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Offline minass

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is life evolving chemistry?
« on: 29/12/2015 19:09:28 »
is life evolving chemistry?


 

Offline puppypower

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Re: is life evolving chemistry?
« Reply #1 on: 30/12/2015 13:48:50 »
Evolution is based on two principles, The first is based on what makes water and oil separate. While the second is the second law of thermodynamics, which states that the entropy of the universe has to increase.

If we mix water and oil, they will separate and form two layers. You can try this at home. Since the entropy of the universe has to increase, then nature will need to find ways to get these two chemically segregated things to mix. One way is to extract things into the water and/or oil, allowing the water and oil to better blend. The membrane of a cell is oily; lipids, but water can freely pass due to protein being extracted into the oil. That was expected.

The other is to chemically modify the water or the oil thereby making it easier for the two the mix; so entropy can increase. The water is simple and stable so there in not much we do there. The oil, on the other hand, by being organic and carbon based has many more options. This was the place where the entropy was able to increase, best, with chemical changes to organics continuing to occur. 

The DNA, which is sort of the king of the organics in terms of life, is the most hydrated molecule in the cell. The DNA is organic; oily, but has been modified to be able to blend in water, with its most hydrated molecule status, meaning it is at the pinnacle of the entropy chain. Further entropy occurs not by altering the basic nature of the DNA, but by altering genes and by altering others things, using the surface of the DNA; transcription.

There is still second law potential with the water, even for the king. Periodically, cells duplicate the DNA to make more and more of the terminal organic and even make changes with the hope that more and more water and oil can merge as one.
 

Offline minass

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Re: is life evolving chemistry?
« Reply #2 on: 09/01/2016 11:35:00 »
So you mean that if i mix oil and water in a flask, then life will be created because entropy has to increase?
 

Offline minass

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Re: is life evolving chemistry?
« Reply #3 on: 18/01/2016 17:46:50 »
To make it simple, if you have complex organic chemical reactions, then the infinite stereochemical isoforms will develop infinite possible interactions, and if you add external energy, then chemical equillibrium will not likely occur that easily.
On the other hand, if you have a system of complex chemical reactions then most of them will lead to a dead end. But some will not, and so those will continue. After a huge amount of time, only those that can be sustained will be selected in a way. So the chemical system will evolve in a way...But technically, isn't life a sum of self-sustainable chemical systems after all?
 

Offline puppypower

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Re: is life evolving chemistry?
« Reply #4 on: 20/01/2016 14:10:08 »
Water and oil do not mix. Take some cooking oil and water and shake it hard for ten minutes. If you let this settle, the water and oil will separate into two layers. The random mixture or emulsion, that took you ten minutes to make, will not remain. Rather, order will appear from the chaos.

Water and organics create a potential with each other. There is no organic material that can perfectly blend in water and not add some potential. The result is water and organics systems, from pre-life to life, will attempt to lower the water-organic potential, resulting in order. For example, water and lipids tend to form bi-layered membranes. This is not a random thing, but it forms because it defines a lower energy shape in the water. It does not take millions of years, but can form in minutes.

Let me we go back to oil and water, because this is the simplest binary system; water and oil will separate. The second law states that the entropy of the universe has to increase. However, since water and oil wants to separate, this fights against entropy. But the second law says the entropy needs to increase and the system needs to become less ordered. One round-about way to do this is to add/dissolve things to the water and oil, so each phase gains entropy. Another way is to chemically alter the water and/or the oil so they can blend better. Water is already very simple so its remains unchanged over time. The change needs to come from the organics.

Water is setting a lowest energy floor, pushing the organics and water into order.  The entropy has to increase, but with water fighting back. There are still ways to satisfy both potentials at the same time, such as extraction and chemical change. Water is always pushing while changes occur, with some changes able to better satisfy both the water and the entropy. This is the direction of evolution.

If you took the water out of life, at any level, from an entire life form, to a cell, to any enzyme and substituted any other solvent, life will not appear. In fact, enzymes, will work properly. Everything was built/evolved based on the push back that water generated.

