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Author Topic: Was RNA and protein assembled by accident?  (Read 877 times)

Offline Robertt

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Was RNA and protein assembled by accident?
« on: 09/04/2016 01:29:40 »
Hi,
I am new to this site so bare with me. ha
I need some much needed help, I am currently in a debate of sorts with a person and he sent me this, I would appreciate any info on how to answer it. I have a few idea's but looking for some guidance. I believe he is hinting at a god behind these things. But since science does not know all.. some cases we do, but saying god is behind it is an extraordinary claim that has no evidence to back it up. So Occams's Razor can come in and take over. But I would like to know about the subjects in question below are answered by science or rather points to science but not known as of yet.
- Cheers
Here it is:
"thank you so much for the complete breakdown of my comments but then all your points still have God filled in gaps you left wide. Tell me, the universe started by accident or external force? Proteins are made from right handed amino acids but the only one simulated in the lab is left-handed,how come? RNA is assembled by accident? Why do onions have longer DNA than highly evolved humans? Has there been any evolved tardigrades? Can a 75 million years old dinosaur soft tissue of collagen and blood vessels be that old?"
« Last Edit: 13/04/2016 16:01:41 by chris »


 

Online chiralSPO

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Re: Need some assistance:RNA is assembled by accident?
« Reply #1 on: 09/04/2016 02:16:30 »
I have some answers for a few of these...

Proteins are made from right handed amino acids but the only one simulated in the lab is left-handed,how come?

Simply not true. Like, at all. Most labs study amino acids that are the same handedness as those that occur in biology, because (big surprise) those are the ones we want to learn more about and (big surprise) those are the easiest to get because we can isolate them from living organisms. That is not to say we cannot make them on our own. We can make both the left handed and right handed amino acids from scratch in the lab, and we study both.

RNA is assembled by accident?

Hard to know exactly what the question is here. Once the nucleobases of RNA are formed, they will naturally come together to form strands. If the question is regarding how the nucleobases formed initially, I don't know the answer myself, but they are not particularly complex molecules, and many direct precursors have been observed in abiotic systems (no life involved...)

Why do onions have longer DNA than highly evolved humans?

Evolution is a process that involves adding new genes, removing old genes, and altering old genes. The length of a DNA sequence does not have much relationship with "how advanced" the organism is. As far as we can tell, there is a lot of DNA that does not encode for proteins, and there are a lot of things plants need to do on a cellular level that animals do not (we eat food, they make their own food...)

Has there been any evolved tardigrades?

There are several different species of tardigrades, and some are more closely related than others. They reproduce sexually, so individuals are genetically distinct from their parents. Sounds like evolution to me...
 
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Online chiralSPO

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Re: Need some assistance:RNA is assembled by accident?
« Reply #2 on: 09/04/2016 02:42:48 »
Also, a few comments about "god gaps"

We will always have gaps in our understanding. Whether it is biology, evolution, cosmology, or acoustics... Invoking God when we don't have the answer is at best setting religions up for failure. In the past, reilgious figures and texts have made claims about how the world works, or why things are they way they are, and have repeatedly been shown to be false (or probably not true). Questions have since come up that couldn't have been contemplated millenia, centuries or even decades ago (What does the bible say about quantum teleportation?), and we have repeatedly seen religious figures persecute the scientists, philosophers and inventors that have raised the questions they couldn't answer or provided the answers the haven't questioned.

When discussing the evolution of animals, (or any other species) our fossil record is very sparse in some regards. We don't have an obvious map of the evolutionary tree from one fossil to the next because there have literally been billions of generations, creating countless different variations from one organism to the next. Our own taxanomic differentiation and classification of species is imperfect and imprecise. And if we go by fossil record alone, every time a new fossil is found that links one organism and one of its ancestors, two new gaps are formed (we went from the AB gap to an AC gap and a CB gap).

