[Kryptid]

One cannot depend on mathematic and computer simulation, since physics game engines use the same types of math/simulation and these allow us to have infinite lives. It is too easy to stack the deck by reverse engineering the needed self serving assumptions; ends justices the means.

You seriously think that the infinite lives feature in a video game is a product of simulated physics? Either way, you can't make a broad-spectrum claim that "It's a simulation, so it's flawed". You need to point out specifically what is wrong with it. In what way does it not demonstrate the principle of natural selection and random mutation?

[Bored chemist]

Why is DNA not shown with its hydrating water in textbooks since

For simplicity.
In the same way that, for example, the reaction of  zinc with hydrochloric acid isn't shown as involving H₉O₄⁺ and Zn(H2O)₆ ²⁺

It's enough of a pain in the neck doing it for that simple case.
Showing the water in the case of DNA would just clutter things up.

[puppypower]

Why is DNA not shown with its hydrating water in textbooks since

For simplicity.
In the same way that, for example, the reaction of  zinc with hydrochloric acid isn't shown as involving H₉O₄⁺ and Zn(H2O)₆ ²⁺

It's enough of a pain in the neck doing it for that simple case.
Showing the water in the case of DNA would just clutter things up.

To me it would be more useful to show the full reality of DNA and water to young students, upfront, and then teach them starting with the simplified approach. By showing the full story in advance, youthful expectations, are more open for furthering discovery. It not like showing the water is obscene. Showing DNA without its water is perverted in terms of reality, since nobody has ever used dehydrated DNA as a template.

The problem is the analysis, even at advanced levels, never goes beyond the original textbook over simplification. Instead the overly simplified approach is increasingly fudged with statistics, to compensate for lack of conceptual validity. What was already made obsolete by 1960, has lingered for over 60 years, due to this deceptive approach. It is time to change and let nature run its course.

I can accept Darwin's theory of natural selection, since survival of the fittest will apply, whether you believe in evolution or creation. It is a logical approach for change and persistence, since utility and durabilty do make a difference, whether humans or chosen race.

Where I depart is connected to the overly simplified version of generic theory, that has been integrated into evolution, since it does not take into account water, even though genetic templates will not work without water. How does biology get away with this and why does the rest of science accept these half baked concepts as infallible? Are they all birds of a feather, providing mutual cover? The Physicists and Chemists should speak up, at the very least. But hey provide cover, for some reason.  Is everyone afraid of being black balled by peer pressure if yo point out the emperor is naked, like DNA is naked without water.

Who in their right mind can expect a theory of evoluton to work, if to leaves out a critical variable and replaces it with rolling dice; statistical oracles. That mystical spook stuff; oracle approach, has no place in science. It may be useful to big pharm, but only if they can maintain inflated medicine prices to offset the high costs of oracles.

[puppypower]

One cannot depend on mathematic and computer simulation, since physics game engines use the same types of math/simulation and these allow us to have infinite lives. It is too easy to stack the deck by reverse engineering the needed self serving assumptions; ends justices the means.

You seriously think that the infinite lives feature in a video game is a product of simulated physics? Either way, you can't make a broad-spectrum claim that "It's a simulation, so it's flawed". You need to point out specifically what is wrong with it. In what way does it not demonstrate the principle of natural selection and random mutation?

The DNA will not work as a template without water. The current theory of mutations does not take into account the water, therefore it is conceptually flawed. How can you defend  the results of a conceptually flawed theory? You have to rig the system, with statistical oracles, to make it appear conceptually sound to the untrained eye?

Let me give an example to show who this works. Gravity is based on mass and distance. This is two varible analogy of DNA and water. Say we developed a theory of gravity based only on mass. We leave out distance and empirically and statistically simulate distance, but we never reach a rational state. Throwing the ball of mass M, from Joe to John, becomes an empirical crap shoot instead of a reliable event based on a rational relationship. Then we will make this the center piece of another theory, such as sending a man to moon. This wishful application will require using a game engine so it appears to work like a charm for funding solicitation.

Don't let your feelings about me get in the way of common sense and reason, since I can be irritating and frustrating. A scientist will maintain cool reason and common sense, and not be controlled by emotions, sentiment and even the fear of the  black ball, if the truth be known or accepted in public.

Explain to yourself, how we can leave out, one of two main variables and expect the analysis  to be conceptually sound? After that explain how this half baked theory can now be extrapolated and become the center piece of another theory? There is no logic that can defend this. The resistance is purely emotional induced by the irrational nature of the oracles being used.

[Kryptid]

The current theory of mutations does not take into account the water,

You have to be kidding me...

What is the water supposed to do to change anything? It obviously isn't going to get rid of mutations, since all living things contain water and they still mutate.

[Bored chemist]

To me it would be more useful to show the full reality of DNA and water to young students, upfront, and then teach them starting with the simplified approach.

To you, and to nobody else.
Not to scientists; not to teachers.

Explain to yourself, how we can leave out, one of two main variables

It isn't variable.
You have, at length, laboured the point that there is always water, and that's true. Life simply doesn't exist without it.
So, it's not a variable, it's a constant.

