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Is life only a system of evolving chemical reactions?

Debate and discussion of any biological questions not pertaining to a particular topic.

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Is life only a system of evolving chemical reactions?

Postby minasole » Thu Dec 24, 2015 5:15 pm

Is life only a system of evolving (and selected) chemical reactions over long periods of time?
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Re: Is life only a system of evolving chemical reactions?

Postby claudepa » Thu Dec 24, 2015 9:11 pm

Hi. Could the question be also: Is biology only a part of chemistry ? I have no answer but a personnal experience. A long time ago during my phD in biology I identified a new chemical reaction involving DNA. I had then a very interesting collaboration with organic chemists who successfuly reproduced this reaction with small molecules. This was a confirmation of my results. However we did not agree on the notion of affinity between molecules. At this time (may be it is different now in chemistry, I do not know) chemists had not this notion of affinity between molecules, only the notion of reactivity. (the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,...) is very important in biology.
Is this also part of evolving chemical reactions ?
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Re: Is life only a system of evolving chemical reactions?

Postby minasole » Sat Jan 09, 2016 1:02 pm

claudepa wrote: (the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,...) is very important in biology.
Is this also part of evolving chemical reactions ?

Yes! But most of all i think it reflects the different conditions that generated these molecules. Biological reactions we observe are a tiny part of a larger group of reactions in which they belong..
If you search enough, there will be a pure chemical explanation for this difference in affinity (perhaps different stereochemistry?)

claudepa wrote:Hi. Could the question be also: Is biology only a part of chemistry ?

Chemistry can break down into physics. However there are difficulties into breaking down biology into complex organic chemistry (although the latter can pose a great variability of isoforms, thus enhancing complexity, selection and evolution over time that will eventually favour reactions with sustainability in the long term). However, there is a problem mainly with respect to thermodynamics and creation of order…

We think of life as a miracle and order because, for instance, some might say that a cell is much more ordered than its components, which means that a cell is an ordered and not a chaotic system.

However, I am skeptical with this interpretation because don’t forget that a cell never exists in isolation.
Imagine you have a flask with water that is heated with fire. The molecules of water will start speeding randomly toward various directions. Virtually, what you are doing here with the cell argument is ignoring the fire and the majority of other water molecules and focusing only on subset of 1 or 2 specific molecules. These molecules will be perceived as gaining speed without an obvious reason,..
Maybe sometimes our fate is to focus on the tree rather than the forest..
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Re: Is life only a system of evolving chemical reactions?

Postby claudepa » Sat Jan 09, 2016 6:16 pm

claudepa wrote:
(the reaction with DNA was much faster than with the small model molecules for an affinity reason). We of course know that the affinity between molecules (antibody-antigen, transcription factor-DNA sequence,...) is very important in biology.
Is this also part of evolving chemical reactions ?

Yes! But most of all i think it reflects the different conditions that generated these molecules. Biological reactions we observe are a tiny part of a larger group of reactions in which they belong..
If you search enough, there will be a pure chemical explanation for this difference in affinity (perhaps different stereochemistry?)

I agree that biological reactions and chemical molecules used by biology are selected among a much larger group. A good example is adenine used by cells for very different purposes. Other examples are D sugars and L amino acids. I indeed believe that the very high affinity between macromolecules has a stereochemical cause. When these macromolecules meet their surfaces is modified until a minimum of energy is reached. The point I raised was only a semantic one, it seems pure chemistry but may be is not involved in the sentence: chemical reactions.




claudepa wrote:
Hi. Could the question be also: Is biology only a part of chemistry ?
Chemistry can break down into physics. However there are difficulties into breaking down biology into complex organic chemistry (although the latter can pose a great variability of isoforms, thus enhancing complexity, selection and evolution over time that will eventually favour reactions with sustainability in the long term). However, there is a problem mainly with respect to thermodynamics and creation of order…

We think of life as a miracle and order because, for instance, some might say that a cell is much more ordered than its components, which means that a cell is an ordered and not a chaotic system.

The more I advance the more I imagine (may be I am wrong) a cell as a very ordered system. When I see videos of viruses going from the membrane to the nucleus travelling on microtubules, when I know that vesicles going out of the Golgi are targeted for their destination, I really see the cell like a city with roads and highways.

However, I am skeptical with this interpretation because don’t forget that a cell never exists in isolation.
Imagine you have a flask with water that is heated with fire. The molecules of water will start speeding randomly toward various directions. Virtually, what you are doing here with the cell argument is ignoring the fire and the majority of other water molecules and focusing only on subset of 1 or 2 specific molecules. These molecules will be perceived as gaining speed without an obvious reason,..
Maybe sometimes our fate is to focus on the tree rather than the forest..
minasole

Cell exist in isolation but may be they will not live a long time in this situation. I like a video showing islotated cell moving on a glass plate towards an amino acid for which they have receptors at the membrane. They look really like small animals.

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Re: Is life only a system of evolving chemical reactions?

Postby minasole » Sun Jan 24, 2016 10:20 am

claudepa wrote:
The more I advance the more I imagine (may be I am wrong) a cell as a very ordered system. When I see videos of viruses going from the membrane to the nucleus travelling on microtubules, when I know that vesicles going out of the Golgi are targeted for their destination, I really see the cell like a city with roads and highways.


