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Abiogenesis Update


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#1 Guest_Keith C_*

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Posted 16 June 2009 - 11:06 AM

This article from NY Times gives an abiogenesis update.
New Glimpses of Life’s Puzzling Origins
In the last few years, four surprising advances have renewed confidence that a terrestrial explanation for life’s origins will eventually emerge.
1. One is the discovery that simple fatty-acid molecules will spontaneously form stable membranes, which admit small molecules and retain larger molecules like RNA without the presence of special pores and pore proteins. These essentially form protocells which spontaneously divide. Next step is to try adding a replicating DNA system.

2. Discovery of a quite unexpected route for synthesizing nucleotides. Instead of making the base and sugar separately under the right conditions the base and sugar could be built up as a single unit. This eliminates the need to link base and sugar before forming RNA.

3. Dr. Joyce reported in Science earlier this year that he had developed two RNA molecules that can promote each other’s synthesis from the four kinds of RNA nucleotides. “We finally have a molecule that’s immortal,” he said, meaning one whose information can be passed on indefinitely. The system is not alive, he says, but performs central functions of life like replication and adapting to new conditions.

4. 'Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.
The chemists have now been granted an unexpected absolution from their original syn problem.
Researchers have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.'
http://www.nytimes.c...ence/16orig.htm

This item is not about abiogenesis, but the unusual bacterium shows how life can survive under extreme conditions.
Tiny Frozen Microbe May Hold Clues To Extraterrestrial Life
A novel bacterium -- trapped more than three kilometres under glacial ice in Greenland for over 120,000 years
H. glaciei is small even by bacterial standards – it is 10 to 50 times smaller than E. coli. Its small size probably helped it to survive in the liquid veins among ice crystals and the thin liquid film on their surfaces. Small cell size is considered to be advantageous for more efficient nutrient uptake, protection against predators and occupation of micro-niches and it has been shown that ultramicrobacteria are dominant in many soil and marine environments.
http://www.scienceda...90614201734.htm
If modern examples of this species can be isolated it might provide a snapshot of 120,000 years of evolution.

#2 Adam Nagy

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Posted 16 June 2009 - 12:44 PM

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#3 Adam Nagy

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Posted 16 June 2009 - 12:48 PM

Since you want to focus on bacteria, I want to show you one of the best questions I've seen raised regarding proposed evolution:

http://www.icr.org/a...eyond-bacteria/

#4 Arch

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Posted 16 June 2009 - 06:17 PM

Since you want to focus on bacteria, I want to show you one of the best questions I've seen raised regarding proposed evolution:

http://www.icr.org/a...eyond-bacteria/

View Post


Again I've been watching some Ted Talks and this one touches on the point your article makes, although it's not directly relevant.

http://www.ted.com/t...gy_evolves.html

In this talk Kevin Kelly says that all life (from bacteria through to humans) is all equally evolved. I would think that the original bacteria wasn't able to survive as well as modern bacteria. To compensate some bacteria evolved towards more complexity, while others stayed bacteria and evolved different traits. Depending on circumstances one or the other may have been more beneficial.

Regards,

Arch.

#5 Guest_Keith C_*

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Posted 16 June 2009 - 06:26 PM

Since you want to focus on bacteria, I want to show you one of the best questions I've seen raised regarding proposed evolution:

Link given is an article from the Institution of Creation (ICR) website:-
Why Did Life Evolve Beyond Bacteria?
by Brian Thomas, M.S.
The first paragraph in this article mentions (with citation) a recent lecture given by Harvard geochemistry professor Charles Langmuir. The last paragraph of the article, quoted completely reads:-
In his lecture, Langmuir described a series of “evolutionary steps” through which life evolved from initially toxic conditions. There is no place in Scripture, plainly read, for a vast age of anoxic bacteria, then one of aerobic bacteria. Fortunately for scriptural history, there is also no geologic evidence for any time on earth when oxygen was not present, and there is certainly no biological evidence that indicates anything other than life having been created from Life.
http://www.icr.org/a...eyond-bacteria/

On first scanning this, I was left with the impression that Langmuir asserted that Earth had always had an oxygen-containing atmosphere.

