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  Topic: Abiogenesis discussion thread, No trolls please, we're adults< Next Oldest | Next Newest >  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Oct. 10 2008,11:13   

OK, here's a silly question.

How expensive is it to do a Miller-Urey experiment? Is it now in the range of high school science fair project? (Not Bronx High School of Science or Intel/Westinghouse Science Talent Search variety)

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 10 2008,11:37   

Quote (dvunkannon @ Oct. 10 2008,17:13)
OK, here's a silly question.

How expensive is it to do a Miller-Urey experiment? Is it now in the range of high school science fair project? (Not Bronx High School of Science or Intel/Westinghouse Science Talent Search variety)

That's a really good question, not a silly one!

If you wanted to run "the original" from scratch, that would take a few thousand dollars (arc generators, vacuum pumps, specialist glassware, autoclaves, chemicals etc). If your school has a few items like vacuum pumps, some basic chemical glassware, basic chemicals etc, then you'd save a lot of cash.

The really troublesome part for the "home lab" is getting clean kit to run the experiment in. You have to determine that your equipment is completely free of biological contaminants and that your chemicals are sourced from biological contaminant free sources. Depending on what kit you have available to you this will be either relatively trivial or spectacularly hard.

Smaller scale, science project type experiments might be accomplished with pretty standard glassware. Wikipedia has a pretty bog standard overview of the basics, it'll give you and idea of what you'd need.

The trick will be "deconvoluting" the resulting mixture to get a clear analysis. Since I'm not sure either a) how profound/accurate the data out of the end has to be, or b) what kit/training you'd have available I can't really answer properly.

Louis

--------------
Bye.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Oct. 12 2008,07:47   

ok, I thought the analysis would be the expensive part!

As you say, this is for the original experiment. Are there versions of the experiment that would be cheaper to do, yet be as interesting in the results?

I was very interested in the synthesis of organics in a frozen ice, referenced in an article a few posts upthread. Can the same concentration effects be obtained through the crystallization of (for instance) salt instead of ice?

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 12 2008,12:35   

Quote (dvunkannon @ Oct. 12 2008,13:47)
ok, I thought the analysis would be the expensive part!

As you say, this is for the original experiment. Are there versions of the experiment that would be cheaper to do, yet be as interesting in the results?

I was very interested in the synthesis of organics in a frozen ice, referenced in an article a few posts upthread. Can the same concentration effects be obtained through the crystallization of (for instance) salt instead of ice?

The Miller-Urey type experiments (synthesis of biologically useful molecules/monomers from gases + electricity) are all going to suffer from the problems I mention above. It's really dependant on what the school has. For example, I'd imagine basic glassware, basic chemicals, ovens and reasonable vacuum pumps are all there already. These will certainly get you 90% of the way. Like I said, evacuating the reaction glassware and making sure it's clean might well be the tricky part. Hospital autoclaves/UV irradiation/high temp ovens etc all will help and these are things that a school lab might legitimately have.

The expensive/hard part is the making sure stuff is clean and sealed, once that's done running the experiment is cheap and easy. All the reagents are super cheap and easy to get hold of, and it doesn't take an enormous amount of electricity to run.

Analysis could be troublesome for two reasons: a) it'll be messy and b) if working on a small scale it'll be tricky to get enough material for easy analysis (getting enough material for analysis is simple, getting enough material for an easy life is harder!). If I were you I'd look up the original references from the Miller Urey expt and see how they analysed their products. Purifying and NMRing (for example) all your goo is going to be laborious but ultimately very accurate. Getting IR spectra of the resulting gooey mixture and identifying the stuff in it is in principle simpler (i.e. it takes less practical effort) but is more of an intellectual challenge (i.e. knowing something about spectroscopy is necessary). It's all cheap to do in terms of finance, it's not cheap in terms of time.

As for ice/salt/clay crystals and concentration effects, sure these are more than possible, but they make the experiment more complex rather than simpler. Just from an experimental design point of view you've increased the number of variables you have to manage, and that's before you get into the practicalities. I'd suggest the original approach is much simpler.