If we started life with another solvent, that solvent will provide its own push back. However, no other solvent can push against carbon and organic compounds as hard as water. This is why if you add other solvents, in exchange for water, there is not enough push back to allow anything to work. Water is the chemical basis for natural selection since all changes needs to address the push of water.

The DNA is the most hydrated material in the cell. This means it is designed to define the lowest potential with water, by being composed of so much water. The DNA was logical respond to the 2nd law in water. This was one of the milestones.

 
 

Offline alancalverd

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Re: is life evolving chemistry?
« Reply #5 on: 20/01/2016 16:56:48 »
I think you will find that DNA contains no H2O, but cell cytoplasm contains lots. But don't be put off by the facts, PP. 
 

Offline minass

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Re: is life evolving chemistry?
« Reply #6 on: 26/01/2016 10:47:36 »
puppypower: Is there a way to experimentally test in order to prove or falsify this?

Evidence so far are not supportive because life on earth is the only example we have, despite the fact that water is the most abundant substance in the Universe
« Last Edit: 26/01/2016 10:49:47 by minass »
 

Offline puppypower

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Re: is life evolving chemistry?
« Reply #7 on: 27/01/2016 13:46:46 »
I think you will find that DNA contains no H2O, but cell cytoplasm contains lots. But don't be put off by the facts, PP.

I remember years ago wondering why adenine (A) and cytosine (C) had more possible hydrogen bonding hydrogen, than it forms in base pairs along the DNA. This can be seen below. The extra hydrogen bonded hydrogen are on the -NH2 groups of adenine and cytosine. My first theory was maybe the two hydrogen would switch like a binary switch. At that time I was still biased by the biology tradition of naked DNA i n vacuum, that did not include water.

Later I learned that these extra hydrogen, are used by water. Investigations have also shown that water hydrogen bonds as two separate helixes along the DNA; double helix of water. See the diagram below. The degree of this hydration will determine the phase of the DNA, with beta DNA the most common to life. The educational system does seem to teach the reality of the DNA in water, based on the latest science data. It seems to prefer to perpetuate a retro approximation of naked DNA.  Why does biology ignore hard data, in favor of horse and buggy science from 1950?


 

puppypower: Is there a way to experimentally test in order to prove or falsify this?

Evidence so far are not supportive because life on earth is the only example we have, despite the fact that water is the most abundant substance in the Universe

When protein fold, they form exact folding, not governed by the laws of statistics. The probability is 1.0 or the fold is a sure thing. This is due to the impact of water on organics, since protein folding is driven by hydrophobic interactions; water scares the protein to fold perfectly, since this allows it to avoid water and minimize potential.

Other proposed solvents for life elsewhere, used to perpetuate the random mythology, are just not scary enough. The protein do not have the same phobia. Organic solvents are more protein friendly and will lead to randomness. If you use other solvents the retro random assumption may still apply. Other solvents give hope for the ole glories days. Water is different since it can scare; phobic, the protein to perfection. Water has to be talk down to maintain confusion for the retro theory. How is perfect protein folding possible, if we assume a random assumption of the universe and life? I would like to hear that explanation. Such an explanation has never been offered.

Proteins are also all left handed helixes. A random assumption would assume left and right helices should occur in equal amounts. All the left handed protein in the cell are like throwing a coin thousands of times and always getting heads. What are the odds for that?  Why is the random misinformation being taught at the same time they teach left handed helixes? Does anyone see the paradox? Students need to ask these questions. Bit don't expect a rational answer since this is none.

Water is the future of biology, since water based order allows global control over cells. Maybe biology needs to undergo cell division. One daughter cell of biology can stay retro and random, like a museum, while the other can use modern water data and assume order. Then we can allow natural selection.
« Last Edit: 27/01/2016 13:57:31 by puppypower »
 

Offline minass

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Re: is life evolving chemistry?
« Reply #8 on: 02/02/2016 13:42:18 »
I don't think that anyone thinks that water is not crucial for life on earth. It's like viewing a house built with some kind of bricks and assume that these bricks are essential for this house. Of course they are.
However there are two things:
a)Maybe other similar solvents can support (at least primitive) life under special circumstances
b)Water alone is insufficient to create life. Other ingredients are needed as well...
 

