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Author Topic: Where is the evolution tree for DNA?  (Read 2167 times)

Offline Robertt

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Where is the evolution tree for DNA?
« on: 29/04/2016 03:04:43 »
Hi, I was sent this meme (attached) and was wondering what it meant and how to argue against it... Is this guy who sent the meme talking about the phylogenetic tree?

Appreciate any help. Thanks.


 

Offline RD

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Re: Where is the evolution tree for DNA?
« Reply #1 on: 29/04/2016 03:51:59 »
Atavisms are evidence for evolution in DNA ... http://www.talkorigins.org/faqs/comdesc/section2.html#atavisms_ex1
 

Offline evan_au

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Re: Where is the evolution tree for DNA?
« Reply #2 on: 29/04/2016 13:10:23 »
The DNA of every living creature records the evolution tree of DNA (or at least, it's leaves).

With a complete genome of multiple species, scientists can work backwards to estimate what this tree might look like if some of the earlier branch-points were still alive. (Earlier attempts with tracing just a single gene were somewhat random and inconsistent.)

It suggests that the Creator designed the creatures from a common design pattern held by their ancestors, as recorded in the DNA.

Now, where did DNA come from - that's a mystery.
RNA is almost certainly part of the story.
 

Offline evan_au

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Re: Where is the evolution tree for DNA?
« Reply #3 on: 30/04/2016 03:45:10 »
When talking to Christians (or Jews or Muslims), I would start with Genesis 1:24
Quote from: Genesis
God said, Let the earth bring forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so.
See: https://www.biblegateway.com/passage/?search=Gen+1&version=KJV

This says that young are similar to their parents - but not exactly identical to either of their parents.
This links to the modern idea of inheritance with variation (which postdates Darwin).
We now understand that this process of inheritance happens through DNA, and leaves a trail which is recorded in the DNA.

See: https://en.wikipedia.org/wiki/Heredity
 

Offline puppypower

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Re: Where is the evolution tree for DNA?
« Reply #4 on: 03/05/2016 13:57:57 »
DNA is the most hydrated molecule in the cell. What that means is DNA contains more chemically bound water than any other molecule in life. In fact, the DNA double helix contains a double helix of bound water in the major and minor grooves. DNA needs about 30% water by weight to be active.

RNA contains more chemically bound water per weight of RNA, than DNA, because the RNA has more polar groups to bind water. However, RNA is much smaller than DNA. Both RNA and DNA evolved based on a push by the water. Life evolved RNA first, then DNA came second which is consistent with the amount of total bound water.

In chemistry there is a concept called activity.  Activity of water is the potential for water to hydrogen bond with other materials; things will dissolve in water. The activity of pure water is defined as 1.0. As we add materials to the water, and the water hydrogen bounds to these materials, the activity of the water will decrease below 1.0. When all the water has hydrogen bonded to all the other materials, the activity is zero; 0.

Because the DNA is the most hydrated molecule in the cell, the activity of the water, near the DNA is minimal. In fact, the DNA defines the lowest water activity in the cell. The water of the cell, will set activity potentials with all the organics, attempting to make the organics blend better in water. The DNA evolved and evolves by means of the push of water, until the DNA can become one with water. This was always the goal in mind.

To predict whether DNA is the end template, or whether there will be another type of genetic material in the future, one would need to assess whether it is possible to define a template with an even lower total activity in water.

One interesting application is to compare replicating cells to cells that are not yet engaging in cell cycles. The cells that engage in cell cycles will make DNA, while those who are not, will only make RNA.

During cell cycles, synthesis is very high as the cell makes provisions for two daughter cells. All these extra needed materials will  lower the activity of the bulk water. This means less potential between the bulk water (lower activity) and DNA in cells engages in cell cycles. This means it become harder to make RNA. DNA is preferred, because it has slightly lower activity needs per weight compared to RNA.


 

Offline alancalverd

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Re: Where is the evolution tree for DNA?
« Reply #5 on: 03/05/2016 18:00:37 »
Quote
DNA is the most complex molecule in the universe

Proof, please, preferably with a numerical definition of complexity. And whose DNA?

I smell bullshit.
 

Offline puppypower

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Re: Where is the evolution tree for DNA?
« Reply #6 on: 05/05/2016 11:55:38 »
DNA is actually quite simple. DNA is a polymer that consists of a small variety of monomer units. There are only four bases, one type of phosphate and one type of cyclic sugar. Each monomer has one phosphate group, one cyclic sugar and one of the four bases. The total length of the DNA may be long, but its composition is based on the polymerization of just four sub-units.

 

Offline puppypower

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Re: Where is the evolution tree for DNA?
« Reply #7 on: 07/05/2016 13:37:59 »
Let me infer a few things about the DNA from its basic repeat units, which are called nucleotides. This is show below. All the repeat units have the phosphate and the cyclic sugars. The main difference are the bases, which can be one of four, which is shown below the first diagram.