Don't be disheartened by my apparent negativity, I like the idea very much and think it's very possible (obviously) but I really do need an idea of what kit you have available to you because without that knowledge I can't really get down to specifics. All these type of abiogenesis experiments have the same basic issues: contamination, deconvolution, analysis. Whatever you do you'll need to deal with those.

Louis

--------------
Bye.

  
Albatrossity2



Posts: 2778
Joined: Mar. 2007

(Permalink) Posted: Oct. 17 2008,07:01   

New data from old vials - NY Times story about analysis of some of the original materials produced in the Miller-Urey experiment.

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
- Pattiann Rogers

   
fusilier



Posts: 208
Joined: Feb. 2003

(Permalink) Posted: Oct. 17 2008,07:16   

Quote (Albatrossity2 @ Oct. 17 2008,08:01)
New data from old vials - NY Times story about analysis of some of the original materials produced in the Miller-Urey experiment.

There's a Panda's Thumb post on the topic, including a chart showing proportions of the various aa's and amines.

--------------
fusilier
James 2:24

  
J-Dog



Posts: 4361
Joined: Dec. 2006

(Permalink) Posted: Oct. 17 2008,07:46   

I wonder if anybody is working with a "new" soup mixture?  Perhaps composed of the same chemicals found around the "hot holes" found on the ocean floor?

http://query.nytimes.com/gst....ted=all

--------------
Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Dr.GH



Posts: 1954
Joined: May 2002

(Permalink) Posted: Oct. 17 2008,10:34   

Quote (J-Dog @ Oct. 17 2008,05:46)
I wonder if anybody is working with a "new" soup mixture? Perhaps composed of the same chemicals found around the "hot holes" found on the ocean floor?

Yeah

Amend, J. P. , E. L. Shock
1998 摘nergetics of Amino Acid Synthesis in Hydrothermal Ecosystems Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blochl, Elisabeth, Martin Keller, Gunter W臘htersh舫ser , Karl Otto Stetter
1992 迭eactions depending on iron sulfide and linking geochemistry with biochemistry PNAS-USA v.89: 8117-8120

Foustoukos, Dionysis I., William E. Seyfried
2004  "Hydrocarbons in Hydrothermal Vent Fluids: The Role of Chromium-bearing Catalysts" Science Vol 304 1002-1005

Horita, Juske,  Michael E. Berndt
1999 Abiogenic Methane Formation and Isotropic Fractionization Under Hydrothermal Conditions. Science 285 (5430): 1055

Huber, Claudia, Gunter W臘htersh舫ser
1997 鄭ctivated Acetic Acid by Carbon Fixation on (Fe,Ni)S Under Primordial Conditions  Science v. 276: 245-247

Huber, Claudia, Gunter W臘htersh舫ser
1998 撤eptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life  Science v.281: 670-672

Claudia Huber and Gnter W臘htersh舫ser
2006 殿-Hydroxy and a-Amino Acids Under Possible Hadean, Volcanic Origin-of-Life Conditions

Claudia Huber and Gnter W臘htersh舫ser
2006 迭eply to Bada et al 2006 Science 16 February 2007:
Vol. 315. no. 5814, pp. 937 - 939

Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K.
1999 摘longation of oligopeptides in a simulated submarine hydrothermal system Science 283(5403):831833.

{My refutation of creationist J. Sarfati regarding Imai, et al}

Shock, Everett L.
1990 敵eochemical Constraints on the Origin of Organic Compounds in Hydrothernal Systems Origins of Life and Evolution of the Biosphere v.20: 331-367

W臘htersh舫ser, Gunter
2000 撤erspective Science v.289 : 1308

There are papers that are critical of the idea as well.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Leftfield



Posts: 98
Joined: Nov. 2006

(Permalink) Posted: May 13 2009,15:06   

Is this new news to those following this thread?

Chemist Shows How RNA Can Be the Starting Point for Life



If that's old news, let me recommend this headline instead:

Ancient Figurine of Voluptuous Woman Is Found

--------------
Speaking for myself, I have long been confused . . .-Denyse O'Leary

  
k.e..



Posts: 2873
Joined: May 2007

(Permalink) Posted: May 13 2009,15:20   

Quote (Louis @ Oct. 12 2008,20:35)
Quote (dvunkannon @ Oct. 12 2008,13:47)
ok, I thought the analysis would be the expensive part!

