Jump to content


Abiogenesis Update


  • Please log in to reply
101 replies to this topic

#41 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 20 June 2009 - 01:48 PM

September. I've been exposed to a lot of arguments and so far i've seen through all of them. Feel free to try but i'm skeptical about your ability to find a good argument for creationism. Though i have an open mind so don't be discouraged.

My turn to ask

What would convince you evolution is true?

View Post


Show me the evolutionary pathway of any protein, starting from a primitive sequence through all mutations to a present sequence.It doesn´t need to be the right one, only a viable one.Showing the function and selective value of each step.

#42 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 20 June 2009 - 02:07 PM

"Though the changes produced in any one generation are small, differences accumulate with each generation and can, over time, cause substantial changes in the organisms. This process can culminate in the emergence of new species." -
Wikipedia

define specie first.

So like I said..... What's stopping mutations from accumulating?
What discerns when the change is large enough to the point of where you can no longer accumulate mutations that would further change the genotype/phenotype?


The combinatory explosion.The number of useless proteins is infinite comparing to useful ones.So, it´s impossible to find a pathway from one protein to another using random mutations.

#43 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 21 June 2009 - 05:00 PM

Answer posted to question, 'What stops mutations from accumulating?'

The combinatory explosion.The number of useless proteins is infinite comparing to useful ones.So, it´s impossible to find a pathway from one protein to another using random mutations.

I think this is an opportunity to illustrate the difference between the creationist and the scientific approach.

Creationist:- point to a problem and say 'impossible!'.
In this case if we need a protein with N amino-acids, and we start from a protein of the same length which performs some other function, there are 19 alternative amino-acids which could be tried in each of the N positions.
The number of alternatives to search is then 19^N, which is extremely large if N is 10 or greater.

Scientific:- explore the problem and understand it before looking for conclusions.
There are 2 separate combinatorial explosions:- the number of proteins and the number of search paths.
Start protein........... target protein, length N ( representing amino-acids by 20 single letters)
.....A.............................Z
.....B............................ Y
.....C............................X
......:.............................:

Both start and target sequences represent possible real effective proteins. The start protein is produced by a duplicated gene and the target protein performs some alternative function so that the change is a gain-of-function, ie the target makes the organism containing it 'fitter' than the starting organism..
We also know that many AA substitutions are neutral (because the position is far from the active sitre and/or because the new AA is similar to the old one). All we have to do is find a pathway consisting only of neutral or beneficial changes and avoiding all deleterious steps.
. .
Mutation occurs one amino-acid at a time. If we consider only direct changes, ie a change which goes immediately to one of the 'correct' amino acids, there are N possible first steps, Then we have N - 1 positions to choose from for the second step etc.
Total number of direct paths = N x (N-1) x (N-2) ...........x 2 x 1. = N! = N factorial.
However, we can really change the first position to either Z or any of the other 18 choices. This gives 19^N as the number of choices for the first step. Second step has 19^(N-1) choices. Total number of paths is then 19^{N + (N-1) + (N-2) .....2 + 1}
= 19^(N x N/2)
The total number of available paths is greater, by a factor of 19^(N/2), than the maximum possible number of deleterious sequences. This means that there is a very good probability of a feasible pathway to the target sequence without being blocked by deleterious sequences.

If there is a problem preventing mutation accumulation, I don't think you have found it.

#44 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 22 June 2009 - 02:17 AM

Answer posted to question, 'What stops mutations from accumulating?'

I think this is an opportunity to illustrate the difference between the creationist and the scientific approach.

Creationist:- point to a problem and say 'impossible!'.
In this case if we need a protein with N amino-acids, and we start from a protein of the same length which performs some other function, there are 19 alternative amino-acids which could be tried in each of the N positions.
The number of alternatives to search is then 19^N, which is extremely large if N is 10 or greater.

