A research project

nroberts · 12-14-2007, 09:23 AM

I was reading Darwin's Dangerous Idea and I came across a discussion of the beginnings of life...from the ooze. Well, the problem is that DNA is incredibly complex. 10 billion years is not enough time for it to occur, statistically, given the rules of chemestry and physics as starting points and allowing the components to float around in a puddle.

But, there are many theories that account for it by starting smaller...as one would expect. Basically, there are some molecules that will replicate and are very simple. They in turn would have evolved into the more complex and stable forms. However, there's no fitness function on molecules. Or is there?

Given a completely random chance that a given string of molecules will copy itself we STILL end up with order from non-order. I have begun experimenting with this idea on my computer. Last night I developed a simple genetic algorithm with no fitness function. It just randomly selected from the old generation and copied into the new.

Starting with a completely random set of strings, within 100 generations we will arrive at around 3 distinct strings from 100. Adding mutation that number changes drastically depending on how well the strings copy themselves. So, for instance, a mutation rate of 50% never really arrives at anything, even given a billion generations to evolve in, but a mutation rate of 1% will arrive at around 5-10 distinct strings at the end of a 100 generation cycle.

This just shows that completely random selection can resolve to a pattern of order. The likelihood of randomly starting with a uniform density is very rare. That you'd still have it at the next generation even more so...and so on. What this doesn't show is that stable copying could have evolved.

The next step I wish to go through is to base the mutation rate on the strings themselves, just as it works in Chemestry. The G and C components of DNA if strung together copy more successfully that other strings of molecules. If I impose something like this on the genetic algorithm, I expect that the pattern will quite normally resolve to sequences having these characteristics.

None of this is ground breaking of course...it's all based on other people's work. But it's interesting to me at any rate so I thought I'd share.

mentor · 12-14-2007, 09:32 AM

I heard a new hypothesis the other day that speculated it started on the surfaces of mica, inbetween the flat layers. Mica is super abundant, and it's structure lends itself to forming a sort of template where molecules in solution are forced to interact in specific formations which could have greatly accelerated the formation of the complex molecules needed for life.

The idea is that the ooze was not in a puddle or sea, but in the very small gaps between layers of mica. (clay has also been considered a substrate for the early formation of these molecules).

mentor · 12-14-2007, 09:34 AM

the mica hypothesis greatly reduces your odds of reproducing the complex molecules because it forces you to work in two dimentions rather than three.

nroberts · 12-14-2007, 09:57 AM

Quote:

Originally Posted by mentor

I heard a new hypothesis the other day that speculated it started on the surfaces of mica, inbetween the flat layers. Mica is super abundant, and it's structure lends itself to forming a sort of template where molecules in solution are forced to interact in specific formations which could have greatly accelerated the formation of the complex molecules needed for life.

The idea is that the ooze was not in a puddle or sea, but in the very small gaps between layers of mica. (clay has also been considered a substrate for the early formation of these molecules).

Yeah, simulating such is a future direction for this project.

The_Heretic · 12-14-2007, 01:06 PM

Quote:

Originally Posted by nroberts

I was reading Darwin's Dangerous Idea and I came across a discussion of the beginnings of life...from the ooze. Well, the problem is that DNA is incredibly complex. 10 billion years is not enough time for it to occur, statistically, given the rules of chemestry and physics as starting points and allowing the components to float around in a puddle.

Actually this all depends on what chemical compounds occurred in whatever abundances at the time. Amino acids themselves aren't that complicated, and the arrangement of them into strands also is the most likely of chemical reactions between them [dehydrolysis]. The concept of monomeres and polymeres.

Quote:

But, there are many theories that account for it by starting smaller...as one would expect. Basically, there are some molecules that will replicate and are very simple. They in turn would have evolved into the more complex and stable forms. However, there's no fitness function on molecules. Or is there?

There's enthalpy and entropy acting on molecular reactions.

Quote:

Given a completely random chance that a given string of molecules will copy itself we STILL end up with order from non-order. I have begun experimenting with this idea on my computer. Last night I developed a simple genetic algorithm with no fitness function. It just randomly selected from the old generation and copied into the new.