Have you ever thought that maybe this “magical” small city only differs from chaotic chemistry in the fact that this system you described sustains itself and all procedures are repeated (pretty much) the same again and again?? Don’t forget that one of the most important properties of a cell is self-sustainance.
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Re: Is life only a system of evolving chemical reactions?

Postby claudepa » Sun Jan 24, 2016 11:14 am

I am nor a chemist nor a thermodynamician. I know only of the basic types of chemical reactions that take place in a cell. What is amazing is their number, around 1 million chemical reactions per second in a bacteria I believe (anyway a huge number). Also amazing the efficiency of the nanomachines: A DNA polymerase is able to associate thousands of DNA base pairs per second. And all this works perfectly well without interferences that we could imagine chaos would create. What about the dissipative (ordered) structures that chaos could generate if I remember not too wrongly Ilya Prygogine ?
OK a cell repeats the same reactions but it also responds to the environment through numerous signals to the membrane and then expressing the required genes. In multicellular organisms, as we are, all the DNA program of the cell is here to insure the positive role of the cell in the body. If mutations occur a whole machinery is present to correct these mutations and prevent the cell going wrong. Nothing is perfect and only when this system is overflowed will problems such as cancer occur. Thanks to Louis Pasteur we know that every cell comes from an other cell. It therefore comes from very far, 3.5 billions years, may be 4 billions say now some researchers. Nobody knows if there are several origins of cells or only one. Chemists have not yet succeeded to artificially create a cell. Even when the genes are synthetic cytoplasm and membrane are not.
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Re: Is life only a system of evolving chemical reactions?

Postby BrianEvans » Mon Jan 25, 2016 5:25 am

To be more specific, life is self-propagating information capable of detecting environmental conditions and responding to them. The chemistry of biological systems is a tool through which these responses are expressed. Some chemical arrangements, like lipid membranes, are used mostly for mechanical reasons like durability and polarity. Others, like neurotransmitters and receptor proteins, are employed because their interaction follows a specific algebraic function and thus computationally behaves as that function. This allows the lifeform to chemically represent and analyze external information internally and respond to it.

The life isn't actually in the chemistry. It's in the genetic information that expresses a total design for a self-propagating and adapting chemical machine. This information's form is an emergent property of nucleic acid structure, but nucleic acids are just very convenient substrates on which to represent a chemical instruction set. A completely accurate translation of this information structure to another medium (such as a digital electronic representation) would be "life" just as much as the one implemented through chemistry.
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Re: Is life only a system of evolving chemical reactions?

Postby claudepa » Mon Jan 25, 2016 10:16 am

Life is in DNA ? Life is in chemical reactions ? Membrane only mechanical ? But ATP synthesis is linked to membranes! Difficult for me to know what is the most important, I mainly see that the whole system works perfectly well. In around 100 yeras of research it has been possible to identify how the system works (I consider that the discoveries of these 100 years are absolutely extraordinary, and even the discovery of cell existence is not so ancient in the history of science) . But DNA without proteins to read it is like a tape without tape recorder. And without DNA, no proteins. Researchers speak of a precellular RNA world where RNA would have had at the same time both the functions of DNA for information and of proteins as executive agents. But again this is only speculation. When chemists will (or if they succeed) succeed to create such chemical autoreproducting assemblies of molecules it will be much more convincing.
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Re: Is life only a system of evolving chemical reactions?

Postby minasole » Sat Jan 30, 2016 7:26 pm

BrianEvans wrote:The life isn't actually in the chemistry. It's in the genetic information that expresses a total design for a self-propagating and adapting chemical machine. .

What about prions? They don't seem to have no genetic information at all.
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Re: Is life only a system of evolving chemical reactions?

Postby claudepa » Sat Jan 30, 2016 10:16 pm

Good point with the prion. It is autoreproducible without nucleic acid. But then it is a question of definition of life. Prion as well as viruses could probably be chemically synthetized. At this time it seems very difficult to do it for a cell. If we should define life as all organism composed of cells, including ones with only one cell, (not the usual definition!) the question would remain unsolved. Furthemore it seems that the actual theory is that viruses are very old but appeared after cells. There are therefore presumed as a product of cells.
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Postby minasole » Wed Feb 17, 2016 11:36 am

This is only a problem of semantics. I dont see why prions are not living material. They are excluded from our definitions because they don't fit our DNA models of life. But my prediction is that more such entities (non DNA) will be discovered in the future. At this moment, prions are only different from the rest of life on the fact that they are a much more simple set of chemical reactions...
Biology in theory can be reduced down to chemistry, which can be reduced down to physics, however, things grow tremendously complex and its not worth it.
On the other hand, I think that mathematical models cannot apply to biological systems that easily. 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, etc, etc....Moreover, they can be manipulated until they work.
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, 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.
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Postby chemnorm » Thu Feb 18, 2016 9:25 am

What an interesting topic
http://www.chemnorm.com :lol:
ChemNorm-the professional Phytochemical and Natural product R&D service provider.
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