Scientific:- explore the problem and understand it before looking for conclusions.
There are 2 separate combinatorial explosions:- the number of proteins and the number of search paths.
Start protein........... target protein, length N    ( representing amino-acids by 20 single letters)
.....A.............................Z
.....B............................ Y
.....C............................X    
......:.............................:
             
Both start and target sequences represent possible real effective proteins.  The start protein is produced by a duplicated gene and the target protein performs some alternative function so that the change is a gain-of-function, ie the target makes the organism containing it 'fitter' than the starting organism.. 
We also know that many AA substitutions are neutral (because the position is far from the active sitre and/or because the new AA is similar to the old one).  All we have to do is find a pathway consisting only of neutral or beneficial changes and avoiding all deleterious steps.
       .                               .
Mutation occurs one amino-acid at a time.  If we consider only direct changes, ie a change which goes immediately to one of the 'correct' amino acids, there are N possible first steps,  Then we have N - 1 positions to choose from for the second step etc.
Total number of direct paths = N x (N-1) x (N-2) ...........x 2 x 1. = N! = N factorial.
However, we can really change the first position to either Z or any of the other 18 choices.  This gives 19^N as the number of choices for the first step.  Second step has 19^(N-1) choices.  Total number of paths is then 19^{N + (N-1) + (N-2) .....2 + 1}
= 19^(N x N/2)
The total number of available paths is greater, by a factor of 19^(N/2), than the maximum possible number of deleterious sequences.  This means that there is a very good probability of a feasible pathway to the target sequence without being blocked by deleterious sequences.

If there is a problem preventing mutation accumulation, I don't think you have found it.

View Post


I think your explanation is no sense.
1 - How do you quantify the number of deleterious sequence ?
2 - Neutral mutations cant be recognized by natural selection
3 - Mutations far from active site can disrupt the 3d structure of a protein
4 - If the mutation is silent ie code for the same amino-acid then we have no new function, no evolution.
5 - each step has 19^N possible mutations, I dont know why you think it´s factorial
6 - Try show an example , instead of wishful thinking.

#45 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 22 June 2009 - 06:22 AM

I think your explanation is no sense.
1 - How do you quantify the number of deleterious sequence ?
2 - Neutral mutations cant be recognized by natural selection
3 - Mutations far from active site can disrupt the 3d structure of a protein
4 - If the mutation is silent ie code for the same amino-acid then we have no new function, no evolution.
5 - each step has 19^N possible mutations, I dont know why you think it´s factorial
6 - Try show an example , instead of wishful thinking.

Items 1 - 4 and 6 are irrelevant.
Only #5 requires comment.
5 - each step has 19^N possible mutations, I dont know why you think it´s factorial
I was considering what I called 'direct changes' ie mutation at one position is to the amino acid in the target protein at that position.
For first step there are N positions to choose from. After 1 of these has been changed, there are only N-1 to choose from for the second step etc. That is what introduces the factorial.

The important part of my post was the next part - where I include the possibility of indirect paths. The total # of paths is far greater and your conclusion that all will be blocked is extremely uncertain.

#46 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 22 June 2009 - 07:39 AM

Items 1 - 4 and 6 are irrelevant.
Only #5 requires comment.


No, they are not.

5 - each step has 19^N possible mutations, I dont know why you think it´s factorial
I was considering what I called 'direct changes' ie mutation at one position is to the amino acid in the target protein at that position.
For first step there are N positions to choose from.  After 1 of these has been changed, there are only N-1 to choose from for the second step etc.  That is what introduces the factorial.


Oh, yes ? So what will stop the other positions from keeping mutating ?

#47 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 22 June 2009 - 08:29 AM

Who ever said the environment was oxygen free??  All that was said is there was no free oxygen.  That means O2 was not present.  Oxygen was still bonded to other elements to form compounds, one of which was water.

View Post


If you have water and sunlight you will have free oxygen and through a process called Photodissociation

Anouther way of saying the same thing is that water and oxygen is a reversible reaction:

H2O ------> <- H2 + 1/2 O2

So when you have water you will free oxygen and hydrogen.

Also the peptide reaction is very very difficult in water because the reaction is reversible:

AA = amino acid

AA + AA ----> <-- Peptide + H2O

Posted Image

The shear volume of water forces Chemical equilibrium back to the left side of equation. Abiogenesis need copious amounts of AA's in close proximity to be viable. AA reaction in water is provides neither.

#48 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 22 June 2009 - 08:44 AM

How does any life-form survive with no ozone because of the oxygen-less enviroment? UV rays kill, mutate, and sterilize. Especially unfiltered UV rays.
Water would block the UV
And if anything it would help accelerate the mutations.
"How does rain form and fall in a oxygen-less enviroment?"

