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How Was The First Cell Made?


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#18 CraigD

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Posted 04 December 2016 - 01:04 PM

Biology perpetuates a conceptual problem for itself, than makes the question of the formation of life harder to answer. Biology assumes life is organic-centric; DNA, RNA and Protein. The fact remains, lab tests have shown that none of these molecules will work if we take away the water. Lab tests have also shown you cannot substitute any other solvent and make the DNA or the proteins work.

I agree that biologists are “organic-centric”, focuing most study on molecules like DNA and the proteins expressed by the genes encoded in DNA, rather than the fact that DNA need water for function, but don’t see how this is a problem.

There’s simply much more to study with large, complicated molecules like DNA than small, simple ones like H2O. A typical geneome, like the human one, is about 10,000,000,000 times larger (about 3.3 x 109 base pairs, about 1011 AMU) than a water molecule (18 AMU). Studying the genome allows biologists to understand and change the traits of biological organisms. Studying water does not.
 

From this basic data, I would conclude that life is based on a partnership between water and organics, with both parts needed to create life.

The team approach, like the husband and wife, means there not just one way, but two ways at the same time, with compromises needed to reached, to reflect the needs of each, with these compromises having sweet spots; milestones. Lowest potential is when both husband and wife are satisfied with the result.

I think you’re erring in taking your “partnership” analogy literally, H-bond.

The water in a biological organisms can’t have multiple states like “satisfied” and “not satisfied”. Unlike an organism like a human, water doesn’t have structures like neurons that allow it to think, remember, and plan.
 

One useful observation, that tells us somethings about the evolution of life, is DNA is the most hydrated molecule in the cell.

Can you back this claim up with a link or reference, H-bond :QuestionM I wasn’t able to with a quick web search.

As you correctly point out in your post, if DNA isn’t surrounded by a layer of water, it doesn’t assume its B form, and doesn’t function. But many other structures in the cell don’t function unless surrounded by water. I don’t see how one can say they are more or less hydrated than the cell’s DNA. Water it vital to all intra- and extra-cellular biological activity.

#19 exchemist

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Posted 05 December 2016 - 01:57 AM

I agree that biologists are “organic-centric”, focuing most study on molecules like DNA and the proteins expressed by the genes encoded in DNA, rather than the fact that DNA need water for function, but don’t see how this is a problem.

There’s simply much more to study with large, complicated molecules like DNA than small, simple ones like H2O. A typical geneome, like the human one, is about 10,000,000,000 times larger (about 3.3 x 109 base pairs, about 1011 AMU) than a water molecule (18 AMU). Studying the genome allows biologists to understand and change the traits of biological organisms. Studying water does not.
 
I think you’re erring in taking your “partnership” analogy literally, H-bond.

The water in a biological organisms can’t have multiple states like “satisfied” and “not satisfied”. Unlike an organism like a human, water doesn’t have structures like neurons that allow it to think, remember, and plan.
 
Can you back this claim up with a link or reference, H-bond :QuestionM I wasn’t able to with a quick web search.

As you correctly point out in your post, if DNA isn’t surrounded by a layer of water, it doesn’t assume its B form, and doesn’t function. But many other structures in the cell don’t function unless surrounded by water. I don’t see how one can say they are more or less hydrated than the cell’s DNA. Water it vital to all intra- and extra-cellular biological activity.

All H Bond is saying, really, is that water appears to be a uniquely good solvent for the molecules used in earthly life. One can make a plausible argument that water is very likely to be involved in any conceivable life, whether on the Earth otherwise. Hence the obsession of NASA with liquid water on Mars and elsewhere, for example.  

 

But this poster has form - on another forum, under the name Wellwisher - for dressing up this simple idea in a sort of mysticism, which is completely unscientific. 



#20 HydrogenBond

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Posted 06 December 2016 - 03:35 PM

All H Bond is saying, really, is that water appears to be a uniquely good solvent for the molecules used in earthly life. One can make a plausible argument that water is very likely to be involved in any conceivable life, whether on the Earth otherwise. Hence the obsession of NASA with liquid water on Mars and elsewhere, for example.  

 

But this poster has form - on another forum, under the name Wellwisher - for dressing up this simple idea in a sort of mysticism, which is completely unscientific. 