As you say, this is for the original experiment. Are there versions of the experiment that would be cheaper to do, yet be as interesting in the results?

I was very interested in the synthesis of organics in a frozen ice, referenced in an article a few posts upthread. Can the same concentration effects be obtained through the crystallization of (for instance) salt instead of ice?

The Miller-Urey type experiments (synthesis of biologically useful molecules/monomers from gases + electricity) are all going to suffer from the problems I mention above. It's really dependant on what the school has. For example, I'd imagine basic glassware, basic chemicals, ovens and reasonable vacuum pumps are all there already. These will certainly get you 90% of the way. Like I said, evacuating the reaction glassware and making sure it's clean might well be the tricky part. Hospital autoclaves/UV irradiation/high temp ovens etc all will help and these are things that a school lab might legitimately have.

The expensive/hard part is the making sure stuff is clean and sealed, once that's done running the experiment is cheap and easy. All the reagents are super cheap and easy to get hold of, and it doesn't take an enormous amount of electricity to run.

Analysis could be troublesome for two reasons: a) it'll be messy and b) if working on a small scale it'll be tricky to get enough material for easy analysis (getting enough material for analysis is simple, getting enough material for an easy life is harder!). If I were you I'd look up the original references from the Miller Urey expt and see how they analysed their products. Purifying and NMRing (for example) all your goo is going to be laborious but ultimately very accurate. Getting IR spectra of the resulting gooey mixture and identifying the stuff in it is in principle simpler (i.e. it takes less practical effort) but is more of an intellectual challenge (i.e. knowing something about spectroscopy is necessary). It's all cheap to do in terms of finance, it's not cheap in terms of time.

As for ice/salt/clay crystals and concentration effects, sure these are more than possible, but they make the experiment more complex rather than simpler. Just from an experimental design point of view you've increased the number of variables you have to manage, and that's before you get into the practicalities. I'd suggest the original approach is much simpler.

Don't be disheartened by my apparent negativity, I like the idea very much and think it's very possible (obviously) but I really do need an idea of what kit you have available to you because without that knowledge I can't really get down to specifics. All these type of abiogenesis experiments have the same basic issues: contamination, deconvolution, analysis. Whatever you do you'll need to deal with those.

Louis

Oh come on it wasn't that hard 6000 years ago, it cost nothing and only took 6 days.

And that recipe sounds more like a meth lab than ....I've got a customer at the door I'll be back.

--------------
"I get a strong breeze from my monitor every time k.e. puts on his clown DaveTard suit" dogdidit
"Abbie Smith (ERV) who's got to be the most obnoxious arrogant snot I've ever seen except for when I look in a mirror" DAVE TARD
"ID is deader than Lenny Flanks granmaws dildo batteries" Erasmus

  
Hermagoras



Posts: 1260
Joined: June 2007

(Permalink) Posted: May 13 2009,16:10   

Quote (Leftfield @ May 13 2009,15:06)
Is this new news to those following this thread?

Chemist Shows How RNA Can Be the Starting Point for Life



If that's old news, let me recommend this headline instead:

Ancient Figurine of Voluptuous Woman Is Found

This seems very nice.  The paper (a letter to Nature) is here.

--------------
"I am not currently proving that objective morality is true. I did that a long time ago and you missed it." -- StephenB

http://paralepsis.blogspot.com/....pot.com

   
Dr.GH



Posts: 1954
Joined: May 2002

(Permalink) Posted: May 13 2009,22:24   

Ten years ago (or so) there was a very good paper in Current Anthropology that matched views of the various "Venus" figures and the perspective of a pregnant woman viewing her own body. The idea was suggested that these were objects made to facilitate pregnancy and delivery.

Actually on topic, I posted my short outline of abiogenesis a while ago at Stones and Bones.

Edited by Dr.GH on May 13 2009,20:26

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Dr.GH



Posts: 1954
Joined: May 2002

(Permalink) Posted: May 14 2009,09:42   

There is a recent article on the prebiotic formation of an RNA.

The Nature abstract ->

http://www.nature.com/nature....lang=en


A Nature commentary ->

http://www.nature.com/nature/journal/v459/n7244/full/459171a.html

Subscription required to read the articles.

