I, personally, have very little background in physics compared to most other scientists. I am fairly young, so I suppose that is to be expected. I still can't help but be perplexed with what seems to me as over-complicating the system. These are just my thoughts on the matter. Feel free to correct any errors. I'll blame my ineptitude in the field and my youth.

Are DNA mutations random or purposeful?

Evolution is change. Changes that occur during DNA replication and because of radiation exposure all have chemical causes, and I think that at the very least some portion of them are random, if not all. Not all genes exposed to the same radiation will mutate, but certain mutation catalysts are more likely to affect certain genes/enzymes than others. It is arguable that DNA has a mechanism that scans its own DNA before it replicates and makes small changes purposefully, but from everything I know, that is unlikely. DNA makes mistakes that are not beneficial more frequently than beneficial ones. When we talk about say, brown bears moving north and evolving into polar bears, it's likely that the cause of the gene mutation was environmental (not meaningful, a chemical difference) since more than one animal had to have had this mutation upon birth to procreate and overthrow the brown bear, it's unlikely that the change was 100% random.

Randomness is not necessarily the way we think it is. If we introduce a set of genes into a new environment, with a different chemical make-up, it isn't odd that these slightly different chemicals could cause a gene mutation during replication of offspring. However, since not all DNA strands undergo the change, it is possibly that while they have a cause, whether or not they will occur is random; unpredictable. On the other side of the coin, every single organism has a slightly different chemical make-up, organisms that do not mutate could be more resistant to mutation because of their own nucleic chemistry. Is this natural selection? Not necessarily. An organism who passes on a stronger resistance to mutation could miss out on a beneficial mutation, while an organism with a weaker resistance to mutation could have a mutation that ends its life in the embryonic stage of life.

Is DNA scanning itself and purposefully making changes, like slightly altering Sonic hedgehog so a whale can conquer the ocean? Or are simple chemical reactions from the environment causing these genes to be more likely to mutate, and the organisms' offspring which does end up surviving more easily than those that didn't, and we find natural selection as an observation?

Is that all we are? Just a bunch of aggregate particles functioning in a meaningful system? What is energy made up off? What are thoughts made up off? What is gravity made up off? What is mass made up off?...ect

Energy itself is a lot more ubiquitous and a more intrinsic part of our lives than we usually consider. Matter is made up of energy; the ability to create a force over a distance in the universe from the very smallest event within the tiniest of particles to the very largest between celestial objects in the universe. Einstein suggested that matter such as the molecules and atoms are really very large collections of energy particles. There exist energy particles such as the photon that transfer energy between different types of matter.

Under some conditions some of these energy particles could be liberated from the atoms in different forms such as light and heat. When we feel the weight of an apple in our hand we are really feeling the weight of the energy particles in the apple. When you smash particles of matter into one another at sufficient energy levels instead of breaking apart they fuse forming new matter. In everyday life if two cars collide you get smashed up cars and pieces of cars. But in quantum mechanics when two cars collide you may end up with a bus or an oil tanker - the energy of the collision becoming new matter.

I've thought for some time that the "unexplainable forces" can be explained with the same notions that explain everything explainable thus far. Positive versus negative. Equilibrium. Particles versus anti-particles, which at some point, during the first moments of the universe's birth, particles overthrew anti-particles and began to form the universe and life as we know it. Supposedly, the anti-counterpart of energy is energy itself, but I don't believe it is quite that simple. Positive/negative does not need to be electromagnetic. We measure energy in the form of waves, so is it likely that the opposite of this wave is the negative space around it?

From observations, the constituents of the universe are:

Matter: 5%

Dark Matter: 25%

Dark Energy: 70%

The dark energy may be due to a cosmological constant that's gained enough of a reign in the vast reaches of outer space 7 billion years after the big bang in such that it could reverse any sort of gravitational contraction and set the universe into a global expansion.