Is that the impression you got on the first reading?
This was sufficiently surprising for a geochemistry professor that I checked the reference given.
http://www.news.harv...0/11-earth.html
He is reassuringly orthodox. There clearly is substantial evidence for a time when there was little or no free oxygen in Earth's atmosphere.

*****************************
The main argument of the Thomas article is:-
"animal and plant life is more vulnerable than microbial life to environmental variations, .....(i.e., is “less fit” to survive the changes).
... ....if increased survivability is what drives evolution, then why did life evolve upwards from microbes?
If —fitness—is removed from the equation, then what remains to drive it(evolution)?

.....since bacteria are earth’s superior survivors, they should be all the life this planet has ever seen. ............................
And yet the earth is populated by a variety of living things, including humans, who are supposedly the most evolved species.
[presumably implying some divine intervention]

If this really is an argument for creation, why should god's special creation be so vulnerable?
I will ignore minor errors, like 'most evolved species'. All lines of descent cover the same time range.

Whether evolution explains it or not, geology, geochemistry and the fossil record document 4 billion years of evolution rather than creation 6,000 years ago.
But evolution does explain it -when viewed correctly.
The criterion for fitness is replication rates under current conditions - without any thought for tomorrow.
As someone said, a chicken is an egg's way to create another egg. Dawkins said the essentially the same thing, - that genes create bodies in order to make more genes.
The other piece of wisdom about eggs is not to put all your eggs in one basket. This does not have to be a pre-established policy. It may be that only those species which did this have left descendants to keep the tradition going.

Evolution does this by having species diverge, effectively into different baskets. Mutation, genetic crossing over and s@x are all processes which help long-lived diploid organisms compete with single-celled organisms.
Intelligence may be the next arena of competition. Can humans use their intelligence to out-compete microbes and solve problems like global warming, or will the earth have to wait for another major innovation?

#6 Bruce V.

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Posted 16 June 2009 - 09:37 PM

4.  'Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.
The chemists have now been granted an unexpected absolution from their original syn problem.
Researchers have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.'
http://www.nytimes.c...ence/16orig.htm


View Post


Chiral chemicals (chemicals that are the same handed) have almost identical melting and freezing points. Separating out stereoisomers (chemicals that are the same handed) is almost impossible to do by manipulating physical properties like temperature. (It can be done with light) Why, because there essentially the same chemical. Rather than being ABCD there are ABDC.

Posted Image

Versus

Posted Image

The other problem is that solutions that are all one the same handed will racmetize in time. They will go back to a 50/50 mixture.

The other question I had is what are the temperature cycles we are talking about and how fast do they have to occur? Is this scenario even realistic.

#7 Bruce V.

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Posted 16 June 2009 - 09:49 PM

This item is not about abiogenesis, but the unusual bacterium shows how life can survive under extreme conditions.
Tiny Frozen Microbe May Hold Clues To Extraterrestrial Life
A novel bacterium -- trapped more than three kilometres under glacial ice in Greenland for over 120,000 years
H. glaciei is small even by bacterial standards – it is 10 to 50 times smaller than E. coli. Its small size probably helped it to survive in the liquid veins among ice crystals and the thin liquid film on their surfaces. Small cell size is considered to be advantageous for more efficient nutrient uptake, protection against predators and occupation of micro-niches and it has been shown that ultramicrobacteria are dominant in many soil and marine environments.
http://www.scienceda...90614201734.htm
If modern examples of this species can be isolated it might provide a snapshot of 120,000 years of evolution.

View Post



How old is Greenland? It certainly is less that 120,000 years.

Its small size probably helped it to survive in the liquid veins among ice crystals and the thin liquid film on their surfaces. Small cell size is considered to be advantageous for more efficient nutrient uptake, protection against predators and occupation of micro-niches and it has been shown that ultramicrobacteria are dominant in many soil and marine environments.