(Hat tip to wattsr1 at TWeb)

Edited by Dr.GH on May 14 2009,07:44

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Reed



Posts: 274
Joined: Feb. 2008

(Permalink) Posted: May 14 2009,23:29   

Quote (Dr.GH @ May 14 2009,07:42)
There is a recent article on the prebiotic formation of an RNA.

The Nature abstract ->

http://www.nature.com/nature....lang=en

Carl Zimmer has a nice post about this

  
J-Dog



Posts: 4361
Joined: Dec. 2006

(Permalink) Posted: Feb. 03 2010,17:04   

HOT PRIMORDIAL SOUP THEOREY COOLS OFF

NEW THEOREY SAYS IT'S ALL ABOUT LOUIS
(well the chemistry anyway...)

Abiogenesis = All About Teh Chemistry

Quote
In rejecting the soup theory the researchers turned to the Earth's chemistry to identify the energy source which could power the first primitive predecessors of living organisms: geochemical gradients across a honeycomb of microscopic natural caverns at hydrothermal vents. These catalytic cells generated lipids, proteins and nucleotides which may have given rise to the first true cells.


added in edit:  I just visted Panda's Thumb and see that this is a headline story over there.  I guess great minds think alike sometimes it is better to be lucky than good.

--------------
Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Dr.GH



Posts: 1954
Joined: May 2002

(Permalink) Posted: Feb. 04 2010,18:07   

Quote (J-Dog @ Feb. 03 2010,15:04)
Quote
In rejecting the soup theory the researchers turned to the Earth's chemistry to identify the energy source which could power the first primitive predecessors of living organisms: geochemical gradients across a honeycomb of microscopic natural caverns at hydrothermal vents. These catalytic cells generated lipids, proteins and nucleotides which may have given rise to the first true cells.


added in edit: I just visted Panda's Thumb and see that this is a headline story over there. I guess great minds think alike sometimes it is better to be lucky than good.



This was a classic "Science Paper Jerked-off by Science Reporter Hack."
This was delt with at the Amazon.com DB.

Edited by Dr.GH on Feb. 04 2010,16:11

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Mar. 24 2010,10:23   

Despite my utter failure to keep several promises about updating this thread in a meaningful manner, I thought I'd just share this:

Mechanical self replicators.

Louis

--------------
Bye.

  
Henry J



Posts: 4045
Joined: Mar. 2005

(Permalink) Posted: Mar. 24 2010,10:42   

But the experiment was designed by an intelligence!!one!!!

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Mar. 24 2010,10:43   

Quote (Henry J @ Mar. 24 2010,15:42)
But the experiment was designed by an intelligence!!one!!!

But it's a European Intelligence. Dutch even.

Which therefore means that sexual liberation,  homosexuality and pot smoking are ok.

Q.E.D.

Louis

--------------
Bye.

  
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Feb. 20 2011,14:15   

Quote (Louis @ Mar. 24 2010,05:23)
Despite my utter failure to keep several promises about updating this thread in a meaningful manner, I thought I'd just share this:

Mechanical self replicators.

Louis

So how would you react to the statement:

"Amino acids do not self assemble into proteins."

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Feb. 20 2011,14:53   

Quote (Alan Fox @ Feb. 20 2011,20:15)
Quote (Louis @ Mar. 24 2010,05:23)
Despite my utter failure to keep several promises about updating this thread in a meaningful manner, I thought I'd just share this:

Mechanical self replicators.

Louis

So how would you react to the statement:

"Amino acids do not self assemble into proteins."

I'd ask which words were being weaselled about before agreeing or disagreeing. ;-)

Louis

--------------
Bye.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 20 2011,20:07   

Quote (Louis @ Feb. 20 2011,15:53)
Quote (Alan Fox @ Feb. 20 2011,20:15)
 
Quote (Louis @ Mar. 24 2010,05:23)
Despite my utter failure to keep several promises about updating this thread in a meaningful manner, I thought I'd just share this:

Mechanical self replicators.

Louis

So how would you react to the statement:

"Amino acids do not self assemble into proteins."