A scientist will maintain cool reason and common sense, and not be controlled by emotions, sentiment and even the fear of the  black ball, if the truth be known or accepted in public.

A true scientist will ask for evidence.
And that's what I'm doing.
What evidence is there for this weird claim that you have to include lots of water in the drawing of DNA?

[puppypower]

To me it would be more useful to show the full reality of DNA and water to young students, upfront, and then teach them starting with the simplified approach.

To you, and to nobody else.
Not to scientists; not to teachers.

Explain to yourself, how we can leave out, one of two main variables

It isn't variable.
You have, at length, laboured the point that there is always water, and that's true. Life simply doesn't exist without it.
So, it's not a variable, it's a constant.

A scientist will maintain cool reason and common sense, and not be controlled by emotions, sentiment and even the fear of the  black ball, if the truth be known or accepted in public.

A true scientist will ask for evidence.
And that's what I'm doing.
What evidence is there for this weird claim that you have to include lots of water in the drawing of DNA?

If applied science is good enough, and an approximation is close enough, one does not have to include the water. However, if you wish to extrapolate to other areas of science, like evolution, then you need a sound pure science foundation, and not an approximation method. 

[Bored chemist]

if you wish to extrapolate to other areas of science, like evolution, then you need a sound pure science foundation, and not an approximation method.

In what way would water be important to evolution of life on Earth?
As I have pointed out, water is always there.

I'm still waiting for evidence for your claim.

[xersanozgen]

Natural selection process is a routin for other organisms except humanity. Humanity has a success  against nature about this subject. We human protect every weak peoples due to our emotional/humanly alliance of values (of course there are some  exceptions).

However, this success has caused new/extraordinary  -good and bad- evolutions for humanity. Because the candidates of natural  selection wants to generate and keep some humanly organisations for their survival. They work to be competent for sportive positions and they focus to fortune, chair, force etc. Some of them gets bad roles like animals or they may become gang.

[Kryptid]

except humanity

Despite our technology, humanity is far from immune to natural selection. There are still many lethal diseases that we can't cure.

[Bored chemist]

By the way, am I the only one who finds it particularly hard to take someone seriously when they refer to themselves as "Magister"?

[Colin2B]

....it (is) particularly hard to take someone seriously when they refer to themselves as "Magister"?

The word ‘****’ comes to mind
Oh dear, it doesn’t like T W A T
I wonder why not?

[puppypower]

Natural selection process is a routin for other organisms except humanity. Humanity has a success  against nature about this subject. We human protect every weak peoples due to our emotional/humanly alliance of values (of course there are some  exceptions).

However, this success has caused new/extraordinary  -good and bad- evolutions for humanity. Because the candidates of natural  selection wants to generate and keep some humanly organisations for their survival. They work to be competent for sportive positions and they focus to fortune, chair, force etc. Some of them gets bad roles like animals or they may become gang.

Humans practice artificial selection.

if you wish to extrapolate to other areas of science, like evolution, then you need a sound pure science foundation, and not an approximation method.

In what way would water be important to evolution of life on Earth?
As I have pointed out, water is always there.

I'm still waiting for evidence for your claim.

Water is responsible for selection at the nano-scale. Natural selection is more about bulk selection; global organics plus water equals a full critter. The role of water has been in affect since the beginning of abiogenesis, and still continues today. If a mutation is to be accepted, it comes down to the water, since water deals with the details of the nanoscale. Decisions for selection will be based on equilibrium in water

For example, protein folding is induced, by the water. Water would prefer lower its potential by hydrogen bonding with other water. Water-water hydrogen bonding, in liquid water, is energetically favorable, due to the large number and high strength of aqueous hydrogen bonding. This energetically favorable induction, will attempt to lower any surface tension with dissolved organics, thereby inducing protein folding in repeatable ways not governed by statistics. Water does not play dice with the universe. It likes sure things. Human like playing god and use dice to cover their mistakes

Depending on the amino acid sequence, this will dictate how the protein will be folded and therefore the final configuration and final purpose for the folded protein. Not all folded protein will become enzymes. Some are more suitable for scaffolding. Water will decide based on maximizing itself. Potentially new proteins, which result from changes on the DNA, which have no equilibrium spot, will be recycled. If they do find an equilibrium spot they will be accommodated.

Equilibrium in water is not just based on single protein. Proteins will also converge with other protein, as well as with RNA and DNA. These merged relationships are all based on that which lowers the surface tension in water. Packing proteins for DNA have long organic side groups with terminal charges. These are high potential in water and use DNA to lower potential.

Junk genes on the DNA make no sense in terms of coding genes. However, they play a role in terms of inducing configurational potential along the DNA. The analogy is every amino acid in an enzyme  is not directly involved in catalytic action. However, all amino acids will have some support role in the overall structure.

The water induces a global enzyme configuration with the goal of lowering water potential. This can induce tension on certain amino acids within the collective. In the case of the DNA, the junk genes are more exposed to the water, than the amino acids inside a protein. The overall DNA-protein shape although minimizing water potential, can nevertheless induce local potential along DNA which can impact the local water.

