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On the origins of life


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#1 minos

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Posted 03 November 2013 - 02:25 AM

Current definitions of life find it difficult to normally include viruses and prions without adding sub-definitions, exceptions, etc.  Viruses and prions are the simplest known organisms and one idea is to study the functions of the most simple organisms and let them dictate what is life and build a new model and accommodate it in the larger scale. As we know, viruses as living beings exist only in a changing state.

But all life exists only in a changing state and living material can be further reduced and divided till the point we have a single chemical reaction. So , life is a sum of countless chemical reactions. Obviously in the past they were much fewer so we must assume that a source of energy (sun) caused a burst of reactions in terms of number and complexity. But giving energy to increase the number of reactions just leads to mindless chaotic and random reactions. It also suggests that each organism is a system of random chemical reactions, or else a chemical mindless automaton.

This seems pretty naïve as a conception because we know that reactions follow very precise patterns and in fact, can be viewed as being directed by other complex processes and pattern driving structures. But..a) If we consider the whole living system as a unique individual entity, it seems not to have any specific pattern and B) remember who is the reference frame! YOU! Or else a sum of chemical reactions, inside the system which it judges. The cause observed by the result.

After all, what would happen in a growing number of random chemical reactions after billions of years?  A) Eventually some sticky reactions would lead to adhesion of molecules that would attract others as well, converting the procedure from diffuse to multifocal, allowing forms to be created, B) the reactions with repeatability that occur in a somewhat cyclical manner would survive in the long term, because they will not lead to a dead end and c) the reactions that will survive after billions of years  will do it because these specific reactions pose surviving capacities over other. From our point of view (perspective) B is perceived as reproduction and C as evolution. What I try to say is that even we were indeed some automaton chemical reactions, even the fact that these reactions continue to happen makes them successful to our eyes regardless of how this happened. These reactions survived and there was a history behind this.

Human position in the system can explain everything. Both life and fire are chemical reactions but fire is very simple with no functional resemblance with us to perceived as life.

Proposed experimental testing:

Due to the fact that even the most simple organisms are very complicating and their precise interreactions with the environment are difficult to be estimated, it is difficult to create an experiment to test IF living beings actually behave as chemical automatons. Here are some ideas though:

  A If a living organism is a sum of chemical reactions, then the components of food intake are the first substrates and the excreted products are the last elements. By changing the food and also the pace of feeding, one can observe the way the organism performs some functions, for instance if the organism is an automaton, in certain feeding conditions one can observe extreme outlier values. The latter won’t be observed if the organism is self-regulating (self sustained).

B) Testing if feeding identical organisms (clones) with the same food in an identical manner and under identical conditions would produce exactly the same amount of waste products plus the error factor ε, or noise, produced by various unpredictable factors. Only if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results.

The factor ε must follow a normal distribution as known by statistics.

C) If we have clones of the same simple organism and we study them into the same conditions and we give the exact food, then if these organisms are just random chemical reactions, their lifespan could be predicted as a result of multiple linear regression. The dependent variable y (or else the lifespan) would be: y=a+a1x1+a2x2+…….aνxν+aωxω+ε where ε is the error variable and x1,x2…xν the various explanatory variables and a,a1,a2…av the effects or regressor coefficients and aωxω measures the feeding speed effect.
If these clones share everything in common(e.g environmental factors, temperature etc) except the pace with which they are fed  and if we secure that actually these organisms absorb exactly the same nutrients, but differ only in the pace they absorb them, then all the parameters of the linear regression will be the same for all clones except the speed factor, or else lifespan=y=aωxω+B+ε (where B=a+a1x1+a2x2+….avxv and it is the same for all organisms), or else we have a simple linear regression. Thus, if we avoid extremes in feeding pace and we assume no collinearities caused by it, then at a certain pace range we would expect lifespan to be linearly correlated with the feeding pace. (ATTENTION: The regressors x do not represent the reactions, but rather represent  the effects of some “x” factors. Once again, if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results. I agree that it is difficult to completely isolate the system from all possible disturbing factors, but if their influence is chaotic and random for all experimental individuals, i think that their influence as a total can be satisfactorily represented by ε , or else the error term or noise in the formula of the final linear regression.

D) One can also test the way the living forms and their functions are decaying when they move to more hostile conditions on earth, such as extreme temperatures, deep ocean etc. Do they decay as if they where random chemical reactions or in an other way, e.g. self-sustaining organsms?

 

 



#2 bob1

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Posted 03 November 2013 - 11:54 AM

And your point is???

 

All your experimental designs are completely untestable, and as such unscientific...



#3 minos

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Posted 15 November 2013 - 07:12 AM

Maybe my experimental designs were unsuccesfull, but i call anyone that can contribute, to propose his ideas.
Also, I am looking forward to listening your opinion about the theoretical concept.
 