I'd ask which words were being weaselled about before agreeing or disagreeing. ;-)

Louis

Agreeing with Louis. (The safe option, except in MC)

Of course, they do self assemble, and pop out a water molecule. Then a little while later, the reaction reverses. Which side of the reaction represents most of the reactants in equilibrium depends on a lot of things. In pure water, the amino acids win. In concentrations (think very salty water of evaporation pools, water bubbles trapped in ice, etc) the peptide can win.

Your friendly creo, like BA^77, is happy to quote studies all day long based on the pure water results. Ignores the salty water results. The salty water usually has some helpful metal ions floating around, as well.

There is also the consideration that the above analysis is useful for two AAs becoming a dipeptide. Once you start thinking about longer chains, you realize you actually have a population of peptides, length 1 to n, all possibly breaking and ligating. But because longer peptides start folding, some ligation points get hidden, stabilized by other bonds, etc. As a result, they are more stable than you'd expect the unfolded peptide to be.

So OOL doesn't need the whole ocean to be "primordial soup" to get started. The reactions can be favorable in tidal pools (considering that the Moon was quite a bit closer, tides 3.5 billion years ago were huge, so these pools could have covered large inland areas), polar ices, the top millimeter of the tropical ocean, near ocean vents, and still be unfavorable in most of the volume of the oceans.

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
OgreMkV



Posts: 3282
Joined: Oct. 2009

(Permalink) Posted: Feb. 20 2011,21:27   

I recent report suggested that clays can form armored vesicles in which small amino acids can enter, but larger proteins cannot exit, thereby increasing the concentration radically.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Feb. 21 2011,03:05   

Quote
I'd ask which words were being weaselled about before agreeing or disagreeing. ;-)


I guess the pedant might pick on "protein" and claim a minimum number of residues before a peptide qualifies as a protein. There might be some weaselling over whether "no true protein" lacks biological function.

I emailed Professor Szostak who was kind enough to respond:

Dear Alan,

Amino acids can easily react with each other to form short random sequence peptides, some of which may have performed important functions in very early, primitive life forms. Peptides can form either by drying amino acids at moderately elevated temperatures, or even by reacting with each other while dissolved in water, in the presence of certain high energy compounds such as COS, a compound found in volcanic gases. So forming peptides is not chemically difficult.

Proteins, composed of longer polypeptide chains, arose much later, after the long series of evolutionary developments that led to the emergence of the translational apparatus and the genetic code. Earlier catalysts were probably RNA or something similar, perhaps acting together with very simple peptides.

I hope this is helpful,

Jack


So is it the case that the only known current way for any proteins or peptides to appear in living organisms is via ribosomal synthesis from DNA/RNA?

  
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Feb. 21 2011,03:13   

Quote (dvunkannon @ Feb. 20 2011,15:07)
Quote (Louis @ Feb. 20 2011,15:53)
Quote (Alan Fox @ Feb. 20 2011,20:15)
 
Quote (Louis @ Mar. 24 2010,05:23)
Despite my utter failure to keep several promises about updating this thread in a meaningful manner, I thought I'd just share this:

Mechanical self replicators.

Louis

So how would you react to the statement:

"Amino acids do not self assemble into proteins."

I'd ask which words were being weaselled about before agreeing or disagreeing. ;-)

Louis

Agreeing with Louis. (The safe option, except in MC)

Of course, they do self assemble, and pop out a water molecule. Then a little while later, the reaction reverses. Which side of the reaction represents most of the reactants in equilibrium depends on a lot of things. In pure water, the amino acids win. In concentrations (think very salty water of evaporation pools, water bubbles trapped in ice, etc) the peptide can win.

Your friendly creo, like BA^77, is happy to quote studies all day long based on the pure water results. Ignores the salty water results. The salty water usually has some helpful metal ions floating around, as well.

There is also the consideration that the above analysis is useful for two AAs becoming a dipeptide. Once you start thinking about longer chains, you realize you actually have a population of peptides, length 1 to n, all possibly breaking and ligating. But because longer peptides start folding, some ligation points get hidden, stabilized by other bonds, etc. As a result, they are more stable than you'd expect the unfolded peptide to be.