This is pure evolutionist story telling. No scientist would have speculated such a thing before. Is there really a correlation between longevity and size. If the cell was larger you would have the opposite spin: Large cell size is advantageous because...

#8 Bruce V.

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Posted 16 June 2009 - 09:52 PM

Is that the impression you got on the first reading?
This was sufficiently surprising for a geochemistry professor that I checked the reference given.
http://www.news.harv...0/11-earth.html
He is reassuringly orthodox.  There clearly is substantial evidence for a time when there was little or no free oxygen in Earth's atmosphere.

View Post



How do you get an amino acid from an oxygen free environment?

Posted Image

Without and atmosphere what would prevent hydrogen and oxygen from escaping into space?

If free oxygen escapes the earth than the much lighter hydrogen will as well. You can not assume free oxygen escapes and then turn around and say that hydrogen doesn't also escape.

That is why, Langmuir said, chemicals such as antioxidants developed, to protect against oxygen’s damaging effects.


How exactly does this happen? Seriously.

#9 Bruce V.

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Posted 16 June 2009 - 10:17 PM

1.  One is the discovery that simple fatty-acid molecules will spontaneously form stable membranes, which admit small molecules and retain larger molecules like RNA without the presence of special pores and pore proteins.  These essentially form protocells which spontaneously divide.  Next step is to try adding a replicating DNA system.


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How are these fatty acid molecules made it the first place? Will these fatty acids react with RNA? What are the side reactions? Keq? Does RNA have a code to reproduce these fatty acids as well? Of course not.

Are these stable membranes 3-D like a sphere, if not what is the point?

#10 Adam Nagy

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Posted 17 June 2009 - 06:14 AM

Bruce, stop being so critical and just believe. :(

#11 Guest_Keith C_*

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Posted 17 June 2009 - 08:07 PM

How do you get an amino acid from an oxygen free environment?

Without and atmosphere what would prevent hydrogen and oxygen from escaping into space? 

If free oxygen escapes the earth than the much lighter hydrogen will as well.  You can not assume free oxygen escapes and then turn around and say that hydrogen doesn't also escape.
How exactly does this happen?  Seriously.

Quite seriously, I think your first step should be to read the account of Langmuir's talk at:-
http://www.news.harv...0/11-earth.html
Then ask questions.

Chemical convention is that 'oxygen free' means that O2 is not present or else is at extremely low concentration. It does not mean that oxygen-containing chemicals like water, CO2 and CO are absent.

The earth's gravity is sufficient to keep water, O2, N2 and heavier gases in the atmosphere. Hydrogen and helium are the light gasses which can escape.

I have never said oxygen escapes. Earth's early atmosphere contained little or no free O2. It was the evolution of photosynthesis in blue-green algae which started accumulation of free oxygen in the atmosphere. This occurred over millions of years. Then organisms found out how to use oxygen to get energy by oxidizing food. It was in this period that living cells began making chemicals like vitamin C as protection from byproducts of respiration.

You also asked "How old is Greenland".
Your fairy-tales probably put it at 6,000 years old.

Greenland itself contains some of the oldest rocks on earth - at least 3.8 billion years.
It is the ice-sheet over Greenland which contains some ice which fell as snow about 120,000 years ago.

#12 Sif

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Posted 18 June 2009 - 12:19 AM

Oh dear Adam...

The whole reason it's taking them so long to create life in a lab is that they have to simulate natural processes. If they wanted to, they could just stick molecules together and make it. They recently made a protobiont in a lab. Of course protobiont isn't alive but it is a subject to natural selection.

http://en.wikipedia....wiki/Protobiont

And scientists are figuring it out quite fast. The earth had all the world oceans as a laboratory and millions of years.

#13 Adam Nagy

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Posted 18 June 2009 - 06:05 AM

Hi darling Sif, ;)

Welcome to the boards. :)

The whole reason it's taking them so long to create life in a lab is that they have to simulate natural processes.