Evaporation
"Low barometric pressure changes the laws of evaporation. A newly forming atmosphere would have low barometric pressure. Which would lower the boiling point of water. The earth was hotter back then. Add all that together and you get oceans of boiling water, atmospheric mosture that would never condense into rain because it's to hot. And UV rays that would kill anything that tried to form in pond scum that was 98% very toxic to all life. Sound like the odds are just right  "
Low pressures is usually what causes storms in the first place.

The earth being hotter doesn't mean you wouldn't have condensation. The earth was cooling as more water vapor was being emitted. Since the water vapor was helping to establish an atmosphere along with volcanic ash trapping gases. Which there was tons of volcanic activity on a young earth.

I think if you wager in all the variables that you left out..... Life was bound to occur via abiogenesis.

View Post


I hope I answered you objections in the previous post.

Low pressure and high temperatures would also radically increase the amounts of free oxygen and hydrogen.

My opinion is abiogenesis is impossible. We have no early earth scenario's on how 6 of the 20 amino acids could have been created.

My wife needs the computer -so more on this later if you are interested.

#49 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 22 June 2009 - 09:08 AM

If you have water and sunlight you will have free oxygen and through a process called Photodissociation.

Anouther way of saying the same thing is that water and oxygen is a reversible reaction:

H2O  ------> <-  H2 + 1/2 O2

So when you have water you will free oxygen and hydrogen.

This site, specifically on photo-dissociation of water, is a bit more pesimistic than you.
http://answers.yahoo...07045616AAfd4jT
Photo-dissociation is simply saying that if a H2O molecule is hit hard enough it will come apart.
Calling combustion of hydrogen reversible is effectively saying that water comes apart spontaneously, at least to some measurable extent. I suggest you find what the actual equilibrium constant is, and calculate how extensive that dissociation would be.

Also the peptide reaction is very very difficult in water because the reaction is reversible:

The shear volume of water forces  back to the right side of equation.

If you research very hard, you might find out the % water in the human body and also the protein content (perhaps as grams per kg of body weight).
You might also be able to find the equilibrium constant for peptide hydrolysis and see how consistent that is with the protein in the human body.

Ultimate realization might be that living processes are not always restricted by equilibrium constants.
If you get to that point, we can go further.

#50 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 22 June 2009 - 11:33 AM

This site, specifically on photo-dissociation of water, is a bit more pessimistic than you.
http://answers.yahoo...07045616AAfd4jT
Photo-dissociation is simply saying that if a H2O molecule is hit hard enough it will come apart.

Calling combustion of hydrogen reversible is effectively saying that water comes apart spontaneously, at least to some measurable extent.  I suggest you find what the actual equilibrium constant is, and calculate how extensive that dissociation would be.

View Post


Hi Kieth,

Are you saying that Photo-dissociation is not relevant in your early earth scenario? What would the sun effect be on water without an atmosphere?

You are right that the equilibrium constant is extremely low. Meaning that the reverse reaction is very low. However, when you have an ocean that covers 2/3 of the earth than even a low number has to be accounted for- it is not insignificant. Especially considering the earth had no atmosphere, temperatures were higher and the the atmospheric pressures were lower.

If you research very hard, you might find out the % water in the human body and also the protein content (perhaps as grams per kg of body weight).
You might also be able to find the equilibrium constant for peptide hydrolysis and see how consistent that is with the protein in the human body.

Ultimate realization might be that living processes are not always restricted by equilibrium constants.
If you get to that point, we can go further.

View Post



If you get to that point, we can go further.

Are you trying to be obnoxious. Stop patronizing me!!!

Ultimate realization might be that living processes are not always restricted by equilibrium constants.


You are equating biochemistry with chemistry. Biochemistry has a metabolism, or photosynthesis, catalytic enzymes, cell walls and the other doesn't. In short biochemistry has an information laden system that directs energy whereas standard organic chemistry does not.

In short Biochemistry takes into account entropy (Keq, free energy) much differently than does standard chemistry.

Interesting quotes for this article: The Implausibility of Metabolic Cycles on the Prebiotic Earth

The catalytic properties of enzymes are remarkable.  They not only accelerate reaction rates by many orders of magnitude, but they also discriminate between potential substrates that differ very slightly in structure.  Would one expect similar discrimination in the catalytic potential of peptides of length ten or less?  The answer is clearly “no,” and it is this conclusion that ultimately undermines the peptide cycle theory.