This is also a misconception. Not only can self replication chemistry happen it happens mroe often than scientists once thought. There are certain hydrocarbons that self replicate.

Quote:

Starting with a completely random set of strings, within 100 generations we will arrive at around 3 distinct strings from 100. Adding mutation that number changes drastically depending on how well the strings copy themselves. So, for instance, a mutation rate of 50% never really arrives at anything, even given a billion generations to evolve in, but a mutation rate of 1% will arrive at around 5-10 distinct strings at the end of a 100 generation cycle.

This just shows that completely random selection can resolve to a pattern of order. The likelihood of randomly starting with a uniform density is very rare. That you'd still have it at the next generation even more so...and so on. What this doesn't show is that stable copying could have evolved.

The next step I wish to go through is to base the mutation rate on the strings themselves, just as it works in Chemestry. The G and C components of DNA if strung together copy more successfully that other strings of molecules. If I impose something like this on the genetic algorithm, I expect that the pattern will quite normally resolve to sequences having these characteristics.

None of this is ground breaking of course...it's all based on other people's work. But it's interesting to me at any rate so I thought I'd share.

The thing is the sciences are why we got as far as we did. So given enough time these questions also would be worked out, and probably sooner than we think.

nroberts · 12-14-2007, 02:24 PM

Quote:

Originally Posted by The_Heretic

Actually this all depends on what chemical compounds occurred in whatever abundances at the time. Amino acids themselves aren't that complicated, and the arrangement of them into strands also is the most likely of chemical reactions between them [dehydrolysis]. The concept of monomeres and polymeres.

DNA replication involves more than just the strand itself.

At any rate, what you are saying is exactly what this experiment shows. Even with no selection function more than just randomness the algorithm works and forms order from chaos.

Quote:

This is also a misconception. Not only can self replication chemistry happen it happens mroe often than scientists once thought. There are certain hydrocarbons that self replicate.

Uhh...that's exactly what this experiment assumes. Perhaps you didn't understand it. Simply saying a lot of different stuff can replicate doesn't explain the order we see.

Thanks for the input though. I think you assume I'm a lot more ignorant than I really am but that's your right.

Environment Man · 12-14-2007, 03:15 PM

Your first paragraph was very good. Then you lost me with your fiction.

Your computer program proved nothing. The fact of the matter is even with limitless time DNA will not spring from any random arrangement of elements. Nor any amount of lightning strikes and even given an infinite amount of time.

The magic involved in this leap is much more magical than the so-called 'God did it' proposition of creation science. You say 'chance did it' but get pissed when we say 'God did it.' Well God is a much more scientific explanation than chance. AND YOU KNOW IT.

Comicsartist · 12-14-2007, 03:34 PM

Quote:

Originally Posted by Environment Man

Your first paragraph was very good. Then you lost me with your fiction.

Your computer program proved nothing. The fact of the matter is even with limitless time DNA will not spring from any random arrangement of elements. Nor any amount of lightning strikes and even given an infinite amount of time.

The magic involved in this leap is much more magical than the so-called 'God did it' proposition of creation science. You say 'chance did it' but get pissed when we say 'God did it.' Well God is a much more scientific explanation than chance. AND YOU KNOW IT.

Um...No, and neither do you. It is your opinion that God did it, but that doesn't mean you're right. I might actually agree with you to a point, but that still doesn't mean it's correct.

Environment Man · 12-14-2007, 03:47 PM

Quote:

Originally Posted by Comicsartist

Um...No, and neither do you. It is your opinion that God did it, but that doesn't mean you're right. I might actually agree with you to a point, but that still doesn't mean it's correct.

If you apply logic and science you have no choice but to agree with me, even if there is still some doubt. What you do not have a choice to do is suspend all of physics and established science and leap to spontaneous generation of DNA and life.

nroberts · 12-14-2007, 04:00 PM

Quote:

Originally Posted by Environment Man

If you apply logic and science you have no choice but to agree with me, even if there is still some doubt. What you do not have a choice to do is suspend all of physics and established science and leap to spontaneous generation of DNA and life.

Actually, that's incorrect. Anyone has the choice to believe any old stupid thing they want. It IS the right of everyone to believe what they want. It's also the right of others to think they're ape shit nuts...I mean, if you really believe in Santa and you're not 5...I'm going to question your sanity. Equally so if your concept of God is an anthropomorphic super being in the sky.