Offline puppypower

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Re: is life evolving chemistry?
« Reply #9 on: 03/02/2016 00:11:50 »
Protein in water will fold with perfect folds. This has been demonstrated for over 50 years. Protein folding, in turn, is driven by hydrophobic interactions. In other words, protein folding is not so much due to the protein wanting to be bind to itself. Rather the protein has to fold to avoid contact with water. Water contact with an open protein creates potential, which needs to be minimized. The water is driving the protein into a perfect fold, since this will minimize the potential of the water.

If we use other solvents, the question to ask is, will that solvent still allow perfect folding of proteins, since perfect folding is necessary for enzyme function? The answer is no. Rather protein folding in all other solvents will follow the rules of statistics. Those who wish to preserve the random approach to life would do better with other solvents.

The reason other solvents will cause randomization in folding is, if you use organic solvents, for example, their hydrophobic equivalent (their push) to make the protein fold, is much weaker. For example, if you used an alcohol instead of water, the protein will not fold properly, because the alcohol can dissolve both the polar and organic aspects. If the protein does not fold properly, the active side is not active.

I am a development person, so if a boss said, I need to use another solvent, like an alcohol, to make protein equivalent fold perfectly. What would need to happen is I  would need to design a protein equivalent, with different atoms, so the solvent now has sufficient push to make perfect folding. This may be possible, but it will not be something that is common to the universe. Amino acids can be found all over the universe. Amino acids polymerize into protein, but protein only fold perfectly in water.

The idea of perfect folding needs to explained using statistical arguments. The quote I showed suggested after 50 years nobody can explain perfect folds with statistical arguments. It has stumped the stars.

In my opinion, the reason biology has never evolved beyond statistics is connected to this and other pure science not being self sufficient in terms of resources. Science discovery, although important to help us better understand nature, does not generate resources to be self sufficient. It is for of a money pit. Therefore science depends on Government and Industry to provide funding. If you follow the money, this is the bottle neck, that does not allow the change.

From the POV of bio-business, like the medical and pharmaceutical industries, they need science bodies and mass production due to the numbers of projects. Statistics provides a useful cookie cutter approach,that is easy to do, since it places things in a black box, so all you need to know is the facade. This allow mass production and the science assemble line. If you open the black box; admit the protein has perfect folds, then science would need to become more customized. This is not good for the assembly line.

Relative to Government, they have laws and regulations that require compliance and oversight to compliance.This is also better served by the assembly line, since the assembly line is consistent and easy for bureaucrats to deal with. They would not like having to deal with custom works all the time.

Since money;industry and power; government are providing the funding, they will prefer the cookie cutter even if it falls short. If science had been more self sufficient, we would be decades ahead.

We need to discuss perfect protein folding and see if we can offer a statical explanation. If not, we need to discuss the powers to be and how they will be mad of the truth is known. This is naked science venus political science.
« Last Edit: 03/02/2016 00:16:15 by puppypower »
 

Offline chiralSPO

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Re: is life evolving chemistry?
« Reply #10 on: 03/02/2016 00:28:16 »
Puppypower, I disagree whole-heartedly that statistics don't apply to proteins. I have addressed this elsewhere:

Proteins do NOT fold into a specific shape with a probability even close to 1.

Synthesis of a polypeptide chain does not guarantee that the chain will fold into what would be the "correct" shape of the protein as produced in a cell. A whole range of foldamers (peptides with the same sequence of amino acids, but folded differently) will be sampled. Sometimes there are one or two foldamers that are thermodynamically preferred over the others, but there will still be a distribution.

Taking a protein of the "correct" shape and denaturing it (pushing it to sample more foldamers than it would in biological setting) usually ruins the shape permanently (it rarely goes back to the original shape), even if no covalent bonds are broken.