I would like to focus on adenine. The heat of formation for adenine is the most endothermic of the four bases. What this means is adenine is the most reduced. In the cell, water defines the lowest chemical potential in the cell; floor, with adenine setting the highest potential with the water, relative to the fours based on the DNA. Since the DNA is dissolved in water the impact of the adenine, is to add the most potential to the water of the four bases.

The starter zones on the DNA, used to initial the transcription of genes, make use of repeat base patterns that contain a lot of adenine. Adenine is used to make the starter zones "hot" so they are easy to find by enzymes. I use the term "hot" in the sense of energizing to the water.

It is not coincidence that adenine is also the base used for ATP, which is the main energy molecule of life. Life uses this "hot" base for energy. The other bases can also be used but these are cooler.

If we compare tRNA (transfer RNA) to rRNA (ribosomal RNA) both of which are made on the DNA template, since tRNA is smaller, these areas on the DNA have more adenine rich starter zones, per unit length of DNA, than does rRNA. This means that the area of the DNA, used to make tRNA are hotter. Junk DNA, is even cooler than the zones on the DNA that make rRNA. The net affect is the adenine distribution on the DNA, concentrated as the starter zones, allows the DNA to define potential gradients based on three zones; "hot, warm and cool". These gradients are expressed via the water, and are reflected in the " heat" of the hydrogen binding of water. 

As an analogy, say we have a tank of water with a heater. The heating of the water will set up a convection, as warm water rises and cool water sinks. Next, say we add ice cubes. These will set up their own convection as cold water sinks and warmer water rises. Say well also add warm water balloons for an intermediate convection. In terms of the DNA, the gradients between "hot" , "warm, and "cool" is expressed by material convections, which have the impact of balancing the potential in the water. The DNA is fixed, but the water is changeable based on other things. In evolution, even before the bells and whistle of modern cells were defined, the gradients would help define a selection process with respect to what works to cool the DNA.

ATP is a "hot" molecule. The diffusion of ATP, defines it own convection, seeking "cool" areas, such as the -OH zones on enzymes. During cell cycles the amount of ATP produced by the cell will rise. This causes the entire cell to get warmer and then "hot". This change will not only cause equilibrium material changes to reflect the "heating", but it also makes the DNA become hotter. One way to heat the DNA, is with improper base pairs. When the bases do not base pair properly, potential is added to the DNA.

The question becomes, is this directed? The defects that form on the DNA are mostly corrected by proofreading enzymes. These enzymes will move along the DNA and stop at the improper base pair ; hot spots. The enzyme changes the DNA to cool the water. For an improper base pair to persist, the proofreader somehow needs to ignore the "hot" typo. One way to do this is to make the local water cooler, from outside, so the improper base pair does not look hot to the proofreader.

As an analogy, say you were writing a novel and an editor is reviewing it. You may purposely add some bad spelling because the character talks that way. You don't want the editor to change this misspelling, since it has a context in the story. You need to warn the editor in advance. It comes back to gradients and convection using the water itself; cool water shroud. Now the editors does no think you are a poor speller
 

Offline Trish Maynes

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Re: Where is the evolution tree for DNA?
« Reply #8 on: 18/05/2016 14:11:34 »
I think this article would help... doi: 10.1126/science.aad2808

 

Offline evan_au

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Re: Where is the evolution tree for DNA?
« Reply #9 on: 18/05/2016 23:20:51 »
Quote from: Puppypower
Let me infer a few things about the DNA from its basic repeat units
I agree that it is valuable to look at the detailed structure of DNA. But the OP is asking "where did this come from"?

But if you only look at the detailed structure, you miss out on higher-level functions like genes and chromosomes, and epigenetic control over gene expression. And the OP is asking "where did this come from"?

Quote
The question becomes, is this directed?
I think this is the question that was driving the OP.
 

Offline puppypower

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Re: Where is the evolution tree for DNA?
« Reply #10 on: 19/05/2016 13:40:13 »
DNA is the most hydrated molecule in the cell. The high degree of hydration of the DNA means the DNA is very water friendly, and therefore exerts low potential with the water.

As an analogy for the evolution of the DNA, picture water quickly flowing in a stream. If we add a bunch of odd shaped stones, water will tumble and abrade the stones until they all become smooth. As they become smooth there is less and less turbulence for further erosion. DNA is the smoothest stone in the cell.

In terms of a chemical explanation, if we burn any and every organic material in the cell, in the presence of oxygen, water will be one of the final two products. CO2 will also be a product, but the CO2 is a gas that has limited solubility in the water. At the temperatures of life, the final accumulating product of combustion in the cell is water.

In terms of the cell and life, water defines the energy floor of the cell. The high degree of hydration of the DNA implies that the DNA exists fairly close to this energy floor. DNA is very stable due to its low energy.

