Fraggle Rocker
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There's a whole thread on that.
Denial of Evolution V
- Thread starter Hercules Rockefeller
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Try synthesizing an enzyme or protein from a gene and you'll find a veritable plethora of algorithms Nature has handed down.
Not "in the beginning". The cell wall evolved to nurture and protect the nucleus.
Says who?
And you mean "evolution". Cells evolved.
Sure it is. That's what one of the essential qualities of Brownian motion, which one of the essential processes affecting spontaneous precipitation of reactants out of solution.
You mean in cosmology? In biology, specifically in understanding evolution, it's a fundamental working principle. Why would you say otherwise?
But this is not a cosmology question, so how does it pertain to evolution of life?
Indeed all science must be thrown out if our only goal is to dismiss it through epistemics rather than to apply it in order to understand nature. Oh, wait, that's why we study science, isn't it.
And no, many scientific endeavors are specifically directed at understanding particular random processes.
Evolve upward from chemicals to any life form.
Let me see it.
====================
Evolution in a test tube
Sunday, 21 February 2010
by Wilson da Silva
SAN DIEGO: Can life arise from nothing but a chaotic assortment of basic molecules? The answer is a lot closer following a series of ingenious experiments that have shown evolution at work in non-living molecules.
For the first time, scientists have synthesized RNA enzymes – ribonucleic acid enzymes also known as ribozymes - that can replicate themselves without the help of any proteins or other cellular components.
What’s more, these simple nucleic acids can act as catalysts and continue the process indefinitely.
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One thing needed for abiogenesis, that is always left out of the analysis, is the directional impact of water during abiogenesis. Water molecules form extensive networks of order within the liquid phase. Organics dissolved in water are under the constraints of this aqueous network. The result is not random but has to conform to the free energy of the water.
The impression often created is life formed from organics in a vacuum, like a gas phase with random interactions. But in reality the organic precursors of life were in water, which forms an extensive hydrogen bonded network that is even denser that its solid state.
Once the organics are in water the organics become hydrated and exist as water/organic composites. The composite has to conform to the extensive aqueous network that has free energy constraints. It is not organic in an ideal solution without bonding interactions. RNA has more attached water by weight than it does the ideal organic atoms.
For example, if we add oil to water, agitate and stop, the two phases will separate. Immediately, it is not about random interaction of oil molecules in a vacuum. Rather all the oil molecules are forced by the free energy within the water to interact in a restricted space; oil beads up. If there are straggler oil molecules, they will find the oil phase by following the free energy gradient.
If you look at water and oil, if this was an ideal solution, the oil and water would completely dissolve maximizing entropy. In the real world, the observed phase separation into two phases leads to a lowering of entropy. This is energetically possible because the phase separation lowers the overall free energy by minimizing surface (tension) energy. You gain in one way, but lose in another with the net lowering the free energy.
Since entropy needs to increase, there is an inherent push to increase entropy away from the phase separation minima. There is a potential for chemical modifications since these can allow the entropy to increase. But we are still restrained by the aqueous matrix and its free energy. There is a sequence based on lowering free energy while increasing entropy. For example, as we add polar groups, the hydration changes, so the restricted space expands.
I work under the assumption that the organics and water are equal partners in life, with water the matrix that initially led the process. For example, the simple oil/water separation, followed by lowering free energy via phosphate attachment; lowers surface energy while increasing entropy. This leads to semi-permeable membrane partitions. This then leads to the aqueous entropic force. Now we have an entropy increase generating a directional force.
With osmosis we can control the level of aqueous entropy by putting pressure on either side of the osmotic device. Reverse osmosis allows us to lower water entropy. A simple pressure/force at a membrane impacts the free energy of the aqueous matrix by entropy and therefore organic equilibria.
If you wish to quicken abiogenesis, all we need is crude ion pumping to tweak the entropic force, so we can have the inside of the membrane space under the influence of higher free energy.
The membrane potential makes the inside of the membrane negative due to the ability of potassium to diffuse out because of the potassium gradient. The DNA, RNA as well as ATP all contain negative charge. This situation will set up global free energy potential due to charge repulsion. Lowering this free energy moves specific materials in both directions to shield the charges. In cells configurational potentials are still in effect and are a drawback to earlier times. Stuff knows were to go simply by following free energy gradients. Later free energy is increased further by moving things to higher potential so they more active.
The impression often created is life formed from organics in a vacuum, like a gas phase with random interactions. But in reality the organic precursors of life were in water, which forms an extensive hydrogen bonded network that is even denser that its solid state.
Once the organics are in water the organics become hydrated and exist as water/organic composites. The composite has to conform to the extensive aqueous network that has free energy constraints. It is not organic in an ideal solution without bonding interactions. RNA has more attached water by weight than it does the ideal organic atoms.
For example, if we add oil to water, agitate and stop, the two phases will separate. Immediately, it is not about random interaction of oil molecules in a vacuum. Rather all the oil molecules are forced by the free energy within the water to interact in a restricted space; oil beads up. If there are straggler oil molecules, they will find the oil phase by following the free energy gradient.
