by RAZD
03-27-2004 7:52 PM


Re: Viruses, prions and curious implications
quote:
AbbyLeever:
You still have not shown where I say that viruses or prions are living.

Wow, big letters! You MUST be right! LOL!

Here, let me use even bigger letters so I will be even more right.

I have shown BOTH of your offered supports to be flawed.

Yep, that’s my claim and that’s fact.

quote:
AbbyLeever: Until you do that your argument is all based on a false assumption of what I said.

Nope, I addressed what you said. I’ve shown BOTH of your supports to be flawed and now you’re attempting to distance yourself from your errors. We all understand.

quote:
Abbyleever: You are in error. Again.

Nope, you are.

quote:
AbbyLeever: I have no need to converse with fools who repeat their mistakes.

Tsk tsk...stooping to personal attacks...already!

quote:
AbbyLeever: Especially after being corrected.

You haven’t corrected me one iota. On the other hand, I have shown BOTH of your offered supports to be flawed.

Enjoy


This message is a reply to:
 Message 62 by RAZD, posted 03-27-2004 7:52 PM RAZD has responded

Replies to this message:
 Message 67 by RAZD, posted 03-27-2004 8:56 PM DNAunion has responded

RAZD
Member
Posts: 20332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.7


Message 67 of 142 (95222)
03-27-2004 8:56 PM
Reply to: Message 66 by DNAunion
03-27-2004 8:22 PM


Re: Viruses, prions and curious implications
Poor fool.

ALL you have shown is that viruses and prions are not living.

And I have not claimed they were living

The fact is that your whole argument, that your ample demonstration via books quotes that viruses and prions are not living shows my arguments to be flawed, is based on the mistaken belief that I said they were. The fact is that you continue to attack something that is not there. After being shown that fact several times. The only conclusion is that you are congenitally incapable of either (q) seeing the truth or (8) admitting you made a mistake even to yourself. As such I will take pity on you and no longer reply to your posts. This will allow you to declare victory and assuage your ego.

AND -- You still have not shown where I say that viruses or prions are living.

You made your bed and you lie in it.

Enjoy.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist


This message is a reply to:
 Message 66 by DNAunion, posted 03-27-2004 8:22 PM DNAunion has responded

Replies to this message:
 Message 68 by DNAunion, posted 03-27-2004 9:33 PM RAZD has not yet responded

DNAunion
Inactive Member


Message 68 of 142 (95232)
03-27-2004 9:33 PM
Reply to: Message 67 by RAZD
03-27-2004 8:56 PM


Re: Viruses, prions and curious implications
quote:
AbbyLeever: Poor fool.

Tsk tsk...another personal attack. That makes two from you...zero from me. Let's all keep that in mind, shall we.

quote:
AbbyLeever: ALL you have shown is that viruses and prions are not living.

Nope, what I've shown is that BOTH of your supports are flawed. That was my original point, and still is.

quote:
The fact is that you continue to attack something that is not there.

Nope, the fact is I trashed your flawed supports, and since then, you've tried to distract everyone by moving the goal posts.

quote:
The only conclusion is that you are congenitally incapable of either (q) seeing the truth or (8) admitting you made a mistake even to yourself.

The options are (q) and (8)??? LOL! You're so steamed you can't even type correctly!

quote:
AbbyLeever: As such I will take pity on you and no longer reply to your posts.

You won't reply anymore? You mean I don't get to be called names by you anymore? Darned!

And that you supposedly won't respond anymore doesn't matter anyway since I already won several posts ago.

quote:
You still have not shown where I say that viruses or prions are living.

I've shown exactly what I intended to...that BOTH of your offered supports are flawed. You haven't even attempted to show otherwise.

Enjoy.

[This message has been edited by DNAunion, 03-27-2004]


This message is a reply to:
 Message 67 by RAZD, posted 03-27-2004 8:56 PM RAZD has not yet responded

DNAunion
Inactive Member


Message 69 of 142 (95241)
03-27-2004 9:48 PM
Reply to: Message 62 by RAZD
03-27-2004 7:52 PM


Re: Viruses, prions and curious implications
quote:
AbbyLeever: I didn't claim that you made errors

quote:
AbbyLeever: You are in error. Again.

This message is a reply to:
 Message 62 by RAZD, posted 03-27-2004 7:52 PM RAZD has not yet responded

DNAunion
Inactive Member


Message 70 of 142 (95262)
03-27-2004 10:26 PM
Reply to: Message 14 by RAZD
03-16-2004 9:48 PM


Re: Building Blocks
AbbyLeever has linked to or posted his “famous” conclusion on building blocks several times. I thought I’d take a look at his support.

quote:
Abbyleever:

Conclusion
From these building blocks it should be clear to a rational mind that the building blocks needed for the creation of life were plentiful, not just on Earth but in space in general and from the earliest of times.


Nope. That conclusion does not necessarily follow from the support AbbyLeever presented (he/she seems to have a recurring problem with supporting his/her conclusions!).