Almost all proposals of hypothetical metabolic cycles have recognized that each of the steps involved must occur rapidly enough for the cycle to be useful in the time available for its operation.  It is always assumed that this condition is met, but in no case have persuasive supporting arguments been presented.  Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of the reverse citric acid cycle was present anywhere on the primitive Earth, or that the cycle mysteriously organized itself topographically on a metal sulfide surface?  The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity.  The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated.  If it has, it has been ignored.  Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own.


The 2 previous quotes show that metabolic systems are laden with information.

Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers.  However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help



#51 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 22 June 2009 - 07:12 PM

Are you saying that Photo-dissociation is not relevant in your early earth scenario?  What would the sun effect be on water without an atmosphere?

You are right that the equilibrium constant is extremely low.  Meaning that the reverse reaction is very low.  However, when you have an ocean that covers 2/3 of the earth than even a low number has to be accounted for- it is not insignificant.  Especially considering the earth had no atmosphere, temperatures were higher and the the atmospheric pressures were lower.

What makes you think the earth did not have an atmosphere? Only situation I know where this might be correct is before the earth's mass became a reasonable fraction of its present mass. It is earth's gravity which retains the atmosphere. The volatile material making up the atmosphere and later condensed into the oceans would initially be vaporized by the high temperatures produced by impacts.
The initial atmosphere probably did contain substantial amounts of H2, and that would have been quickly lost into space because H2 atoms are light enough to escape earth's gravity.

Heavier molecules like CO2 will not be able to escape and probably formed the major part of the atmosphere, as it still does on Venus and Mars. Venus happens to be 5% smaller than Earth is diameter, about 82% of Earth's mass, yet atmospheric pressure there is about 95 earth atmospheres (about 140 psi instead of 14.7 psi pressure at the surface) and temperature near 450 C. You might reconsider the "atmospheric pressures were lower." part!.
If you get the water dissociation constant, you can use that to calculate the H2 and O2 partial pressures which would be at equilibrium. These gasses would have approximately the same value over the whole earth surface, but is that important or significant?

Are you trying to be obnoxious.  Stop patronizing me!!!

Since I have had to correct almost all of this part of your last post, and I suspect you are still not convinced that your 'ideas' about the early earth are still correct, I think I am entitled to have a little fun at your expense.
You could perhaps try harder to check your ideas before posting them.

You are equating biochemistry with chemistry. Biochemistry has a metabolism, or photosynthesis, catalytic enzymes, cell walls and the other doesn't.  In short biochemistry has an information laden system that directs energy whereas standard organic chemistry does not.

In short Biochemistry takes into account entropy (Keq, free energy) much differently than does standard chemistry.

It might help me understand this if you explain where you learned biochemistry.

Interesting quotes for this article:  The Implausibility of Metabolic Cycles on the Prebiotic Earth
The 2 previous quotes show that metabolic systems are laden with information.

It might help me understand this if you explain where you learned biochemistry.
Biochemistry is simply chemistry which occurs in cells, and the standard chemical concepts of energy and entropy etc apply in exactly the same way as in 'ordinary' chemistry.
What is different is that frequently there are two or more reactions coupled together. In this way, a reaction can be driven far from equilibrium by using the free energy available from another reaction which goes spontaneously.
You are correct that membranes, or at least the active transport through pores in membranes, is an important part of how cells function.

Based on the problems with your posts, I doubt whether you can do anything except quote mine in the Orgel paper.
However, you should read this article:-
http://www.nytimes.c...ence/16orig.htm
particularly about the new synthesis of nucleotides and consider what other novel chemistry might exist. Orgel starts his thinking from the reactions going on in today's cells and entirely different paths might be more effective and simpler.

#52 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 23 June 2009 - 02:18 AM

If you research very hard, you might find out the % water in the human body and also the protein content (perhaps as grams per kg of body weight).
You might also be able to find the equilibrium constant for peptide hydrolysis and see how consistent that is with the protein in the human body.

Ultimate realization might be that living processes are not always restricted by equilibrium constants.
If you get to that point, we can go further.

View Post


That´s irrelevant in abiogenesis.There´s no living process.No protein to prevent hydrolysis.

#53 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 23 June 2009 - 08:28 AM

What makes you think the earth did not have an atmosphere?  Only situation I know where this might be correct is before the earth's mass became a reasonable fraction of its present mass. It is earth's gravity which retains the atmosphere.  The volatile material making up the atmosphere and later condensed into the oceans would initially be vaporized by the high temperatures produced by impacts.
The initial atmosphere probably did contain substantial amounts of H2, and that would have been quickly lost into space because H2 atoms are light enough to escape earth's gravity.