So OOL doesn't need the whole ocean to be "primordial soup" to get started. The reactions can be favorable in tidal pools (considering that the Moon was quite a bit closer, tides 3.5 billion years ago were huge, so these pools could have covered large inland areas), polar ices, the top millimeter of the tropical ocean, near ocean vents, and still be unfavorable in most of the volume of the oceans.

So cycles of wetting and drying at the margin of salt water pools could in theory, if amino acids ware present, result in the build-up of random sequences. Has any experiment been tried or proposed?

PS Thanks for responses, Guys.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Feb. 21 2011,07:09   

Two questions, two (off the top of my head) quick answers:

1)
Quote
So is it the case that the only known current way for any proteins or peptides to appear in living organisms is via ribosomal synthesis from DNA/RNA?


Off the top of my head I can't think of another biochemical method that, in vivo, makes functional proteins. That might be my limitation, but transcription/translation is certainly the dominant mechanism from what I remember. But remember this is a highly evolved system, certainly not what is predicted to have been around earlier.

As for short peptides, I can think of a few ways from a simplistic chemical perspective. After all, a soup of amino acids and a touch of low pH and you get simple dipeptides all over the shop. Eat a bag of alanine and it'll form  dipeptides in your stomach...ok that is slightly facetious because those same conditions could hydrolyse the formed dipeptide, but as the Prof answered, forming short peptides isn't the problem. Getting them to form large macromolecules is trickier

2)
Quote
So cycles of wetting and drying at the margin of salt water pools could in theory, if amino acids ware present, result in the build-up of random sequences. Has any experiment been tried or proposed?


My recollection is that the majority of work has been done on clay surfaces and with mineral catalysis. The wetting/drying cycle thing suffers from the problem alluded too above, hydrolysis of the peptide (amide) bond. The plausible prebiotic conditions of amide bond formation are often suitable for the cleavage of that bond. I have a book at home with a couple of lead references in I can post for you later on.

Again from memory, what has been studied is wetting/drying on clays, or at least oligopeptide synthesis on wet/damp clays. This has proven pretty successful in cases where the rate of formation of the specific amide bond is greater than that of the rate of cleavage of the specific amide bond. Pretty obvious.

As for the "random" nature of the oligopeptides formed, well it won't be so "random". This is a very interesting bit of polymer chemistry. The proportion of the monomer units in a mixed polymer/oligomer isn't simply due to the composition of the original monomer mixture. The interplay between thermodynamic and kinetic parameters comes into play, particularly the ratio between the kinetic constants for the bond formation of each type of bond.

Louis

--------------
Bye.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 21 2011,07:51   

Quote (Alan Fox @ Feb. 21 2011,04:13)
So cycles of wetting and drying at the margin of salt water pools could in theory, if amino acids ware present, result in the build-up of random sequences. Has any experiment been tried or proposed?

PS Thanks for responses, Guys.


Yes, they have been done. BA^77 has a quotemine of a study of dilute salty water favoring AAs over peptides. It is a real scientific paper by a couple of guys who favor eutectic ice OOL theories. I think the references in that paper contain a paper about more concentrated salt conditions. I know I've read it. Basically, when the water molecule comes out, it gets grabbed by the sodium and chloride ions and isn't available to break the peptide bond.

Free energy relationships in aqueous amino acid and peptide solutions containing sodium chloride
Eugene E. Schrier and R. A. Robinson
Journal of Solution Chemistry
Volume 3, Number 7, 493-501, DOI: 10.1007/BF00648134


 
Quote
Abstract
Three systems of the type amino acid or peptide-sodium chloride-water have been investigated over wide solute molality ranges using the isopiestic vapor pressure method. The amino acid employed was L-alpha-alanine, while the peptides were diglycine and triglycine. Equations were obtained for the activity coefficients of these compounds in the salt solutions in terms of the molalities of the solutes. The trace activity coefficients of the peptides were negative at low salt molality and became positive as the salt molality was increased. The limiting interaction parameters were calculated for the systems using the Kirkwood ion-dipole expression and empirical quantities derived from previous work to obtain the salt effect on the nonpolar and amide portion of the molecule. Good agreement was obtained between the calculated values and the experimental results in the case of diglycine, but they diverged in the case of triglycine. The calculated value for L-alpha-alanine is in poorer agreement with the experimental value than for the other amino acids studied previously.
Key words Amino acids - peptides - diglycine - triglycine - isopiestic method - ion-dipole interactions - NaCl

Presented in part at the Second International Conference on Calorimetry and Thermodynamics, Orono, Maine, July 1971.