I read through all of his/her “blocks” on the page linked to and the only biological building blocks mentioned were amino acids and unnamed sugars (acetic acid and pyruvic acid, also mentioned, are not typically considered biological building blocks – they’re not monomers that are linked together to form polymers). Conspicuously missing were nucleotides, the building blocks of nucleic acids, which are the (or at least one of the) primary molecules focused on in OOL research..

As far as polymers of the basic biological building blocks, conspicuously missing were both proteins and RNA (and DNA).

No nucleotides, no proteins, and no RNA!

Seems AbbyLeever draws his own conclusions and mistakenly believes he/she has supported them to an extent that anyone who doesn’t agree with him/her is irrational (“… it should be clear to the rational mind…”). He/she seems blinded to reality.

quote:
AbbyLeever: It also should be clear to a rational mind that the natural processes for forming more complex structures from those basic building blocks were prevalent on the earth at least 3.5 billion years ago in a variety of forms and locations. We are left with a scenario that has a random combination of plentiful and multitudinous organic molecules forming amino acids all over the earth, with a second scenario that has random combination of plentiful and multitudinous amino acids into peptides and proteins, and a third scenario that has random combinations of plentiful and multitudinous peptides and proteins into the first "replicators" (the predecessors to RNA and DNA), a simple 3 step process where the probability of a successful combination is almost inevitable: it is no longer a matter of "if" but of "when" it will occur under these conditions ...

Another conclusion AbbyLeever “forgot” to support. What evidence did AbbyLeever give for self-replicating proteins forming prebiotically? The rational mind knows the answer...0!

Shoot, he didn’t even support the idea that proteins could form prebiotically, let alone self-replicating ones.

quote:
AbbyLeever: ...and once self replication occurs the frequency of replication will necessarily outpace the random action…

Will it? Necessarily? Has AbbyLeever never heard of the error catastrophe?


This message is a reply to:
 Message 14 by RAZD, posted 03-16-2004 9:48 PM RAZD has not yet responded

RAZD
Member
Posts: 20332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.7


Message 71 of 142 (95454)
03-28-2004 6:20 PM
Reply to: Message 15 by One_Charred_Wing
03-17-2004 12:35 AM


Re: Building Blocks and Bridges
For me the search for the elusive transition from non-life to life has to be two pronged:

(1) from the bottom up -- looking for what happens naturally in a variety of environments to build more and more complex molecules from the materials available. This search also includes simulating a variety of early earth environments and possible environments on other planets (mars) or moons (europa). These molecules are the building blocks, making towers from them is the quest.

(2) from the top down -- reducing life to a bare minimum, also in a variety of environments to find what can be done away with from the evolved systems and still have a (possibly crude and likely inefficient) form of life. The variables will likely change with different environments and sources of energy that go with them. This is where LUCA comes into the picture. Taking the skyscraping towers of today and going back through time to the original huts.

As such research is done from both sides an awareness will build about how near one is to the other and bridges can begin to be built ... studies on how to get from tower foundation (D) to small tower structure (42) , very much like the Golden Gate bridge was built from each side of the bay in closing increments even though most engineers of the day said it could not be done.


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist


This message is a reply to:
 Message 15 by One_Charred_Wing, posted 03-17-2004 12:35 AM One_Charred_Wing has not yet responded

secondlaw
Inactive Member


Message 72 of 142 (95970)
03-30-2004 12:42 PM
Reply to: Message 1 by a servant of Christ
03-07-2004 12:38 AM


jump in the mix
I have not seen anything stated about this in the current thread so I thought I would make mention of it.

In short, mathematically speaking, it is impossible for life to come from non-life.

Given the enormity of the 'age' of the universe, still one does not have enough time or probability for proteins to be developed on their own by chance, let alone DNA.

It's one thing to look at the present circumstances and say, "Because we are, it must have happened." But it is a completely different ball of wax to say that it really did all by chance.

I am sure that DNAunion can attest to the intricacies of DNA, and the difficulties that arise when trying to consider this all just coming together at the right time and making life.

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).


This message is a reply to:
 Message 1 by a servant of Christ, posted 03-07-2004 12:38 AM a servant of Christ has not yet responded

Replies to this message:
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MisterOpus1
Inactive Member


Message 73 of 142 (95984)
03-30-2004 1:17 PM
Reply to: Message 72 by secondlaw
03-30-2004 12:42 PM


Re: jump in the mix
quote:
I have not seen anything stated about this in the current thread so I thought I would make mention of it.
In short, mathematically speaking, it is impossible for life to come from non-life.

In short, mathmatically speaking, it is impossible for you to even exist. So how come you are?

quote:
Given the enormity of the 'age' of the universe, still one does not have enough time or probability for proteins to be developed on their own by chance, let alone DNA.