If you attempt to study in details the physiology of a system in human body, for instance acid-base balance from the kidneys, etc, what you get is millions of properties that even a lifetime is not enough for you to learn everything. The most amazing thing however, is that everything is arranged perfectly in a way that even if a single property was different, the whole system would have been in real trouble. Everyone knows things are complex regarding animal (and plant) physiology, but a real study will make you realize that things are much more complex that you have ever even imagined. 
And my question is: How tempting it is to simply assume that all these procedures are random and they gain a meaning only because we (the final result) are the reference frame (e.g the observer)?
This is mostly self evident,but experimental clarification is needed.


#4 minos

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Posted 22 November 2013 - 08:34 AM

Take for instance Krebs Cycle. It is insanely complex! And it is only one cellular process. If you add all the reactions in the human organism, i don't know if the days of earth would have been enough even if one novel reaction was created every single day! What is funny though is that we are the ones that study the process. For observers not involved in the living system (e.g. a space rock), Krebs Cycle reactions are only meaningless reactions...

I want to ask you your opinion.

Are these reactions extremely sophisticated, or we have a case here in which the causes are observed by the result?



#5 bob1

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Posted 23 November 2013 - 11:55 PM

There's nothing novel in this thinking - it has been around at least as long as people have been thinking about the possiblity of extraterrestrial life.  How would we recognize a silicon based life form? for example.  Check out Carl Sagan's books for more.



#6 Greame

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Posted 06 January 2014 - 01:02 PM

The reality is that evolution and creationism are one and the same. Everything is constantly being created, and that creation is always something new and different. Nothing stays the same, not even for a split second. We feel a need to break down and label every single aspect of creation, but the reality is that the term “is” is the only label we need. Everything just is, exactly as it is, in every single moment. Everything influences everything else, and what everything becomes is dictated by what everything currently is all together. Anyway, I really like the post and enjoy the thoughts you share. Keep on sharing great posts!



#7 minos

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Posted 12 January 2014 - 01:48 AM

bob1:

well, as i see, we agree that our specific perception (caused by the fact that we ourselves are reactions)  influences the way we perceive biological phenomena and in extreme cases we can even blur the limit between life forms and simple chemical reactions, especially when they are not close to our own way of functioning. Moreover, as i explained in the beggining of this post, even complex random reactions can be perceived as sophisticated if the reference frame is the result of these reactions. In this case we don't we assume that life is just a sum of chemical reactions spontaneously and randomly occuring on earth, and its only us that get tricked due to our position inside the system.

Simple as that!! No need for smart genes, selfish genes, meteorites, primrdial soups, RNA world and other non working theories.

And apart from the answer it provides to our questions, this is also a knowledge with practical

 meaning. I will explain:

If life is a system of random reactions, this means that genes are only a part of the system of reactions, not the starting point. This explains why till now there have not been developed any gene therapies, as was expected. Replacing a gene rarely fixes everything. Molecular therapies in cancer were also marked with limited success despite high initial expectations. We see lately that tumor cell-stromal interactions are more important that any single tumor cell genetic deregulation. This also means that even second generation sequencing will provide only modest benefit in treating diseases, despite the enthusiasm. Not to mention the limitations in regenerative medicine and life extension research if the random chemical reaction system is the true one. Waste of time, especially for the latter.

Only the whole mapping of reactions can significantly alter the future of humanity and technological leaps during the last decades convinces us that it is only a matter of years. All other efforts are doomed to limited success!



#8 bob1

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Posted 12 January 2014 - 11:55 AM

Possibly you were referring to Greame's post rather than mine...  However:

 

The definitions for life as we know it are relatively constrained - it must metabolize, be self-replicating, homeostatic, self-organizing, adapitive and respond to stimuli, but this still doesn't easily include things like viruses (which most people would recognize as life forms), but does exclude things like prions (thought to be chemical reactions).  Your thought that we are tautologic, is as old as Descartes (Cogito ergo sum), but still doesn't exclude those models we have for the origins of life - all of them assume that there was a random start to life!

 

The fact that we can see the same result every time we trigger a certain gene (in isolation) means that there is indeed hope for gene therapy (there are a few that work in mice, but it takes an incredibly long time, 20 years or more, to get them through regulatory environments.  We have many that work in plants!), the major problem is that we just don;t know enough about the total environment, and have few means (yet, they are coming) of working with the multivariate systems that all cellular environments are.  So the fault is not with how we perceive our chemistry, but rather that we just haven't developed the tools far enough, and as yet don't know enough about all the reactions that are going on (investigate the expansion of the "omes" such as the proteome and metabolome, in biology lately)



#9 minos

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Posted 22 August 2015 - 03:30 AM

A chemical-reaction-only theory of life indicates that life is a sum of chemical reactions that are happening arbitrarily and spontaneously. This means that we would expect that the entropy of the system of reactions both as a whole and for particular organisms to be increasing constantly, albeit the external sun energy that this open system receives.