This also holds for the gaps at the ends of our understanding (rather than between things we understand). Well what's smaller than X? Y is smaller than X. And what is smaller than Y? Z is smaller than Y.... What's bigger than X? W.... What happened before that, and what happened before that, etc. etc. etc.

The scientific process is all about asking these questions, but it also involves looking for the answers. Unfortunately the religious approach has often been one of "we already know--God did it. Case closed!" And it's fine if people don't want to open their own minds to the miraculous world that we live in--even if God did it, don't they want to know how? But I take issue with those who would draw the wool over others' eyes, even if it is their own children.

But now, I have to go light some candles, bless some wine and bring in the shabbos...
 
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Online evan_au

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Re: Need some assistance:RNA is assembled by accident?
« Reply #3 on: 09/04/2016 09:12:33 »
These do sound like questions from a Theistic ("Creation Science") viewpoint.

Most scientists would say "Who created the universe?" is not a scientific question, and cannot be investigated by the scientific method.
Which is interesting, because Richard Dawkins tries to prove scientifically and logically that God does not exist.

The Creation Science organization.
  • Do have contributors with scientific training
  • Validly raise the little mysteries that current research has not answered (yet) and which scientists do not like to discuss in public (perhaps because they may lose their aura of omnipotence - or perhaps because it requires people to think too hard?)
  • Imply that because scientists cannot answer these questions, then their alternative version must be correct.
  • In this sense, the argument of Science and God is a political debate, often with as little credibility as the soundbites currently assaulting our TV sets. 


Addressing the questions raised:
Quote from: Rob itswich
Tell me, the universe started by accident or external force?
This is one of the Big Questions: Where do I come from?
Scientists are using big and expensive tools like the Large Hadron Collider to simulate processes which may have occurred closer and closer to the Big Bang. But this incremental scientific process doesn't tell you what was before the Big Bang, or what caused it.

You can be sure that scientific researchers will try to push forward with even bigger and more expensive versions of the LHC, and searches for gravitational waves and neutrinos from the Big Bang.
But each incremental answer will always leave the infinite regress "...and what caused that?".

Quote
Proteins are made from right handed amino acids but the only one simulated in the lab is left-handed,how come?
Proteins are assembled from 21-odd amino acids; all but one of these (glycine, the simplest) are chiral. That is, they come in "Left" ("L") and "Right" ("D"!)-handed versions.

With some rare exceptions (like antibiotics, and some scent proteins), proteins from all known living things on Earth come in the "L" version (this convention is reversed for sugars).

Chemicals formed from non-living precursors tend to appear in equal quantities of "L" and "D" versions. It is hard to see how you could form functional proteins from this "racemic" mixture. In fact, some of these "D" amino acids seem to be toxic to the organism which ingests it.

So this is one of the outstanding mysteries: How can (predominantly) "L" proteins form from an (almost) equal mixture of "L and "D" proteins from a non-living source?

There have been examples found that can bias the concentration of L and D proteins. Some meteorites have been found with unequal concentrations of L and D. Scientists have come up with lots of theories, but no solid proof, at this time. 
See: https://en.wikipedia.org/wiki/Chirality_(chemistry)#In_biochemistry

One of the problems with research and discussion on the origins of biochemistry is that any examples of early biochemistry were probably eaten by more modern types, leaving no evidence to discover. 

Quote
RNA is assembled by accident?
In life today, RNA is produced by complex proteins, which are produced in the complex ribosome, following detailed instructions from RNA (and usually, DNA too).

The question is: how could the detailed and precise instructions appear in RNA which are needed to produce the complex proteins to create the ribosome which can produce the complex proteins which produce RNA (or DNA)?

It seems like a circular argument.

Scientists have come up with lots of theories, but no solid proof, at this time. 
See: https://en.wikipedia.org/wiki/Abiogenesis

One of the problems with research and discussion on the origins of early life is that any examples of early life were probably eaten by more modern types, leaving no evidence to discover.
   
Quote
Why do onions have longer DNA than highly evolved humans?
Here there is an implicit appeal to human pride, and a slur on the humble onion.