Heavier molecules like CO2 will not be able to escape and probably formed the major part of the atmosphere, as it still does on Venus and Mars.  Venus happens to be 5% smaller than Earth is diameter, about 82% of Earth's mass, yet atmospheric pressure there is about 95 earth atmospheres (about 140 psi instead of 14.7 psi pressure at the surface) and temperature near 450 C.  You might reconsider the "atmospheric pressures were lower." part!.
If you get the water dissociation constant, you can use that to calculate the H2 and O2 partial pressures which would be at equilibrium.  These gasses would have approximately the same value over the whole earth surface, but is that important or significant?
Since I have had to correct almost all of this part of your last post, and I suspect you are still not convinced that your 'ideas' about the early earth are still correct, I think I am entitled to have a little fun at your expense.
You could perhaps try harder to check your ideas before posting them.
It might help me understand this if you explain where you learned biochemistry.
It might help me understand this if you explain where you learned biochemistry.
Biochemistry is simply chemistry which occurs in cells, and the standard chemical concepts of energy and entropy etc apply in exactly the same way as in 'ordinary' chemistry.
What is different is that frequently there are two or more reactions coupled together.  In this way, a reaction can be driven far from equilibrium by using the free energy available from another reaction which goes spontaneously.
You are correct that membranes, or at least the active transport through pores in membranes, is an important part of how cells function.

Based on the problems with your posts, I doubt whether you can do anything except quote mine in the Orgel paper.
However, you should read this article:-
http://www.nytimes.c...ence/16orig.htm
particularly about the new synthesis of nucleotides and consider what other novel chemistry might exist.  Orgel starts his thinking from the reactions going on in today's cells and entirely different paths might be more effective and simpler.

View Post


It takes a member to see the NYtimes article you posted.

The initial atmosphere probably did contain substantial amounts of H2, and that would have been quickly lost into space because H2 atoms are light enough to escape earth's gravity.


Miller Urey assumed no O2 ( a reducing atmosphere) yet assumed copious amount for H2, CH4, CO2 and H20. You can't eliminated O2 and not eliminated H2 because H2 will escape into the atmosphere. Any mechanism that removes O2 as a variable will also remove H2.

Heavier molecules like CO2 will not be able to escape and probably formed the major part of the atmosphere, as it still does on Venus and Mars.  Venus happens to be 5% smaller than Earth is diameter, about 82% of Earth's mass, yet atmospheric pressure there is about 95 earth atmospheres (about 140 psi instead of 14.7 psi pressure at the surface) and temperature near 450 C.  You might reconsider the "atmospheric pressures were lower." part!.



First you post an article that says earth had no atmosphere and no water. Then you discussed both scenarios interchangeably. Later someone else discussed an early earth with little atmosphere and low pressure. So I went with all 6 of early earth scenarios. Now you throw in Mars and Venus. How l am I suppose to answer a question when nobody knows what early earth looked like? Then you throw in remarks like "You might reconsider the "atmospheric pressures were lower." part!." Get real Kieth. Tell me what early earth looked like and support your answers. Give me only one contingency to work with. I will not play your games any longer.


I think I am entitled to have a little fun at your expense.


All you do is play games Kieth. And you don't answer my questions.

I have given up hope talking with you Kieth. You play games with all my posts. You twist words and play semantics games. You act like a know it all yet you never answer a question straight on. You make personal remarks and yet you completely miss my point. I would explain that article you posted from yahoo but I doubt you would understand that it didn't consider Maxwell Boltzmann and statistical thermodynamics.

For example, You missed the point that biochemistry has a machinery to make the chemical reactions proceed. Straight organic chemistry (i.e. abiogenesis) requires using the laws on entropy (Keq, free energy, kinetics...). In nature there is no ATP that can be used to overcome activation energy. But I am sure you missed that point. Or purposely missed that point. As far as quoting from Orgel should be welcomed by a truth seeker. Yet you play games with it. First you say that I don't have the answer and that the papers I quote arn't relevant for some specious unknown reason. You see nothing I post will every satisfy you for any reason. Your logic and science is flawed.

I am putting you on my ignore list. I request you do the same with me.

