How well do we understand DNA?

1. Not well but getting better all the time. Ask me again in 2 years.2. We know that some genetic sequences are more susceptible to mutation than others. My personal opinion is that the rate of mutation has evolved to match the need for it by regulating the level of susceptibility. An organism that mutated too much would have trouble finding mates, while an organism that mutated to little wouldn’t have enough variation in the bank to survive natural selection events. It is also logical that if this is the case, that a stressed population can turn up the rate of mutation by turning down the regulating mechanism with stress signals. Again, certain gene sequences could be more affected than others so you would have your random module in the sequences most likely to result in viable variations and less in the ones that would result is non-viable variations.3. Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.That’s my take on this.

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

Interesting Sylas, thanks.I don't equate expendable with junk, but rather with redundant, and I think it is entirely valid to have redundant systems that rarely get used. Those "highly conserved" sequences would certainly qualify for preserved redundancy, and this may be a secondary function of the extra sequences - to keep the "conserved" sequences operational. An offshore sailing vessel with no redundancy in it's life support systems is asking for trouble when any one of them goes down. Redundant genetic material can ensure that a match-up of working genetic sequences during the reproductive process can occur (or rather before, with the repair mechanisms, and multiple copies just means that you have a higher correlation of what is a "good" sequence compared to what is a "damaged" sequence). Or evolution has shown that variation within those sequences is not critical to {structure\life\reproduction} while still being necessary for some function within the system as a whole. This falls into the category I discussed (#2) where a species develops viable variations on a working theme ... like hair color as a raw example ... that ensure enough variations are "in the bank" to provide working answers for {survival\sexual} selection tests, while the ones that are more critical to basic viability {heart function, lung function, nerve function} are more strictly conserved.For there to be "junk" sequences in my mind there would have to be whole sequences that are regularly excluded from the reproductive process, chunks dropped regularly and randomly throughout the population, and I don't see that happening.

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

Proved to exist and proved to cause changes. The fruit fly experiments did this many years ago, recent genetic studies have shown exactly where the DNA was changed and what the change was. There are a several elements here.(1) A {somewhere\manywhere} generator of variation within the code structure itself.(2) The question of {intelligent\random} design influence.(3) The level of involvement of a designer if one is involved(4) A universe "primed" to generate variation.Working backwards through this list:(4): Certainly the ultimate "Intelligent Design" scenario is the {put the whole thing in motion with a maximum degree of variation in all aspects of the universe with the universe "primed" to develop an evolving life where-ever conditions are favorable} and then proceed from there with several alternatives of involvement in "tweaking" the design. As I have said before on other threads, ID ultimately, and properly pursued (click), has no problems with evolution working exactly as science finds it to work. I would be happy to discuss that aspect on the thread linked rather than pursue it here and dilute this discussion.(3): Clearly there is no active, highly involved, hands on designer, or there would be evidence of {his\her\their\its} many perturbations on the natural world. This means that active involvement must be very low and that means that any system involved had to be pre-wired to cover the situations to be encountered. Ultimately this becomes indistinguishable from natural systems ... as in:(2): The problem of the design question is to be able to differentiate {natural\random\unguided} design from {intelligent\intended} design when both can generate very complex and similar solutions. We see software programs now that are set up to evolve solutions to the {programming need} without the programmers needing to know how to solve the {programming need} or even how the code works once evolved.One example of such a {natural\random\unguided} design is the observed natural development of an Irreducibly Complex system. See "A True Acid Test" (click) for an article on this (wish I had a reference that wasn’t as pyric as this though). The key point in it is: Thus we have a natural development of what was touted as a clear sign of {intelligent\intended} design if not the hallmark sign. This single such result invalidates the concept of IC being a sign of ID (and it is time for the ID proponents to reject IC and develop another testable hypothesis if they want to be considered scientific).This {natural\random\unguided} design is sometimes referred to as apparent design — natural processes that results in an appearance of design even though none was involved (or where the ‘design’ selection is natural). Evolution is full of examples of apparent design, from the eye to the hemoglobin molecule to the whole DNA structure. I also have referred to apparent design as the kaleidoscope syndrome: look in one end of the kaleidoscope and you see a wonderful pattern; look in the other end and you see a random jumble of colored bits and beads. The appearance of pattern is caused by the viewpoint, and the random jumble is the reality.(1): A {somewhere\manywhere} generator of variation only needs to be a certain level of susceptibility to mutation from outside triggers, UV radiation, chemical exposure, etcetera. In other words, it can use some stress triggers as mutation agents in addition to low level constant mutation pressures. This too would account for changes in the rates of mutation when stressed. (Certainly when people are stressed they make more mistakes. :laugh

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My personal (deist) belief is that {supernatural} became the universe intentionally primed for maximum diversity and the evolution of life and intelligence in as many ways as possible with one caveat: surprise me ...Enjoy.

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

At least one of those processes, transcription errors during DNA duplication, is capable of dropping sequences, and that is all that is necessary for a stressed population with insuffient nutrients and energy levels to have an advantage in dropping the extra expenditures of protein and energy in the replication of unnecessary sequences.This to me indicates that there should be random "holes" in the genome sequences of different individuals within a total population (or even between cells within an individual). They don't have to be in any high proportion, but they should show up in a regular and persistent and randomly distributed pattern within the total {individual\cell} populations.I also do not see any special benefit to single cell species in this regard, as they don't have any more wastefull an expenditure of resources and energy as every single cell in a multi-cellular species. They are rather more likely to require all their sequences than each cell in a multicell species.This is my opinion on the matter, and we can agree to disagree until more information is available.

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we are limited in our ability to understand
by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}