View Post

Every experiment that was even somewhat attempted under "natural processes" was a dismal failure like the Miller/Urey Experiment. However, if you consider the Miller/Urey experiment as being "natural processes" and/or successful, then I have some ocean front property in Kansas that I'd like to sell you.

If they wanted to, they could just stick molecules together and make it.

View Post

Oh, Really? It's that simple huh? Well, I'm a believer then. Oh wait, we have this little problem of evidence because you have none.

They recently made a protobiont in a lab. Of course protobiont isn't alive but it is a subject to natural selection.

http://en.wikipedia....wiki/Protobiont

And scientists are figuring it out quite fast. The earth had all the world oceans as a laboratory and millions of years.

View Post

Frankenstein parlor tricks are interesting but they are parlor tricks and that's all. They have nothing to do with showing how life evolved. They have everything to do with convincing the public that they're on the cusp of generating the beginnings of evolution when they are merely doing clever biological juggling. Is it fair to say that they've made a believer out of you?

#14 Sif

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Posted 18 June 2009 - 06:58 AM

Hi darling Sif, ;)

Welcome to the boards. :)
Every experiment that was even somewhat attempted under "natural processes" was a dismal failure like the Miller/Urey Experiment

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Excuse me but how was the Miller/Urey Experiment a failure? It was supposed to create amino acids under the simulated hypothetical conditions thought at the time to be present on the early Earth. At first they thought they created 5 amino acids when in fact they created 22 as found out in the 2008 re-analysis of the experiment

http://www.sciencema...ct/322/5900/404

So IF you say "a failure like the Miller/Urey Experiment" you really mean that those were very successful?

#15 Adam Nagy

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Posted 18 June 2009 - 07:24 AM

Excuse me but how was the Miller/Urey Experiment a failure? It was supposed to create amino acids under the simulated hypothetical conditions thought at the time to be present on the early Earth. At first they thought they created 5 amino acids when in fact they created 22 as found out in the 2008 re-analysis of the experiment

http://www.sciencema...ct/322/5900/404

So IF you say "a failure like the Miller/Urey Experiment" you really mean that those were very successful?

View Post

Sif, level with me. How long have you been looking into the creation versus evolution debate? Are you interested in learning why we believe what we believe?

You came in here with your guard up but I would like to know; if you were to discover that there are arguments that you may not be familiar with, would you be interested in giving them an open minded look?

#16 chigaimasmaro

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Posted 18 June 2009 - 01:13 PM

4.  'Prebiotic chemists have long been at a loss to explain how the first living systems could have extracted just one kind of the handed chemicals from the mixtures on the early Earth. Left-handed nucleotides are a poison because they prevent right-handed nucleotides linking up in a chain to form nucleic acids like RNA or DNA. Dr. Joyce refers to the problem as “original syn,” referring to the chemist’s terms syn and anti for the structures in the handed forms.
The chemists have now been granted an unexpected absolution from their original syn problem.
Researchers have discovered that a mixture of left-handed and right-handed molecules can be converted to just one form by cycles of freezing and melting.'
http://www.nytimes.c...ence/16orig.htm

View Post



That was an interesting article Keith. One question that I have though is the article states the following:

Last month, John Sutherland, a chemist at the University of Manchester in England, reported in Nature his discovery of a quite unexpected route for synthesizing nucleotides from prebiotic chemicals. Instead of making the base and sugar separately from chemicals likely to have existed on the primitive Earth, Dr. Sutherland showed how under the right conditions the base and sugar could be built up as a single unit, and so did not need to be linked.



If John Sutherland wasn't using the same chemical setup as what was theorized to be part of the primitive Earth, than how does what the experiment he performed that proves it occurs will naturally? True, he got the single nucleotide to link up, which is cool. But isn't he doing it outside the rules of the game so to speak?