#54 Guest_tharock220_*

Guest_tharock220_*
  • Guests

Posted 23 June 2009 - 01:27 PM

If you have water and sunlight you will have free oxygen and through a process called Photodissociation 

Anouther way of saying the same thing is that water and oxygen is a reversible reaction:

H2O  ------> <-  H2 + 1/2 O2

So when you have water you will free oxygen and hydrogen. 


I'm no chemist, but doesn't water's stability make this very slow without catalysts found in in chlorophyll???

Also the peptide reaction is very very difficult in water because the reaction is reversible:

AA = amino acid

AA + AA ----> <--  Peptide + H2O

Posted Image

The shear volume of water forces Chemical equilibrium back to the left side of equation.  Abiogenesis need copious amounts of AA's in close proximity to be viable. AA reaction in water is provides neither.

View Post


Again, amide hydrolysis is usually acid catalyzed.

You're a jerk for making me attempt to remember chemistry. :blink:

#55 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 23 June 2009 - 01:38 PM

That´s irrelevant in abiogenesis.There´s no living process.No protein to prevent hydrolysis.

The protein itself does not prevent the hydrolysis.
However, your opinion that proteins are very unstable is probably due to the presence of protease enzymes.
"The results indicate that in neutral solution at 25 °C, peptide bonds are hydrolyzed with half-times of approximately 500 years for the C-terminal bond of acetylglycylglycine, 600 years for the internal peptide bond of acetylglycylglycine N-methylamide, and 350 years for the dipeptide glycylglycine. These reactions, insensitive to changing pH or ionic strength, appear to represent uncatalyzed attack by water on the peptide bond."
http://pubs.acs.org/....1021/ja954077c

Other catalysts, such as phosphoric acid, will also catalyze the condensation. Higher temperature promotes condensation by helping remove water.

As to some special 'living process' the important trick in living cells is that reactions with unfavorable equilibria can be driven in the required direction by coupling to other reactions which occur spontaneously.

#56 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 23 June 2009 - 02:01 PM

I'm no chemist, but doesn't water's stability make this very slow without catalysts found in in chlorophyll???
Again, amide hydrolysis is usually acid catalyzed.


You're a jerk for making me attempt to remember chemistry. :blink:

View Post


You are right. Water is very stable and the amount of 0xygen and hydrogen would be very small from the reverse reaction. Photodisassociation is discussed in Origin of life scenarios but you have to establish what early earth environment was before I head down that road again.



You are right again: A catalyst is used to make this reaction go in chlorophyll. The point I was hoping to make is that the peptide reaction is difficult in an aqueous environment.

#57 Bruce V.

Bruce V.

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,153 posts
  • Age: 54
  • Christian
  • Creationist
  • Northern Califiornia

Posted 23 June 2009 - 02:09 PM

Does anyone find it interesting that the first place NASA looks for life is on planets and moons that have water?

#58 Guest_Keith C_*

Guest_Keith C_*
  • Guests

Posted 23 June 2009 - 06:16 PM

It takes a member to see the NYtimes article you posted.

Correct link is
http://www.nytimes.c...ence/16orig.htm
Sorry for the glitch. There is no membership or subscription requirement, but free registration may be required.

Miller Urey assumed no O2 ( a reducing atmosphere) yet assumed copious amount for H2, CH4, CO2 and H20.  You can't eliminated O2 and not eliminated H2 because H2 will escape into the atmosphere.  Any mechanism that removes O2 as a variable will also remove H2.

Hydrogen, which was probably present initially is removed by escaping into space.
Free O2 was not present initially. A large part of the material collected together to form the earth was iron-nickel meteorites ( to form the core). Any oxygen would have reacted rapidly to form oxides.

First you post an article that says earth had no atmosphere and no water.  Then you discussed both scenarios interchangeably.  Later someone else discussed an early earth with little atmosphere and low pressure.  So I went with all 6 of early earth scenarios. Now you throw in Mars and Venus.  How l am I suppose to answer a question when nobody knows what early earth looked like?  Then you throw in remarks like "You might reconsider the "atmospheric pressures were lower." part!."  Get real Kieth.  Tell me what early earth looked like and support your answers.  Give me only one contingency to work with. I will not play your games any longer.
All you do is play games Kieth.  And you don't answer my questions.