That said, you are right. Spontaneous generation of DNA and the companion pieces that go with it could not have happened. It must have either been created or built up from smaller components through time. I don't think anyone claims otherwise but if they do I think it fair to ask for some evidence or question their motives.

12-14-2007, 09:23 AM	#1 (permalink)
nroberts Get Slack! Join Date: Dec 2007 Posts: 338 My Mood: Thanks: 0 Thanked 2 Times in 2 Posts	A research project I was reading Darwin's Dangerous Idea and I came across a discussion of the beginnings of life...from the ooze. Well, the problem is that DNA is incredibly complex. 10 billion years is not enough time for it to occur, statistically, given the rules of chemestry and physics as starting points and allowing the components to float around in a puddle. But, there are many theories that account for it by starting smaller...as one would expect. Basically, there are some molecules that will replicate and are very simple. They in turn would have evolved into the more complex and stable forms. However, there's no fitness function on molecules. Or is there? Given a completely random chance that a given string of molecules will copy itself we STILL end up with order from non-order. I have begun experimenting with this idea on my computer. Last night I developed a simple genetic algorithm with no fitness function. It just randomly selected from the old generation and copied into the new. Starting with a completely random set of strings, within 100 generations we will arrive at around 3 distinct strings from 100. Adding mutation that number changes drastically depending on how well the strings copy themselves. So, for instance, a mutation rate of 50% never really arrives at anything, even given a billion generations to evolve in, but a mutation rate of 1% will arrive at around 5-10 distinct strings at the end of a 100 generation cycle. This just shows that completely random selection can resolve to a pattern of order. The likelihood of randomly starting with a uniform density is very rare. That you'd still have it at the next generation even more so...and so on. What this doesn't show is that stable copying could have evolved. The next step I wish to go through is to base the mutation rate on the strings themselves, just as it works in Chemestry. The G and C components of DNA if strung together copy more successfully that other strings of molecules. If I impose something like this on the genetic algorithm, I expect that the pattern will quite normally resolve to sequences having these characteristics. None of this is ground breaking of course...it's all based on other people's work. But it's interesting to me at any rate so I thought I'd share.
	Top

12-14-2007, 09:32 AM	#2 (permalink)
mentor Senior Member Join Date: Nov 2007 Location: Northern California Posts: 1,407 My Mood: Thanks: 23 Thanked 50 Times in 35 Posts	I heard a new hypothesis the other day that speculated it started on the surfaces of mica, inbetween the flat layers. Mica is super abundant, and it's structure lends itself to forming a sort of template where molecules in solution are forced to interact in specific formations which could have greatly accelerated the formation of the complex molecules needed for life. The idea is that the ooze was not in a puddle or sea, but in the very small gaps between layers of mica. (clay has also been considered a substrate for the early formation of these molecules). __________________ "To explain the unknown by the known is a logical procedure; to explain the known by the unknown is a form of theological lunacy." David Brooks
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12-14-2007, 09:34 AM	#3 (permalink)
mentor Senior Member Join Date: Nov 2007 Location: Northern California Posts: 1,407 My Mood: Thanks: 23 Thanked 50 Times in 35 Posts	the mica hypothesis greatly reduces your odds of reproducing the complex molecules because it forces you to work in two dimentions rather than three. __________________ "To explain the unknown by the known is a logical procedure; to explain the known by the unknown is a form of theological lunacy." David Brooks
	Top

12-14-2007, 03:15 PM	#7 (permalink)
Environment Man Senior Member Join Date: Nov 2007 Location: Catalina Island Posts: 19,728 Thanks: 0 Thanked 36 Times in 32 Posts	Your first paragraph was very good. Then you lost me with your fiction. Your computer program proved nothing. The fact of the matter is even with limitless time DNA will not spring from any random arrangement of elements. Nor any amount of lightning strikes and even given an infinite amount of time. The magic involved in this leap is much more magical than the so-called 'God did it' proposition of creation science. You say 'chance did it' but get pissed when we say 'God did it.' Well God is a much more scientific explanation than chance. AND YOU KNOW IT.
	Top

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