Excuse me but how was the Miller/Urey Experiment a failure? It was supposed to create amino acids under the simulated hypothetical conditions thought at the time to be present on the early Earth. At first they thought they created 5 amino acids when in fact they created 22 as found out in the 2008 re-analysis of the experiment

http://www.sciencema...ct/322/5900/404

So IF you say "a failure like the Miller/Urey Experiment" you really mean that those were very successful?



Geologist have lots of problems with that experiment (See: Heinrich D. Holland, “Model for the Evolution of the Earth’s Atmosphere,” pp. 447-477)

Another problem is once they start introducing either the realistic or naturally occurring atmospheric conditions, the experiment doesn't work. From my knowledge of what I've read it has to be with those specific conditions.

One interesting thing about these sets of experiments, is how did the lightning keep striking the exact same area to form more and more amino acids like in this experiment? From my view, the "failure" in this experiment is actually getting everything grouped together in nature, in a volatile environment and then having lightning strike the same area repeatedly for a week like was done in the experiment. The Miller/Urey experiment was VERY controlled. But I think you already knew that. I guess, the photograph shows lightning, but a question remains for me, to get that type of clouding and lightning formation [ Figure 1, wouldn't you need our current atmospheric conditions to create those type of lightning clouds? Or am I off-base?

#17 Sif

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Posted 18 June 2009 - 01:26 PM

Sif, level with me. How long have you been looking into the creation versus evolution debate? Are you interested in learning why we believe what we believe?

You came in here with your guard up but I would like to know; if you were to discover that there are arguments that you may not be familiar with, would you be interested in giving them an open minded look?

View Post



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?

#18 Justin.EET

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Posted 18 June 2009 - 01:29 PM

That was an interesting article Keith.  One question that I have though is the article states the following:
If John Sutherland wasn't using the same chemical setup as what was theorized to be part of the primitive Earth, than how does what the experiment he performed that proves it occurs will naturally?  True, he got the single nucleotide to link up, which is cool.  But isn't he doing it outside the rules of the game so to speak? 

Excuse me but how was the Miller/Urey Experiment a failure? It was supposed to create amino acids under the simulated hypothetical conditions thought at the time to be present on the early Earth. At first they thought they created 5 amino acids when in fact they created 22 as found out in the 2008 re-analysis of the experiment

http://www.sciencema...ct/322/5900/404

So IF you say "a failure like the Miller/Urey Experiment" you really mean that those were very successful?


One interesting thing about these sets of experiments, is how did the lightning keep striking the exact same area to form more and more amino acids like in this experiment? From my view, the "failure" in this experiment is actually getting everything grouped together in nature, in a volatile environment and then having lightning strike the same area repeatedly for a week like was done in the experiment. The Miller/Urey experiment was VERY controlled. But I think you already knew that. I guess, the photograph shows lightning, but a question remains for me, to get that type of clouding and lightning formation [ Figure 1, wouldn't you need our current atmospheric conditions to create those type of lightning clouds? Or am I off-base?

View Post


Lightning strikes?

You realize that this was atmospheric electric discharges?
Not a lightning bolt striking the ground in the same spot.

Milley-Urey was simulating lightning in the atmosphere that would send electric discharges through the water vapor. That evaporated from the earths body of water.
And for that all you need is sun(adequate distance)/water.

#19 chigaimasmaro

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Posted 18 June 2009 - 02:15 PM

Lightning strikes?

You realize that this was atmospheric electric discharges?
Not a lightning bolt striking the ground in the same spot.

Milley-Urey was simulating lightning in the atmosphere that would send electric discharges through the water vapor. That evaporated from the earths body of water.
And for that all you need is sun(adequate distance)/water.

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ahh my bad. Thank you for correcting the error.
Question though, If this happened in the atmosphere, and rained back down or floated, how did the acids keep from getting destroy once they were formed? If as KeithC says Oxygen was still around, what allowed them to still exist once they came out of the electrical-vaporizing clouds?

#20 Adam Nagy

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Posted 18 June 2009 - 08:10 PM

What would convince you evolution is true?

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If it actually lined up with reality.




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