According to evolutionary theory, every living thing is highly evolved to fit into some ecological niche.
  • Some of those niches might need more DNA than other niches.
  • And some of those organisms may just carry DNA that it doesn't need at the moment, but may be useful if the environment ever changes (and the environment is always changing). 

Quote
Has there been any evolved tardigrades?
Tardigrades are amazing creatures! They survive in environments that would kill most other organisms, even exposure to the vacuum of space on the ISS!

Similar to the previous item, biologists think that tardigrades are highly evolved (and will continue to evolve for as long as they survive).
 
Quote
Can a 75 million years old dinosaur soft tissue of collagen and blood vessels be that old?"
This group takes the Bible as a complete account since the beginning of creation. Counting up the ages of the people mentioned in genealogies ends up with an age of about 6,000 years. So they are look for evidence that the Earth is young.

This question refers to the discovery of soft tissues in dinosaur bones. Normally soft tissues will degrade fairly quickly after death, and you would expect them to be gone after 65 million years (unless they were hermetically preserved in amber, for example). This question is used to suggest that the dinosaurs are not nearly as old as the timeline accepted by scientists.

You can find an account here: http://creation.com/dinosaur-soft-tissue
(You may need to click on the link twice, as they present a welcome page on a first visit...)

In my experience, such discussions usually produce more heat than light, and rarely change deep-seated beliefs on either side.
« Last Edit: 09/04/2016 09:15:25 by evan_au »
 

Offline puppypower

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Re: Need some assistance:RNA is assembled by accident?
« Reply #4 on: 12/04/2016 12:19:28 »
The living state is a result of the co-dependency between water and organics. Water creates the potential that induced the single handed helixes. As a simple visual example, water and oil don't mix. If we try to blend water and oil, they will phase separate into two separate layers. The net affect is water causes the organics of life to lower entropy; separate out of solution. For example, water also causes proteins to fold with exact folds. This eliminates folding randomness; it lowers entropy.

Left handed or right handed only helixes is an extension of entropy lowering. Instead of two equal helixes, the reduction to one helix lowers global entropy.

Because life is composed of lowered entropy structures, induced by water, this creates an entropy potential with the environment; lower than the environment. The result is life needs to increase entropy, but in dynamic ways, like metabolism, so the sum of both  follows the second law; entropy of the universe has to increase.

If both helixes were used, the metabolic potential would be much lower, since there is less entropy potential. The disorder in two helixes, instead of one, would count for part of the needed entropy.

Much of modern biology ignores the impact of water and models many thing in terms of organic only. Organic does not offer a good explanation. making some people assume divine assistance; gods of chaos and chance.
« Last Edit: 13/04/2016 11:45:45 by puppypower »
 

Offline puppypower

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Re: Need some assistance:RNA is assembled by accident?
« Reply #5 on: 13/04/2016 13:45:37 »
If you took a cell and removed its membrane, potassium ions will still accumulate inside the cell, even though the cation pumps, used to concentrate potassium ions, have been removed. The reason is, the protein of the cell and the potassium ions have the opposite affects on the water. The potassium ions accumulates in the cell water to help cancel out the impact of the protein on the water,  allowing the water to return toward its native equilibrium.

Water hydrogen bonds to itself, with hydrogen bonding unique in then sense it is a binary bond showing both covalent and polar bonding characteristics. Potassium ions add disorder to the water shifting the binary of water toward the polar side. Protein pack wth hydrophilic groups on the surface. This tends to favor the covalent aspect of water's hydrogen bonding. The accumulation of potassium in a naked cell, adds polar induction affect to offset the higher covalent protein induction affect, so the balance is able is able to get closer to pure water. It is not magic since there is an enthalpy and entropy difference between the polar and covalence states of hydrogen bonding in water. The offset is being driven by free energy considerations. 