Wow that is old, almost old enough for a creationist to believe!

Newer, but still science from the previous century:
(This is the cite that speaks directly to your question.)

Origins of Life and Evolution of Biospheres
Volume 23, Number 3, 167-176, DOI: 10.1007/BF01581836
Evaporation cycle experiments A simulation of salt-induced peptide synthesis under possible prebiotic conditions
Somporn Saetia, Klaus R. Liedl, Artur H. Eder and Bernd M. Rode

 
Quote
Abstract
Evaporation cycles applied to dilute solutions of amino acids, Cu(II) and NaCl lead to peptides within 13 days. This simulation of possible coastal or laguna processes in a primitive earth environment gives further indications towards the relevance of the salt-induced peptide formation reaction in chemical evolution. The experiments were successfully applied to glycine, alanine, aspartic and glutamic acid. Besides isolated amino acids, also their mixtures with glycine as reaction partner were studied, leading to peptides for all of the aforementioned substances, as well as for valine and proline, which do not dimerize alone. Sequence preferences and some conservation of optical purity were observed.


A follow-up study showing synergies of multiple AAs in the mix:

Origins of Life and Evolution of Biospheres
Volume 29, Number 5, 463-471, DOI: 10.1023/A:1006583311808
Mutual Amino Acid Catalysis in Salt-Induced Peptide Formation Supports this Mechanism's Role in Prebiotic Peptide Evolution
Yuttana Suwannachot and Bernd M. Rode

 
Quote
Abstract
The presence of some amino acids and dipeptides under the conditions of the salt-induced peptide formation reaction (aqueous solution at 85 ーC, Cu(II) and NaCl) has been found to catalyze the formation of homopeptides of other amino acids, which are otherwise produced only in traces or not at all by this reaction. The condensation of Val, Leu and Lys to form their homodipeptides can occur to a considerable extent due to catalytic effects of other amino acids and related compounds, among which glycine, histidine, diglycine and diketopiperazine exhibit the most remarkable activity. These findings also lead to a modification of the table of amino acid sequences preferentially formed by the salt-induced peptide formation (SIPF) reaction, previously used for a comparison with the sequence preferences in membrane proteins of primitive organisms


Dude, its got, like, its own acronym!

http://iupac.org/publications/pac/pdf/2007/pdf/7912x2101.pdf

More from the Rode group. Discussion of SIPF starts on page 9 of the PDF. Now claiming some effect on the growth of homochirality. Woot!

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I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Feb. 22 2011,02:20   

Quote
Dude, its got, like, its own acronym!


Thanks, David. Lots to read, now. Hydrothermal vents? Plausible scenario?

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Feb. 22 2011,11:08   

Quote (Alan Fox @ Feb. 22 2011,03:20)
Quote
Dude, its got, like, its own acronym!


Thanks, David. Lots to read, now. Hydrothermal vents? Plausible scenario?

I'm not seeing how to create a repeated cycle of high/low salt concentration in an undersea vent scenario. Instead, there is the idea of all the little crevices favoring the capture of small AAs while the longer peptides can't escape. Similar to the clay vesicle work that OgreMkV alluded to earlier.

But it also must be said that a lot of what we now see only in undersea vents was happening in the air in a primordial earth. The Zinc World papers go into this (sub-marine vs. sub-aerial) at length. Elevated temperature and pressure, metal particles getting belched out with copious sulfur, etc.

BTW, since I asked about Miller-Urey apparatus at the top of the page, it is cool to see the Rode lab's updated version in that PDF.

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
OgreMkV



Posts: 3282
Joined: Oct. 2009

(Permalink) Posted: Feb. 22 2011,18:05   

Interestingly, relationships among genes for the various processes in photosynthesis and chemosynthesis suggest that chemosynthesis was first and photosynthesis was an adaptation to apply the same solution to light instead of heat.

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
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