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Author Topic:   Excellent paper-peptide self assembly
crashfrog
Inactive Member


Message 46 of 50 (67304)
11-18-2003 8:46 AM
Reply to: Message 36 by Rei
11-17-2003 1:28 PM


quote:
Replies to this message:
Message 37 by DNAunion, posted 11-17-2003 10:32 PM
Message 38 by DNAunion, posted 11-17-2003 10:44 PM
Message 39 by DNAunion, posted 11-17-2003 10:57 PM
Message 40 by DNAunion, posted 11-17-2003 11:22 PM
Message 41 by DNAunion, posted 11-17-2003 11:37 PM
Message 42 by DNAunion, posted 11-17-2003 11:44 PM
Message 43 by DNAunion, posted 11-17-2003 11:55 PM
Message 44 by DNAunion, posted 11-18-2003 12:00 AM
Message 45 by DNAunion, posted 11-18-2003 01:09 AM

This is a little out of control, don't you think, DNA? I know you like to reply like you're programming, but why don't you suspend the fork function, ok?


This message is a reply to:
 Message 36 by Rei, posted 11-17-2003 1:28 PM Rei has responded

Replies to this message:
 Message 47 by Rei, posted 11-18-2003 1:16 PM crashfrog has not yet responded

  
Rei
Member (Idle past 5086 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 47 of 50 (67384)
11-18-2003 1:16 PM
Reply to: Message 46 by crashfrog
11-18-2003 8:46 AM


I've warned him about this - and now I'm going to live up to my word and not respond. I've never found a person with a more annoying "debate" style here - and that says a lot, seing as how we have teenage YECs at this site.

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


This message is a reply to:
 Message 46 by crashfrog, posted 11-18-2003 8:46 AM crashfrog has not yet responded

    
DNAunion
Inactive Member


Message 48 of 50 (67392)
11-18-2003 1:30 PM
Reply to: Message 33 by Rei
11-16-2003 1:57 AM


Re: Peptide self-assembly is one thing...
quote:
Look, do you see me making fun of you?

Uhm, yeah, I do. In fact, in addition to your doing that, I also see you repeatedly taking jabs at me personally, and being condescending - instead of sticking to the discussion - and I also see you stuffing words about religion into my mouth.

All of these come from page 3 of this thread.

quote:
DNAunion, prophet of the God of the Gaps.

quote:
Play "God of the Gaps" all you want, but don't fail to address the meat of the issue.

quote:
I could likewise start sentences with, "Does your invisible friend in the sky ... ".

quote:
DNA, don't be a pain: you know very well that if we knew the exact route that abiogenesis took (even if it were your "poof, here's life!" method), there would be nothing to discuss.

quote:
We're here to discuss theories as to what could lead to enantioselective properties, not trade insults over the gaps in our knowledge.

quote:
Once again, introducing the "God of the Gaps!"

I can just picture creationists in the 1800s now... "You say that the earth is billions of years old... and yet, we know of no way that the sun could be more than a few millions of years old - the best that you can come up with for its energy is "gravitational collapse". What, is there some "mystery, magical energy source" powering it that we don't know of? That has not been demonstrated experimentally.".

The God of the Gaps is continually being forced to move into a new gap. Are you sure you want him in this one?

That is why we discuss possibilities, not absolutes, when we're discussing gaps in scientific knowledge. Shoving a God wherever you see a gap is not a good plan for advancing human knowlege.


quote:
Take a class on chaos theory some time, then get back to me.

quote:
Next week I'll look to see if I can find any studies on the subject; you do your research as well.

quote:
You're back to your old habits of A) splitting up individual posts into multiple, making it very hard to reply to, and B) focusing on personal attacks. If you keep this up, I will cease to respond in this thread. You have been warned; don't expect another warning

quote:
Now we're back to the GL? Nice try at a dodge there

quote:
…since you seem to have this huge problem with the concept of how much of a sample size has been observed:

quote:
You have a very serious problem with the concept of the percentage of total sample size observed that you have displayed again and again, and it gets very frustrating. Please quit pretending that we have observed even a tiny, remotely statistically significant percentage of total possibilities.