But this is in contrast with our long held belief that living beings are characterized by order, and thus a lowering entropy state (see ideas of Schrodiger). But is this really the case?

 

For instance, for a nonliving object, such as a stone, all the reactions of living beings are meaningless. A stone only perceives a chemical unordered chaos. On the other hand, weare what we are because of some properties of these reactions. Hence, through our perspective, there is a lot of order there.

For this reason, if we want to re-examine if entropy of living beings during evolution is actually increasing or decreasing, we must abandon human-created terms such as “order”, and instead check-out for entropy changes using more objective tools such as “heat release”, etc etc.

For instance, I am not sure if life as a totality is characterized by an entropy decrease during , or what happens to an isolated leaf or a baby during its lifetime as it is getting older.



#10 phage434

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Posted 22 August 2015 - 05:49 AM

I think you need to find a few good books on thermodynamics and learn about entropy.



#11 minos

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Posted 30 August 2015 - 07:43 AM

According to the common viewpoint, life is an open system that interacts with external energy. The mainstream viewpoint is that this causes a decrease in its entropy, enabling life to emerge on the first place and to sustain itself, thus avoiding chemical chaos. In return, the system releases entropy to its surroundings so that the 2nd law of thermodynamics is not violated.

 

The common view that the origin of life is characterized by accumulation of order, as order means lower entropy.

 

However, the term order can be very subjective, as an object non involved in life such as a rolling stone can say that it sees no order or no meaning in living systems’ chemical reactions. Just chaotic chemistry. So lets just leave order on the side and calculate entropy changes directly.

 

Does the entropy in living systems actually increase or decrease? If it increases, is it doing so in a pattern that suggests an arbitrary system? Although I am not a physicist I will welcome suggestions on how to calculate changes in the entropy of life over time.

 

Here are some simple approaches: Forgive me for any mistakes…

1)Does the life-associated heat production increase or decrease over time and how? Can life-associated changes in temperature be calculated?

2)Since chemical systems with higher entropy are characterized by increased gas production, does a life-associated gas production increase over time? In a system of decreasing entropy, one would expect a declining life-associated gas production…

Any ideas:?



#12 minos

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Posted 10 September 2015 - 06:25 AM

 
 
Question: If we let alone a cell in an isolated box, the result will eventually be a chemical mixture and not the organized cell. The final disordered mixture is more entropic than the the organized cell. Doesn’t this prove that lowering entropy is a hallmark of life and every organism spends an amount of energy to increase its order?? 
 
Answer: Not necessarily. The story of any individual living being actually is a journey towards gradual decay into disordered chemistry. In the beginning it’s a zygote in which so much information is disclosed about future events, patterns, etc in a very small space. So we can say that a zygote has less entropy compared to later stages. This entropy gradually increases as we become infants, childs, teenagers, adults, etc, because less and less information is carried over time…
A simple cell in isolation will indeed decay quickly, but don’t forget that cells never exist in isolation, and higher organisms are much more complex and they interact with external energy. So the fact that they don’t instantly decay doesn’t necessarily mean that they use energy to decrease their entropy. Never underestimate our inability to fully comprehend the value of huge numbers.
 I will explain:
Lets assume that a human body everyday degrades towards a higher entropic state. Lets assume for this reason, that after each day, the body loses, lets say 100 thousand of chemical reactions. Suppose we have an 80 years old man. He has lived 29200 days. This means that he has lost nearly 3 billion reactions during his lifetime. If the total amount of chemical reactions he has is, lets say 1 trillion, then after 80 years he will be composed of 997 billion reactions, which means virtually still 1 trillion. So the impact of the whole process on the chemical reaction count will be almost negligible. 
Of course, if we stop giving him food, he will degrade faster, but this is an example how can life can be compatible with a gradual loss of entropy.
 
 
 
 
Question: Isn’t a cell is much more ordered than its components?
 
Answer: A cell is much more ordered than its components, but what you forget is that a cell never exists in isolation. It owes its existence and its properties to the fact that it belongs into a more generalized phenomenon that is called life, which is an open system and interacts with external energy. 
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 2 specific molecules. These molecules will be perceived as gaining speed without an obvious reason, thus seeming to decrease entropy, as well as other known laws is such a way that it has to be characterized as an independent phenomenon that has to be studied….
 
 
 
Question: Isn’t glucose and oxygen more ordered than CO2 and water?
Answer: In order to build a house, you take the bricks and put them together. But you don’t build a cell in that way. A cell or a living being is the way it is because of the other living beings, ie because of the existence of what we call life on earth. Cells or living beings never exist in isolation.
 
Question: Isn’t it difficult to measure changes in order in particular organisms or cells? 
Answer: Yes, but if life as a whole is a sum of entropy decreasing entities, then the entropy of the whole system will be decreasing accordingly over time. In this case, the total amount of entropic releases in the environment will be changing over time accordingly. I think this can be measurable....





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