So fill it in with "Godidit" without any verifiable, tested or observed evidence?

quote:
It's one thing to look at the present circumstances and say, "Because we are, it must have happened." But it is a completely different ball of wax to say that it really did all by chance.

Who said it had to happen by chance alone? Why couldn't some events be selectively favored over others?

quote:
I am sure that DNAunion can attest to the intricacies of DNA, and the difficulties that arise when trying to consider this all just coming together at the right time and making life.

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).


I wish I could give credit to myself over the following analogy, but someone else posted it and I simply pasted it. So here's a counter analogy with a little modification of my own:

"Consider the probability of your own existence. Suppose the Earth is as young as many creationists say it is,
about 5000 years old. What then is the probability that you would have been born? Let's generously assume that
the average length of a generation over the last 5000 years has been 30 years. Let's also assume, very generously,
that the average probability of an individual living long enough to have children and then to actually have them
is 95%. The probability that all of your great-great-grandfathers and great-great-grandmothers survived and had
children leading to you (or to anyone) would then be about 1 in 25 million! Somehow we all won the lottery.

This example, is a good example of the posterior probability
fallacy. The probability of an event occurring, after it has already occurred, is exactly 100%. Just because
a given protein is configured in a certain way doesn't mean it couldn't have been just as successfully configured
in a bazillion other possible ways. Abiogenesis, by accumulating positive changes and eliminating
the negative ones, may have ensured life."

And this analogy is being very generous. If you accept an old earth (older than 5000 years or so), the stat. of 1 in 25 million goes through the roof. However, it is a logical fallacy to begin with.


This message is a reply to:
 Message 72 by secondlaw, posted 03-30-2004 12:42 PM secondlaw has not yet responded

Replies to this message:
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RAZD
Member
Posts: 20332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.7


Message 74 of 142 (95988)
03-30-2004 1:42 PM
Reply to: Message 72 by secondlaw
03-30-2004 12:42 PM


Re: jump in the mix and fall on you rface
Ah, the old improbable probability problem ...

The errors in this are multifold and pervasive


  • The calculation is a mathematical model of reality and not the reality itself. When a model fails to replicate reality it is not reality that is at fault but the mathematical model. When a hurricane prediction program crashes because it can't model the first hurricane on record in the South Atlantic, the meteorologists don't go out to the hurricane and say "you can't be here, our model does not allow you to be here" ... they fix the model by looking for and taking out the failed assumptions (ie - that all hurricanes are north of the equator).
  • The probability of winning a lottery by any one ticket is extremely low, but the probability that the lottery will be won is extremely high. How do you reconcile these two very disparate probabilities? By knowing that any one of the millions of tickets is a valid winner if picked. To show that this is not the case for the calculations mentioned (ie -- in order to say "1 out of") you have to show that no other combination works of all the other probabilities. This has not been done.
  • The calculation fails to account for the known pre-existing molecules used in the formation of life that are found throughout the universe, and this failure means the calculation with creation-all-at-once including these molecules is unnecessarily extended downward.
  • The calculation fails to account for combinations of groups of such molecules in smorgas board fashion instead of in assembly line fashion all at once all from nothing. And, all the "failed" experiments are still available to be cut and reassembled into new experiments without having to go through the preliminaries. It fails to account for actual combination process as used in natural assembly of large organic compounds. This failure means that all the ways to reach the final necessary combination are not included and thus it unnecessarily excludes possible combination methods.
  • The calculation fails to account for the fact that the first life need not be as complicated as a modern cell, that the minimum configuration is much simpler as shown by the LUCA studies. This failure means that the calculation is unnecessarily extended upward.
  • The improbability of a thing occurring is not proof of impossibility of it occurring. It could well be that this is the only planet in all the universe that has life on it because it is a very improbably event. And if you divide the surface of the planet into all the different types of environments and do the same for all the other planets and moons and asteroids in the solar system alone you will have billionsXbillions of little experimental crucibles for carrying out experiments and if that is carried out over several billion year periods (4.55 billion year old earth, in a 13.7+ billion year old universe) with multiple "experiments" in a {day?week?month?} time period, and do the same for all the billions of stellar systems throughout the universe it does not take long to create an equally mind boggling number that reduces 1e14billion to a definite probability. I'm at 1e36 already ...

Care to play another game?
{{text in pink has been added by edit}}

[This message has been edited by AbbyLeever, 03-31-2004]


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 72 by secondlaw, posted 03-30-2004 12:42 PM secondlaw has not yet responded

RAZD
Member
Posts: 20332
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.7


Message 75 of 142 (95991)
03-30-2004 1:53 PM
Reply to: Message 73 by MisterOpus1
03-30-2004 1:17 PM


Re: jump in the mix
ahahahahaa I love it.

I used a similar argument to "The probability of an event occurring, after it has already occurred, is exactly 100%" on another board (I said the probability defaults to 1 after it has occurred) and the other person didn't understand it ... that there is no probability that it could not have occurred anymore, for we are here.


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:
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Replies to this message:
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