quote:
Of course, knowing your love of quotes, you'd probably just ignore the article and extract an out of context quote,

quote:
Thank you for being so mature Do most people you debate with end up getting sick of you in the process and leaving? If so, you shouldn't be surprised.

quote:
Do you realize how bullheaded you look when you deliberately ignore what a person is saying?

quote:
2) Exactly what method are you proposing for your deity generating an enantiomeric excess of left-handed amino acids and/or right-handed ribose? Or is this going to remain some unnamed mystery god-magic?

3) How did your as-of-yet unidentified god-magic come to create preferentially one chiral form?

4) How did your as-of-yet unidentified god-magic maintain the chiral preference over an extended period of time? Was there some other chiral catalyst making it?


quote:
Yes, I know, you have far more time for this than I do. Is that something to really be proud of?

quote:
Take a class on chaos theory some time, then get back to me.

--------------------------------------------------------------------------------
Take a class on biochemistry some time, then get back to me.
--------------------------------------------------------------------------------

So typical. You respond to a point with offhand dismissal


So don't try to pretend that only I am to blame. If you start sticking to the discussion, I'll mirror that.

[This message has been edited by DNAunion, 11-18-2003]


This message is a reply to:
 Message 33 by Rei, posted 11-16-2003 1:57 AM Rei has not yet responded

  
DNAunion
Inactive Member


Message 49 of 50 (67840)
11-19-2003 9:26 PM
Reply to: Message 36 by Rei
11-17-2003 1:28 PM


quote:
After all, racemization (of amino acids and ribose) is a thermodynamically spontaneous process, whereas resolution is not.

quote:
Explain?

quote:
The driving force behind racemization - towards equilibrium/racemic mixtures - is entropic (enthalpy remains constant). Going in the opposite direction – towards homochirality – has a positive delta G associated with it (because of the decrease in entropy) and thus is not spontaneous.

quote:
How is there a decrease in entropy?

Okay, for any other people who were interested in the answer.

quote:
“A racemic modification has already been defined as an assembly of equal numbers of enantiomeric molecules, i.e., dextrorotary (+) and levorotary (-) molecules of the same substance. … It might be noted that a racemic modification (or “racemic form”) with equal numbers of two types of molecules corresponds to a more random or disorderly state of affairs than a pure enantiomer (one single type of molecule), therefore there is an increase of randomness and therefore an increase in entropy as one passes from one enantiomer or other to a racemic modification. This process called “racemization” is thus thermodynamically favorable and may be brought about in a number of ways (e.g., by heat, or by treatment with acid, base, metal catalysts).” (Elements of Stereochemistry, Ernest L. Eliel, John Wily & Sons, 1969, p16)

quote:
“Racemization is an energetically favored process since the concentration of the starting enantiomer is reduced by one-half during its operation. … Since [delta]Ho = 0 for the enantiomers undergoing racemization (assuming no intermolecular interactions), it follows that the driving force for racemization is entirely entropic.” (Stereochemistry of Organic Compounds, Ernest L. Eliel & Samual H. Wilen, John Wiley & Sons, 1994, p 425)

quote:
“Racemization is the process of producing a racemic modification [i.e., a “racemic mixture”] stating with one of the pure enantiomers. Since the two enatiomers have the same free energy, the equilibrium mixture will correspond to a 50-50 composition, i.e., it will be a racemic modification. Since the concentration of the pure enantiomer is reduced to one-half of its original value when racemization occurs, the free energy change associated with racemization is [delta]F = RT ln ½ = -RT ln 2.” (Stereochemistry of Carbon Compounds, Ernest L. Eliel, McGraw-Hill, 1962, p33)

[This message has been edited by DNAunion, 11-19-2003]


This message is a reply to:
 Message 36 by Rei, posted 11-17-2003 1:28 PM Rei has not yet responded