If that's true, then dark energy is negative pressure, which creates repulsive gravity. The reason we don't feel the effects of dark energy is because it works over very long distances. It isn't until we compare galaxies that we see the effects. The further galaxies are apart, the weaker the effects of gravity have on them, and the stronger dark energy pushes them. This is actually the reason the universe will never stop expanding. In fact, the universe is expanding faster today than it was a billion years ago. It will continue to expand faster and faster as the strength of dark energy is increased on the galaxies.

Quantum theory suggests that 'empty' space is in fact buzzing with subatomic particles that constantly pop in and out of existence. This produces a 'vacuum energy', which makes space repel itself, providing a physical explanation for the cosmological constant.

So, what is gravity? If we think of the attraction of particles to each other, the universe pulling in on itself isn't very unexplainable, and much like a crystal forming in a solvent. Once the solute has attracted enough particles, it falls out of solution and forms its crystal and is stronger and attracts even more solute particles until the solution is at equilibrium. During this process, the solute is also being pulled apart, which is why the crystal is considered to become stronger as it "grows." Gravity then, is dependent on the mass of an object, and an objects' gravitational pull becomes stronger the more particles it attracts, exponentially. The universe trying to reach equilibrium seems to explain gravity quite elegantly.

What is mass, then? Mass is the amount of "stuff" that makes up a collection of energy or matter. E = mc^2; therefore energy has mass and at the fundamental level, there really is no difference between energy and matter. I don't really know why it seems so complicated and unexplainable. Our system clearly works so well, even with everything that we cannot observe (dark/anti's; whatever is beyond our universe that seems to make it impossible thus far to attain an equilibrium) why do we have to try to make it out to be more complicated than it is? We know that mass determines gravitational pull, we know that different particles have different charges and strengths, and can be pull apart by the anti-forces. We know that our universe has been trying to reach equilibrium since its birth, so it seems silly to me that we try to explain anything to a more complex explanation than positive versus negative.

I know it seems boring, but mass is likely the amount of energy that a collection of energy and the strength of its own electromagnetic bonds, for lack of a better term.

You see, certain forces cause certain things to behave a certain way. A pianist can feel connected to the keys on the piano but he feels an even deeper connection with the melody it produces. Yet without the keys there would be no melody except existing in the deepest recesses of his imagination. My point? You don't need the keys on the piano for the melody to exist in the imagination, but you do need them to manifest it into a reality expressed by the keys on the piano. I wonder if our perceived reality behaves the same way?
The pianist only feels connected to the melody if it is mathematically sound. If it's a horribly choppy, non-melodic string of notes, he will feel no connection to it at all. Would you know what music sounded like if you had never made or heard any before? We are attracted to rhythm, but that's because nature is rhythmic. We find patterns because there are patterns naturally. We seek equilibrium as much as the entire universe tries to attain it.

What are our thoughts? What is consciousness? Is this something that is supposed to make us special? Certainly we must realize that other organisms experience emotions, have thoughts and consciousness, and we all share a common organ. The brain. Brains are amazing, and the result of billions of years of evolving DNA. We have evolved to a point that we are asking why are we here, but it's certainly not unheard of that even a dolphin wonders that while swimming through the ocean. I'm sure many want an answer that is spiritual, but it just isn't.

Thoughts are the result of physical and chemical reactions, and neurology wouldn't be a field of study if that weren't true. Tumors wouldn't change a person's personality if chemical and physical reactions weren't the cause. Memory loss wouldn't cause a person to be devoid of thought if we had some spirit independent of this system we thrive in.

It just seems to me that all possible outcomes are held within the system. The outcomes are obviously related to the possible complexity of the system (or something else I don't know). Compromise the system and obviously the functions of a human being will be compromised. My thing is the manifestation of choice within the system and something I coined as "state of being" and its expression. I feel like its 90% reactions of the system and 10% something else....I don't know. Like the system is the bus but there has to be something driving the bus.

The problem with this logic, is that the bus driver must also have an origin, which leads to an infinite cycle of madness.

There is no reason to expect that the bus isn't driving itself. If energy is the source, it explains everything, drives the system and we only have one question... before matter, there was energy... why was there energy? How did it originate?