When did I post anything claiming no atmosphere and no water?
Try reading post #5 again. The first part of my post is response to Adam Nagy and his link to an ICR site with claim earth always had oxygen atmosphere.
I investigated, and the geochemistry professor quoted in the ICR article definitely mentioned evidence for no free oxygen (or extremely little).

By post #8 you were asking how amino-acids could form if oxygen was absent. I think I answered that clearly in post #11.
In posts #22 and 35, Ikester gets on the 'no oxygen' misinterpretation which I try to answer in post #40.

I have given up hope talking with you Kieth.  You play games with all my posts.  You twist words and play semantics games.  You act like a know it all yet you never answer a question straight on.  You make personal remarks and yet you completely miss my point.  I would explain that article you posted from yahoo but I doubt you would understand that it didn't consider Maxwell Boltzmann and statistical thermodynamics.

My problem is that I really am not sure how much you know, and what you do not know. Whenever I try to explain things simply, you go off at a tangent without asking any questions suggesting problems with my answers.
As to the Yahoo article, the writer had no reason to consider the Maxwell-Boltzman distribution because the energy required is substantially greater than the thermal energy.

For example, You missed the point that biochemistry has a machinery to make the chemical reactions proceed. Straight organic chemistry (i.e. abiogenesis) requires using the laws on entropy (Keq, free energy, kinetics...).  In nature there is no ATP that can be used to overcome activation energy. But I am sure you missed that point.  Or purposely missed that point.  As far as quoting from Orgel should be welcomed by a truth seeker.  Yet you play games with it.  First you say that I don't have the answer and that the papers I quote arn't relevant for some specious unknown reason.  You see nothing I post will every satisfy you for any reason. Your logic and science is flawed.

I specifically wrote:-
"Biochemistry is simply chemistry which occurs in cells, and the standard chemical concepts of energy and entropy etc apply in exactly the same way as in 'ordinary' chemistry.
What is different is that frequently there are two or more reactions coupled together. In this way, a reaction can be driven far from equilibrium by using the free energy available from another reaction which goes spontaneously.
"
You seem to know about Maxwell-Boltzman, ATP, etc and you found the Orgel paper, yet you seem to have trouble realizing that when I mentioned 'coupled reactions' that included high energy molecules like ATP, but without being restricted to that one instance.

#59 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 24 June 2009 - 02:06 AM

The protein itself does not prevent the hydrolysis.
However, your opinion that proteins are very unstable is probably due to the presence of protease enzymes.
"The results indicate that in neutral solution at 25 °C, peptide bonds are hydrolyzed with half-times of approximately 500 years for the C-terminal bond of acetylglycylglycine, 600 years for the internal peptide bond of acetylglycylglycine N-methylamide, and 350 years for the dipeptide glycylglycine. These reactions, insensitive to changing pH or ionic strength, appear to represent uncatalyzed attack by water on the peptide bond."
http://pubs.acs.org/....1021/ja954077c

Other catalysts, such as phosphoric acid, will also catalyze the condensation.  Higher temperature promotes condensation by helping remove water.

As to some special 'living process' the important trick in living cells is that reactions with unfavorable equilibria can be driven in the required direction by coupling to other reactions which occur spontaneously.

View Post


There are special enzymes that keep water away from polymerization.That´s the why amino-acids can polymerise inside cells.In pre-biotic conditions amino-acids cant polymerise, because there´s no polymerization in presence of water.

#60 deadlock

deadlock

    Veteran Member

  • Veteran Member
  • PipPipPipPip
  • 1,196 posts
  • Age: 43
  • Christian
  • Creationist
  • Rio de Janeiro

Posted 24 June 2009 - 02:13 AM

Biochemistry is simply chemistry which occurs in cells, and the standard chemical concepts of energy and entropy etc apply in exactly the same way as in 'ordinary' chemistry.
What is different is that frequently there are two or more reactions coupled together.  In this way, a reaction can be driven far from equilibrium by using the free energy available from another reaction which goes spontaneously.[/color]"
You seem to know about Maxwell-Boltzman, ATP, etc and you found the Orgel paper, yet you seem to have trouble realizing that when I mentioned 'coupled reactions' that included high energy molecules like ATP, but without being restricted to that one instance.

View Post


Now, explain how the other reactions which you think occur spontaneously have to do with abiogenesis.




0 user(s) are reading this topic

0 members, 0 guests, 0 anonymous users