Many scientists have suggested that the pumping of cations; potassium and sodium, is not needed but rather is like a fail safe, since the cells don't need these pumps to accumulate potassium. However, in my humble opinion, the ATP intensive pumping of potassium is being used to force non equilibrium, in the cell water; inducing the constant need for changes in the organics. The ions pumps force a free energy imbalance in the water. Water has it own goals when it comes to chemical selection.

Ion pumping is that one singular change, in the pre-cell, that would have impacted all cellular structures. Potassium pumping would force all the protein to act as a counter measure, so the water can achieve balance. The water will select certain protein and will extrude the rest. The fact that left handed protein are bio-active means that these are more countering to the free energy pressures of the potassium ions on the water.


RNA and Water

There are two type basic types of long chain RNA. One type is used to make ribosomes; rRNA. While the other type is used as templates for protein; tRNA. These roles are not interchangeable, even though both are made of RNA monomer materials. The key difference is the  length. The difference in length have different impacts on the water, and therefore different impacts on what water will need to do for an offset.

The mRNA does not just merge with protein, but it merges ribosomes. While rRNA will directly merge with protein. Each defines a slightly different potential in the water, requiring different tweaks by the water. 

To explain how; the DNA is the most hydrated molecule in the cell. The DNA contains more chemically bound water than any molecule in the cell. in fact, the DNA contains a double helix of water in the major and minor groves of the double helix. The pinnacle hydration of the DNA is why it came last; long term goal. 

If we compare DNA to RNA, the RNA is less reduced/more oxidized; sugar difference, than DNA. Because of this, the RNA should actually define even more hydration than DNA. The DNA wins out because it is a double helix with huge size. But RNA is more potent, in terms of atom to atom hydration. However, it is smaller so it is second in terms of total hydration in one area. 

The net result is RNA, although smaller, shifts the local water in a direction that exceeds the hydrogen bonding induction of DNA, but only on a small local scale. The impact on the water is to shift the water in the nucleus in the direction of too much of a good thing. There is not a deficit in the water, but sort of a surplus. The RNA has to leave the nucleus due to the need of water equilibrium.

The net affect is the RNA (related) molecules will be used by the water to help offset deficit inductions. The larger and more potent rRNA will be used to offset the deficit of proteins; ribosomes precursors. The merger is good for the water. While tRNA offsets the residual potential in the ribosomes/amino acids.

Let me add one more thing; entropy.

In chemistry entropy is a state variable, meaning any given state of matter defines a specific entropy value. Water at 25C has the same entropy no matter who measures it. If the second law is in affect and entropy needs to increase, a new state has to form, since water at 25C defines a fixed value of entropy. This is fixed and cannot increase.

This true at the macro-scale of the water; bulk water at 25C. However, there is a second aspect of entropy, that occurs at the micro-scale. In the glass of water at 25C, are all types of atomic and molecular motion and vibration is being randomly expressed. The only constraint is the sum of this defines the fixed value of the macro-state.

This paradox of opposites; based on scale; micro versus macro, is common to liquid state physics. This is not always taught, mostly because Physics is more in charge of this and tends to define nature with gas and solid state analogies. Liquid state physics tends to be called chemistry. Based on speciality thinking and maybe union rules, liquid state physics is left out when Physics explains things. The organic only approach is an artifact of Physics thinking. It is not consistent with liquids state physics.

The impact of water on life is make life become defined by liquid state physics. What is called random changes on the DNA in biology is true at the micro-state. However, when dealing with liquid state physics, random at the micro-scale is part of a paradoxical pair, with the other aspect of the paradox connected to order on a larger scale. At ribosomes we can have all types of mRNA and amino acids merging that might even be modeled by random, but in the end these are all doing the same basic thing, wth an integrated goal in mind needed to allow life. The second law will increase entropy, which can occur at the micro-scale. But this will require a parallel change in state at the macro-level.
 

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Re: Need some assistance:RNA is assembled by accident?
« Reply #5 on: 13/04/2016 13:45:37 »

 

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