Most starter codons on the DNA use adenine sequences; AAAAA. This is not coincidence since adenine has the most endothermic heat of formation of the bases. It has the most reduction potential and will show up as a hot spot in the water; visible finger print for the enzyme, so it can combine and lower the water potential.

Natural selection, as spoke of by Darwin, deals with fully integrated things like humans or bacteria.  If a mutation occurs, science jumps right to the full human and skip all the steps in the middle. Dice throwinl allows you to gloss over the details. Water is not as caviler. But rather it deals with these details of the nanoscale, adjusting equilibrium, throughout the life form.  If non equilibrium is created it will not be selected.

[Bored chemist]

If a mutation is to be accepted, it comes down to the water,

No.
https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism

[jeffreyH]

Colin who? Never heard of him. Sounds like a wind up to me. May actually be a fake, made up person.

[jeffreyH]

Now here is a Dean I can recognise.
https://en.m.wikipedia.org/wiki/Roger_Dean_(artist)

[jeffreyH]

Poopypower, please spare us having to read all those paragraphs of drivel. Unless you have been head down in your kennel lately, you may have noticed the emergency situation we are in. Stop being a selfish *****.

[hamdani yusuf]

In terms of bacteria and virus, a random assumption could work, in terms of selection, since these tiny entities can form billions of new units; offspring, in a very small time frame. So even if 99.999% of the offspring become defective, due to random approach, the tiny fraction that that randomly  improves, still has lot of units. This approach has a chance for improving the species. But once you get into multicellular species, that breed much slower in time, with far fewer units, this theory breaks down.

It looks like you forgot to take diploidy and polyploidy into account. They provide information backup/redundancy which makes multicellular organisms more resistant to harmful mutations. Beneficial mutations can spread quickly in a population of organisms within a few generations due to sexual selection.

[puppypower]

In terms of bacteria and virus, a random assumption could work, in terms of selection, since these tiny entities can form billions of new units; offspring, in a very small time frame. So even if 99.999% of the offspring become defective, due to random approach, the tiny fraction that that randomly  improves, still has lot of units. This approach has a chance for improving the species. But once you get into multicellular species, that breed much slower in time, with far fewer units, this theory breaks down.

It looks like you forgot to take diploidy and polyploidy into account. They provide information backup/redundancy which makes multicellular organisms more resistant to harmful mutations. Beneficial mutations can spread quickly in a population of organisms within a few generations due to sexual selection.

Wouldn't diploidy and polyploidy redundancy also be conservative toward beneficial changes? The  bigger picture make take some time to develop?  Some change may not appear to later in life, such as medical conditions or overcoming allergies. Fail safe may not want to wait. 

When DNA is duplicated there will be errors in base pairing because of the speed of copying and the amount of units copied. There are proofreading enzymes that reduce the number of errors. Why did proofreading enzymes evolve if mutations are good? The proofreading enzymes are counter productive to both good and bad genetic mutations. Errors are not good, if done randomly, or else there would be no need for proofreader enzymes. If you are a poor typer like me, random errors in typing will seldom lead to something of enhanced clarity.

The next question becomes, why do some typos get past the proofreader enzymes, so as to allow mutations?  This is puzzling since typos are easy to see. Improper base pairing is at higher hydrogen bonding potential. They should all stand out like a sore thumb. As a proofreader works it ways along the DNA, it will feel these hot spots. So why let some hotspots pass so we can get a mutation?

If you use spell check as you type on your computer,  it sometimes correct you, without asking if the correction is proper. I do not type very well so you will often find odd or added words in most of my writings, due to automatic spell check. This may be what proofreader enzymes do, but in the context of some type of programing; configurational potentials in the water and on the DNA that is being proofed.

One way to explain configurational potential is with a loose analogy. Say you are editing a novel based on historical fiction that is set 100 years ago in the deep south. If you are proofing the manuscript, this historical context will have an impact on how you edit and even how you may correct the spelling of certain words. You will alter even correctly spelled modern idioms, so you can maintain historical context. A good mutation needs to build upon something that is already in place; contextual.

[Kryptid]

Why did proofreading enzymes evolve if mutations are good?

Mutations are not, as a whole, good. Nor are they always bad. In theory at least, error correction just reduces the mutation rate to some optimal compromise between good organism function and allowing for the odd mutation here and there so that beneficial mutations will pop up every now and then.

If you are a poor typer like me, random errors in typing will seldom lead to something of enhanced clarity.

That is where natural selection comes it. It edits out the mutations that are harmful to survival. Well, usually. It's also possible that a negative mutation and a positive mutation are paired and thus inherited together as a single unit. If the positive effects outweigh the negative, then selection will work to keep that gene pair and thus the negative mutation.

The next question becomes, why do some typos get past the proofreader enzymes, so as to allow mutations?

Because, (1) it's an imperfect process, and (2) there are long-term benefits from allowing a handful of mutations past (evolution).