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WereKitten said:

So the fact that random mutations selected in a non-random manner can result in building complexity bottom up is something that can amaze and can go against superficial intuition. I can understand that, but a lot of things go against superficial intuition and don't meet the same kind of resistance because they don't touch the sphere of religious beliefs.

Quantum mechanics is based on the hypothesis that reality works with complex numbers. That's horribly unintuitive as it gives some reality to imaginary numbers: every high-school student was probably shocked when a number that squared gave minus one was introduced.

Still, people use lasers every day, accept to be scanned with CAT devices, use appliances based on semiconductor-based diods and transistors. Everything born from quantum mechanics.

That's because they don't have to face the complexities of the underlying theory and its harsh unintuitiveness. They can just use the black box and accept the theoretical work made by physicists and engineer. They won't even try to confute the unintuitive parts of the theory if they are exposed to it, they'll just admit that it works but it's beyond their grasp.

The trouble of evolution by natural selection, on the other hand, is that it seems such a simple idea that everybody think they can understand it fully and quantitatively and mature an informed opinon on it without deeper studies.

One of my pet interests is procedurally generated worlds relating to games.  I have an interest in such things.  I am interested to see the boundaries by which unguided systems can evolve and produce more and more.  Like, can such a system produce a world that would be confused with something created by someone.  As of now, it appears that unguided procedurally generated worlds seem to need a lot of help to get there.  And the work to get one going that produces decent enough content, isn't being done.  I am sure if the video game industry could find one that was sufficient, it would rely on it and not hire level developers.  Unguided development just doesn't feel right to people.  You can even look at unguided game worlds, and see what the Alan Wake developers ran into, where they had to abandon the sandbox, because it wasn't generating results that felt right.

And this is connected to the discussion on evolution.  Natural selection is insufficient to explain how complex functioning systems got there.  Natural selection doesn't add any new features, it merely cuts them out.  What is needed is to understand the mechanics of how features got there.  And there is some work done, but a LOT left to do.  Until this is done, there will still be the gap, and what seems normal to say someone engineered it.

What is being found, particularly in the area of "junk" DNA, is very interesting.  Consider this segment from an episode of Nova, on switch DNA: http://video.pbs.org/video/1503825140/

There is also indication a species may collectively guide its own evolution, in that it can have systems in place that have the mutations be guided so it can adopt to the environment.  For all we know, viruses that circulate among species may actually be part of the genetic make up of that species, and be used to provide the species feedback on what is happening in the environment.  It could act a bit like "white blood cells" and end up culling out genetic code which isn't suitable for the environment the species is currently in. 

There have been experiments run where a species of bacteria rapidly was able to rapidly adopt to a new environment at a rate that wasn't in keeping with random mutation.  It was found that the species of bacteria (I believe it is e coli and I believe someone named Carnes ran the experiment) would be able to switch from one state to another.  Pretty amazing.  I will let others look into it.  I think I am spellined "Carnes" wrong so I can't seem to find it.  I believe Darwin in the Genome goes into it:

http://www.amazon.com/Darwin-Genome-Molecular-Strategies-Biological/dp/0071378227

I also would close here by saying that I believe that there is a lack of understanding by the Evolutionary side to what creationists now say.  Creationists today aren't part of the old Scopes Monkey Trial crowd that says every single species was directly shaped by God.  The argument now is that classes of species are bound within a certain range, and can't jump without help from intelligence on the outside.  That is the debate here, and that is an area that evolutionary scientists are still working on.  There are gaps in understanding the mechanics.  Like, when how the eyeball came about, there is things that aren't even suitable as hypothesis that are proposed, for which there aren't any experiments to be able have a species create an eyeball out of nowhere, or the order by which it would bring in all the components.  In this, there is merely postulations on stuff that sounds reasonable, where each step would work like this:

1. A species develops a "sensor" that can detect light.

2. That sensor then receeds into a socket of a sort.

3. The sensor then begins to get covered with a film that protects it.

4. The flim that covers it begins to refine itself and act as a lens

5. The sensor then beings to grow and duplicate under the lens

6. From here, you then have more refinements that are advantageous, and then BLAMMO there is an eyeball.

Now, is there any science that shows this step can actually happen with genetic code, and whatever else exists in a species?  Nope.  No one even knows how to begin testing this postulation.  Yet, you have Dawkins and others saying that it is possible and plausible, so it make sense.  The drive is to blind the watchmaker, so we can completely not deal with watchmakers ever again... all in the name of showing how to create an eyeball that can see.