If you look at water and oil, if this was an ideal solution, the oil and water would completely dissolve maximizing entropy. In the real world, the observed phase separation into two phases leads to a lowering of entropy. This is energetically possible because the phase separation lowers the overall free energy by minimizing surface (tension) energy. You gain in one way, but lose in another with the net lowering the free energy.
Since entropy needs to increase, there is an inherent push to increase entropy away from the phase separation minima. There is a potential for chemical modifications since these can allow the entropy to increase. But we are still restrained by the aqueous matrix and its free energy. There is a sequence based on lowering free energy while increasing entropy. For example, as we add polar groups, the hydration changes, so the restricted space expands.
I work under the assumption that the organics and water are equal partners in life, with water the matrix that initially led the process. For example, the simple oil/water separation, followed by lowering free energy via phosphate attachment; lowers surface energy while increasing entropy. This leads to semi-permeable membrane partitions. This then leads to the aqueous entropic force. Now we have an entropy increase generating a directional force.
With osmosis we can control the level of aqueous entropy by putting pressure on either side of the osmotic device. Reverse osmosis allows us to lower water entropy. A simple pressure/force at a membrane impacts the free energy of the aqueous matrix by entropy and therefore organic equilibria.
If you wish to quicken abiogenesis, all we need is crude ion pumping to tweak the entropic force, so we can have the inside of the membrane space under the influence of higher free energy.
The membrane potential makes the inside of the membrane negative due to the ability of potassium to diffuse out because of the potassium gradient. The DNA, RNA as well as ATP all contain negative charge. This situation will set up global free energy potential due to charge repulsion. Lowering this free energy moves specific materials in both directions to shield the charges. In cells configurational potentials are still in effect and are a drawback to earlier times. Stuff knows were to go simply by following free energy gradients. Later free energy is increased further by moving things to higher potential so they more active.
RNA is not life without the source form of the cell.
Otherwise, use the RNA on its own and prove it constructs carbohydrates naturally without a cell.
Your opinion is inconsistent with 2009 mainstream.
LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.
http://www.biology-direct.com/content/3/1/29
We therefore have a structural problem. If LUCA evolved in moderate temperatures exactly how is the creature going to construct carbohydrates?
Hint: You need electricity to crack water to create free H and O.
I am not choosing to define life in that sense.
I am saying that chemical operations only result in chemicals.
Given that fact, exactly how would one use chemical operations to cause a result that is not chemical in nature, life.
If TOE is true, then a large number of chemical operations must result in something that has more properties than simple chemicals.
Yet, this violates recursion theory.
Now, perhaps chemical operations are not as simply as we think and conduct additional properties that we cannot detect until it is full blown life.
Either way, TOE is not sufficient to explain life.
Make up your mind. Either you are choosing to define living beings, which are in physical fact large and complex assemblages of chemicals and chemical operations, to be "only chemicals", or you aren't.chinglu said:
According to you, a living being (a large and complex accumulation of chemicals, in physical fact) is "a chemical". That's what you said, above.chinglu said:
Given that, what are you asking?
You have it all wrong.
I am assuming the definitions of life and chemical operators from the mainstream.
Are you claiming I have some interpretation wrong?
I am trying to figure out what you think you're talking about, when you claim that all assemblages of chemicals and "chemical operations" are merely "a chemical", which would include all living beings, but seem to imply that "life" is not.chinglu said:
How do you separate "life" from any and all living beings?
Where the electricity comes from is water in the form of atmospheric water and lightning. The Miller experiment produced many of the simple precursors that would be needed for life. Most contain chemical energy. Carbohydrates are useful for storage, but simple life can live off simple molecules that have accumulated in the water.
After the constant storm clouds depart, and the waters of the earth has been enriched in simple precursor molecules generated from gases. Next, the sun shines and life and photosynthesis develops. I was reading after MIller died, they look at his original vials of water and found more animo acids than his instruments could see; 20 in all. The proportions might tells us what forms first.
In terms of going from precursors to simple life, water brings additional sources of free energy to the table; besides lightning.The first, which I am waiting until the fall (need some time off) to fully develop, is the entropic force which is unique to the living state. This force is demonstrated in osmosis, where an entropy increase within the water (moves from pure water to water/solute) leads to a directed force. It is actually the fifth force of nature and is a unique to the liquid state in which life exists. It allows a random movement at the micro-level to add into a bulk sense of direction at the macro-level. Reverse osmosis allows us to use a simple pressure to decrease aqueous entropy so we can load an aqueous gun with free energy. If I push an osmotic device (reverse osmosis) I can save spontaneous forward force for later, when I flip a switch.
Water also brings changes of free energy within the cell based on changes within surface tension. Picture a chain. A chain cannot transmit pressure, since the chain will collapse like a wet noodle. But a chain can transmit force, over long distances, via tension.
Picture a high tension wire, the limp chain under tension becomes more like a solid, where squirrels can stand on it. Surface tension within a liquid, such as a water and organic interfaces creates something analogous to a pseudo-phase change, from liquid (limp chain) to solid (high tension wire). This causes the aqueous entropy to fall at the surface. The water has to organize to lower free energy, but it does so at the expense of entropy, due to hydrogen bonding considerations.