  
DNAunion
Inactive Member


Message 50 of 50 (67867)
11-19-2003 10:58 PM
Reply to: Message 36 by Rei
11-17-2003 1:28 PM


Some things I forgot to point out earlier.

quote:
Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule
--------------------------------------------------------------------------------
THE homochirality of natural amino acids and sugars remains a puzzle for theories of the chemical origin of life1-18. In 1953 Frank7 proposed a reaction scheme by which a combination of autocatalysis and inhibition in a system of replicating chiral molecules can allow small random fluctuations in an initially racemic mixture to tip the balance to yield almost exclusively one enantiomer. Here we show experimentally that autocatalysis in a chemical reaction can indeed enhance a small initial enantiomeric excess of a chiral molecule. When a 5-pyrimidyl alkanol with a small (2%) enantiomeric excess is treated with diisopropylzinc and pyrimidine-5-car-boxaldehyde, it undergoes an autocatalytic reaction to generate more of the alkanol. Because the reaction involves a chiral catalyst generated from the initial alkanol, and because the catalytic step is enantioselective, the enantiomeric excess of the product is enhanced. This process provides a mechanism by which a small initial imbalance in chirality can become overwhelming.
--------------------------------------------------------------------------------

quote:
First of all, this experiment involved neither amino acids nor nucleotides (nor ribose).

Second, no mention is made of whether or not all of the compounds involved are prebiotically plausible. If they aren’t, this paper has no direct bearing on the origin of life.

Third, as always, we have to remember that this occurred in a lab. That is, what steps were taken to prevent unwanted side reactions? Were any other goal-oriented steps used? If so, how prebiotically plausible were those steps? If they rise to the level of illegitimate investigator interference then this paper has no direct bearing on the origin of life.

However, I must admit, I am quite intrigued. I would like to see the experiment performed on amino acids and nucleotides, using prebiotically plausible molecules and conditions.


First, another of Rei’s claims is false/dishonest. Here’s the context.

quote:

--------------------------------------------------------------------------------
Can you see how, since racemization is a spontaneous process which leads away from enantiomerically pure mixtures and towards racemic ones a slight excess of one enantiomer could be lost?
--------------------------------------------------------------------------------

To lend some support to my last statement there, I’ll quote from an OOL book.

--------------------------------------------------------------------------------
”It has been argued (Bada and Miller 1987) that racemization of amino acids is too rapid to permit amplification (by as yet unspecified reactions) to give rise to homochirality. Carbohydrates are more resistant to racemization than are amino acids. However, they are also chemically less stable, a factor that could equally defeat an amplification cycle.” (Alan W. Schwartz, Origins of the RNA World, chapter 11 of The Molecular Origins of Life: Assembling Pieces of the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p247)
--------------------------------------------------------------------------------

Looks like Rei is facing a bigger problem than she thinks.


quote:
Ah, finally an applicable quote. And my response? It's already been shown to occur. Sorry, there!

And as I’ve shown, Rei’s offered support falls flat on its face. Rei’s doesn’t address amino acids, unlike the quote I presented. Rei’s doesn’t address nucleotides, unlike the quote I presented. In other words, Rei is again pretending to counter me and hoping no one notices. But he failed. Sorry, there!

The second point is, where are the follow up publications that worked with amino acids and/or nucleotides? Since the researchers state that their method could be involved in the origin of homochirality associated with the OOL, then why didn’t they use one of the two main molecules believed to be associated with OOL: amino acids and nucleotides? Okay, well, maybe they got it work with something easier first, something not directly related to the origin of life. But the letter Rei posted is from 1995: that’s 8 years ago. The researchers – and the scientific community at large - have had 8 years to get this to work with amino acids and nucleotides...so where are the publications? I didn't find any and Rei apparently doesn't have one or he would have posted it, instead of the one he did. Evidence of those papers is absent...evidence of absence!? :-)

[This message has been edited by DNAunion, 11-19-2003]


This message is a reply to:
 Message 36 by Rei, posted 11-17-2003 1:28 PM Rei has not yet responded

  
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