In biological systems, the shape of a protein is usually templated and/or shepherded into the right conformation by many other proteins, co-factors, ions, etc., and even then there is a not-insignificant rate of misfolding. Usually the organism has ways of detecting misfolded proteins and destroying (or fixing) them, but sometimes mis-folded proteins accumulate and lead to diseases (https://en.wikipedia.org/wiki/Proteopathy)

Let us also note that proteins are rarely static in biological systems. That proteins change conformations allows them to be "active" machines with the organism (gates open and close, enzymes "turn on" and "turn off", some of them even "walk" https://en.wikipedia.org/wiki/Kinesin).

The handedness of helices in proteins is determined by the chirality of the amino acids themselves. Natural amino acids are all of the same configuration, so it is not surprising that this chirality manifests in the secondary and tertiary structures of proteins.

Continuing to state that proteins fold perfectly will not make it true. I will certainly agree that proteins will not fold the same way in solvents other than water, but that still doesn't mean that water is absolutely necessary for life (although I suspect that this is a reasonable criterion)

For the most part, I agree with minass, unfortunately (as minass has also pointed out) we really don't have enough datapoints about life to answer this question. As far as we know, all life that we have studied evolved from a common ancestor (or pool of ancestors)--it all uses the same DNA/RNA/protein system, the processes of metabolism and reproduction are all very similar on a chemical level, and water is necessary for all. Does this mean that all life in the universe follows these laws? I doubt it, but until we have another tree of life to study, we cannot be certain...
 

Offline minass

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Re: is life evolving chemistry?
« Reply #11 on: 11/02/2016 17:13:24 »
We cannot say however that puppypower is completely wrong about the importance of hydrophobic properties and all the other various factors, such as molecular tension, etc etc. Even the wind and the water stream play a role in complex systems such as biological phenomena.
Biology in theory can be reduced down to chemistry, which can be reduced down to physics, but things grow tremendously complex and its not worth it...
However, I think that mathematical models cannot apply to biological systems that easily (at least not yet, or anytime near). For instance, mathematical models cannot fully represent true biological phenomena because they don't account for the spatial factor. Additionally, they only assume that all chemicals can react with each other without accounting for inhibitory events, or other kind of interactions such as adhesive properties, hydrophobic interactions, water flow, etc, etc.....
Some scientists (even legit ones) introduced some kind of these supposed models into computers, played with complexity and supposedly got some incredible hidden patterns that miraculously emerged, in other words, nothing less than bacteria, flowers, animals, etc...
Now i think this is an example how wrong initial assumptions, when used in wrong ways, can lead us to monstruously misleading conclusions.
If your approach in order to answer how from complex primordial chemistry we got to today’s life is this, then it is life answering to the question how from 1, 2, 5, 8 you got 5689 and you claim: Eureka!!! Its 1+2=15*5=3000*8=5689

On the contrary, I think that in a complex chemical system, due to all the kinds of interactions, which are unpredictable and everytime different, the most sustainable combinations of interactions (or else the resulting mixture) will be slowly selected in a step-by-step fashion, brick by brick, until we get the final mixture that will be super sustainable because it was sculped and shaped by eons of struggles and competitions.


 

Offline alancalverd

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Re: is life evolving chemistry?
« Reply #12 on: 11/02/2016 18:32:23 »

However, I think that mathematical models cannot apply to biological systems that easily (at least not yet, or anytime near). For instance, mathematical models cannot fully represent true biological phenomena because they don't account for the spatial factor.


You are about 120 years behind Pasteur and 60 years behind Watson & Crick. I guess most of the mathematical modelling of protein folding and enzyme specificity can be traced to Kendrew, Klug and Perutz' mathematics in the late 1960's - sadly, their efforts to teach me fell on rather stony ground! But you are entitled to your opinion.   
 

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Re: is life evolving chemistry?
« Reply #12 on: 11/02/2016 18:32:23 »

 

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