The DNA was always meant to be, since its structure is uniquely designed to exist near  the water floor. In terms of evolution, since all the organics set a potential with the water; can be burnt to water, the water constantly works on lowering the organic potential, with the DNA the smoothest stone in the stream.

RNA actually has more hydration per unit of weight, than the DNA. However, the RNA is smaller than the DNA. The DNA has the most hydration due to its huge size.

When RNA forms on the DNA, smaller molecules form that are even closer to the water energy floor. The movement of the RNA, into the cell reflects the needs of water. The RNA acts like an organic surrogate for water, to help the higher potential organics that remain average better in the water.

It is unlikely life could remain stable in any other solvent besides water. The reason is, most organic solvents have more potential than the DNA. They would act like an energy ceiling and not an energy floor for the DNA. Such solvents, like alcohols, will attempt to lower the potential between itself and the DNA, causing the DNA to gain energy, altering the DNA into something less stable. Water is unique in that it is the energy floor for all organics, and can therefore induce the most stable template; lowest energy. 

The only other solvent for a comparable energy floor, might be CO2. However, to obtain the liquid state of CO2 needed for life, reaction kinetics will be slow. Also the RNA and DNA would need to be replaced with a different type of template molecules that have binding sites for CO2, which is not part of any simple chemistry. The hydrogen bonding of water makes life simple and strong.
 

Offline puppypower

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Re: Where is the evolution tree for DNA?
« Reply #11 on: 20/05/2016 13:51:29 »
To better understand how water is the straw that stirs the drink of life, we need to look at hydrogen bonding. The DNA, RNA and protein, to name a few, all make extensive use of hydrogen bonding to determine their bulk secondary, tertiary and quaternary structures. These structures are an evolutionary concession to the potential of the water energy floor; makes the organics come closer to the water. 

Hydrogen bonding is a unique form of chemical bonding. Hydrogen bonds show both polar and covalent bonding characteristics. As a polar bond, the hydrogen bond tries to get as close as possible, to lower the charge potential. While as a covalent bond, the bond spread apart for better overlap of the covalent bonding orbitals; magnetic addition. 

The net affect is a hydrogen bond has two sweet spots, that define minimal energy. One make the bond  closer; polar, and one makes the bond farther; covalent. Ice expands when it freezes, which is unique to water (and antimony). In water, this is due to the bulk of the hydrogen bonds expanding to form the lower energy covalent bond.

The covalent state of the hydrogen bond is slightly more stable, than the polar state of hydrogen bond, with a small energy barrier between the two states. The result is a hydrogen bond is a binary switch. This switch is far more flexible than semi-conductor memory. The two states of the switch are more than just on or off. Each state defines differences in enthalpy, entropy and volume, with the change in volume, as water moves between states, able to exert pressure and do work.

For example, say hypothetically, we have all the binary switches of the hydrogen bonding of water set to polar. This gives us higher entropy, higher enthalpy and lower volume in the aqueous continuum. Say we add organics and then flip the switch to covalent; water gels. The covalent state cause the water to expand, exerting pressure on the organics. There is also a drop in entropy and enthalpy. This gives off energy and restricts the organic; specific shape (entropy state).

Conversely, say we have pure water, which is a distribution of both states. We have an organic molecule dissolved and diffusing in water. The water can locally change its binary switches to reflect the potential that the organic exerts on the water. The local water binary will define information about the organic though the switch profile. Organics typically increase the potential of the water, therefore the water binary goes more polar. The water contracts to squeeze out the organic.

In cells, the surfaces of protein tend to accumulate hydrophilic groups, causing the local water binary switches, in contact with the protein surface, to go more covalent. If we add this affect, with the diffusing organic molecule; glucose, the two affect tweak the potential of each other. The organic will see more covalent due to the enzyme that fixes it shape. While the enzyme sees more entropy; shape shifts slightly; lock opens.

The net affect is everything in the cell impacts the global water average and is defined locally by information in the local water binary. The water average, in turn, impacts the local organics. The transmission of information in the water is the fastest form of information in life, since there is no need for diffusion or structures to break bonds. The hydrogen bonds can simply vibrate between the two states. When anything enters the cell, the water reflects this and is  talking to the DNA; relay information.

Since the DNA is close to the energy floor, it tends to induce the covalent state of the hydrogen bonding in the local water; cooperative hydrogen bonding. Since most organics tend to add energy to the water, there is potential with the DNA; polar impact the covalent, which changes some of the switches on the DNA; getting the DNA ready. Water is like the aid that preps the general before his staff enters. The aid works behind the scenes with his finger in every pie to provide the best information. He also has the consent of the general to expedite anything. This includes helping the general change tactics if needed; new information.



« Last Edit: 20/05/2016 14:01:19 by puppypower »
 

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Re: Where is the evolution tree for DNA?
« Reply #11 on: 20/05/2016 13:51:29 »

 

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