 

 What I am saying is there is an equal partnership between water and the organics of life. During evolution, water remained constant. The result is the biomaterials of life had to evolve in ways that remained tuned to the potentials generated by water. This is why if you remove the water, nothing works, and if try to replace the water with another solvent, the organic of life do not work. These biomaterials are designed to include water as part of the secondary, ternary and quaternary structures. Other solvents generate different potentials which impact activity. 

 

Nucleic acid hydration is crucially important for their conformation and utility [1093], as noted by Watson and Crick [828]. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character [542b]. The DNA double helix can take up a number of conformations (for example, right handed A-DNA pitch 28.2 Å 11 bp, B-DNA pitch 34 Å 10 bp, C-DNA pitch 31Å 9.33 bp, D-DNA pitch 24.2 Å 8 bp and the left handed Z-DNA pitch 43Å 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration.  

 

 

It is not coincidence that B-DNA is both the most hydrated and also the most predominate natural DNA. The DNA evolved toward maximizing water inclusion, to minimize the potential with the water. 
 
When you have two partners, with different needs, they need to come to compromises which benefit both. These sweet spots are not random, but defined by the free energy of the partnership. 
 
The current model is not a partnership, but more like a master (organic) and slave (solvent/water). This is why the consensus assumes any solvent or slave will do. The master has all the authority. The slave does not have the authority to place restrictions on the master. Therefore the whims of the master has uno checks and balances; randomness. Once you add a partner, constraints are placed which restrict options. 


#21 exchemist

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Posted 06 December 2016 - 03:43 PM

 

 What I am saying is there is an equal partnership between water and the organics of life. During evolution, water remained constant. The result is the biomaterials of life had to evolve in ways that remained tuned to the potentials generated by water. This is why if you remove the water, nothing works, and if try to replace the water with another solvent, the organic of life do not work. These biomaterials are designed to include water as part of the secondary, ternary and quaternary structures. Other solvents generate different potentials which impact activity. 

 

 

It is not coincidence that B-DNA is both the most hydrated and also the most predominate natural DNA. The DNA evolved toward maximizing water inclusion, to minimize the potential with the water. 
 
When you have two partners, with different needs, they need to come to compromises which benefit both. These sweet spots are not random, but defined by the free energy of the partnership. 
 
The current model is not a partnership, but more like a master (organic) and slave (solvent/water). This is why the consensus assumes any solvent or slave will do. The master has all the authority. The slave does not have the authority to place restrictions on the master. Therefore the whims of the master has uno checks and balances; randomness. Once you add a partner, constraints are placed which restrict options. 

 

All this is bleedin' obvious, since the available solvent on the Earth at the relevant time happened to be water.

 

Quite plainly, if you take the biochemistry molecules that evolved in the presence of waer as a solvent, and you try to see what they do in another solvent, it will be a a catastrophic failure. That's because they evolved together. You can call that "partnership" if you like but it means little, other than that life on Earth arose in the presence of water and that is why water is important to it.

 

As I say, bleedin' obvious.


Edited by exchemist, 07 December 2016 - 01:34 AM.


#22 HydrogenBond

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Posted 06 December 2016 - 04:36 PM

Let me approach this from another angle. If you look at evolution, natural selection is impacted by the environment. Animals evolve in the context of the environment. If it is a cold or a warm environment, each environment can select differently based on what optimizes the animal to the environment. Water is the chemical environment of life,  on the nanoscale. This nanoscale environment sets the potentials for the selection of chemicals. Even if you assume random changes, unless these are better optimized to the water environment, they will not be selected for evolution. B-DNA, was selected because by containing so much water in its structures it is optimize to the aqueous environment. 

 

You could benefit by doing some studying with respect to the latest discoveries of water. Water is the most anomalous substance in nature with over 70 anomalies. It is a very complex environment for selection. 

 

If we changed the solvent, this is like placing polar bear at the equator. It can thrive in an Arctic Environment, but it may not be selected, elsewhere, because so many things are optimized to the polar weather and environment. 

 

In the current model if a leopard has spots, this is based on its own DNA. The persistence of this subtle change has nothing to do with optimizing the animal to the  environment he hunts in. 

 

Water at the nanoscale is very unique compared to all substances. It is the most anomalous substance in nature. More papers have been written about waters properties that anything else in science. It unique properties allow an environment where life can be selected.