Since entropy would prefer to increase, according to the second law, all we need to do is break one link in that high tension chain so the entire chain will snap, rebound, and relax into higher entropy. Water forms cooperative hydrogen bonding, which distributes the hydrogen bonding over the entire chain similar to a hydrogen bonding version of resonance. All links become stronger, however continued resonance require all links stay intact. If we break any link the entire cooperative resonance is lost and the entire chain snaps, rebounds and relaxes back to liquid with a very large increase in entropy. This will absorb energy and can pull things up energy hills.
ATP is one modern way to break one of the links in a cooperative resonance high tension water wire (more like 2-D surface wire blanket). The ATP needs to covalently absorb water to form ADP and phosphate, which is taken from one link in the surface tension chain, near the active site. The entropy snap and rebound is more powerful than the energy in ATP itself. ATP is a bolt cutter used to break a strong H-bond to generate considerable free energy via entropy.
From the point of view of a physical chemistry, very few chemical mechanisms in biology complete a realistic energy balance, since they all fail to take into account the energy needed to deal with the hydrated water around organics, especially when cooperative hydrogen bonding occurs. It is like trying to push over a tree that is attached to a high tension wire while ignoring the wire. There is not enough energy in the assumed push to do what you say. If you replace water with any other solvent, nothing works right because the cooperative aqueous free energy is no longer there we can amplify the energy we need via entropy increase.
If we go back to lighting and the precursors of life, many water molecules acting in corporation are able to generate tens of millions of volts and enough amperage to light up the night sky. Life makes use of this on a smaller scale, in the liquid state, simply because water and oil don't mix; water gains potential energy. This can be released and tapped into by life.
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I am looking to bootstrap life from chemicals.
Is not not the creation myth of TOE?
So, prior to life, all we have is some form of chemicals.
Now, we need an algorithm to pass from chemicals to life which has different properties.
TOE has no such algorithm.
If not, then TOE is not a science theory but a religion.
TOE must have an effective procedure to prove chemicals emerge into life.
ToE isn't concerned with Abiogenesis as you imply.
You are wrong.
As of 2009, TOE has not explanation for the electron transport mechanism to construct carbohydrates.
In 2009, the genome project proved the gene to protect bacteria from the heat of vents did not come until later in the DNA.
Around vents, you have free sulfur that can function as an electron transport mechanism I guess.
So, since sulfur and Oxygen at in the same column of the periodic chart, then O will do.
But, it is now the consensus that life originated in temperate climates. What is the problem with that?
Unlike volcanic vents where sulfur occurs unbound, in temperate climates Oxygen does not.
So, we have no viable electron transport mechanism to construct food (carbohydrates).
Check the mainstream on this.
I would life to see a proof of this.
I have MIT, Harvard and Oxford links that will show you are wrong.
The theory is not viable if abiogenesis is not viable.
Otherwise, TOE must rest its theory on the magical emergence of life.
Your post indicates a lack of understanding of this conversation.
Whereas, Miller could explain the construction of organic molecules, this is settled science.
We are trying to prove and construct the electron transport mechanism local to the life form.
If you think life forms can survive lightning strikes, then stand on the top of a high building in every thunderstorm.
We need a local controlled source of electricity to crack water for free H and O.
Then, we need a CO2 cracking procedure to extract a free Carbon atom.
Next, we need a factory to assemble the free C, O and 2H into a carbohydrate.
These are the necessary components of a primitive plant life form. It must build its own food.
They don't have the myth written yet. ToE is the onlyu proposed mechanism that fits all the facts, so far, but even if it continues to hold up as well as it has a great many different actual sequences are compatible with it - deciding among them remains a ways into the future.chinglu said:
And after life, some different forms of chemicals. So?chinglu said:
Living beings are completely made up of chemicals, they are "a chemical" as you put it, and all their properties are properties of the organizations of these chemicals.chinglu said:
You can verify this by following embryogenesis - the accretion and organization of chemicals into the living being.
Are you talking about some form of "life" that is not a living being made of chemicals? What would that be?
First off, your assertion that a theory of science does not have to prove its assertions is false.
TOE is required to indicate some mechanism to pass from chemical operations to life.
For example, here is a primitive form of TOE logic claiming life evolved from chemicals. Note, that the simpleton logic does not explain a redox cycle.
http://biology.kenyon.edu/slonc/bio3/origin04.pdf
We are left with the mainstream.
The adaptation to optimal growth temperature (OGT) since the Last Universal Common Ancestor (LUCA) over the universal tree of life was examined, and it was concluded that LUCA was likely to have been a mesophilic organism and that a parallel adaptation to high temperature occurred independently along the two lineages leading to the ancestors of Bacteria on one side and of Archaea and Eukarya on the other side.
http://mbe.oxfordjournals.org/content/28/9/2661.abstract
LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse.
http://www.biology-direct.com/content/3/1/29
So, we must produce a temperate plant life form that is able to build carbohydrates for food.
So, how do you make that happen?
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