Evolution as far as I understand it is fact. The absolute specifics of how it works in all cases are not fully established, there are certainly some tantalizing mysteries, but this is true of all theories. Maths for example holds many unsolved mysteries, however they certainly in no way cast doubt on the theory of Maths!
I think the "confusion" that has arisen in recent years comes from two primary sources; firstly I believe that there is a genuine attempt to discredit evolution by some parts of the conservative religious community (more on this in a bit). Partly this has been fueled by point two; a simple misunderstand of the correct use of the English language.
"Evolutionary Theory", a simple term at first glance that actually causes confusion. It needs to be understood that the scientific community uses the word "theory" (in this context) is a different way to the general public.
A theory is two things. Firstly, (and more commonly used by the layman) it is a proposed proposition to explain the mechanics for a possible outcome or phenomena, nothing more that a hypothesis. For example: "Theoretically if I had four legs I could run faster for longer".
Secondly (and more commonly used by the scientific community) it is a well substantiated explanation of some aspect of the natural world. For example: "Theoretically the sum of two numbers is the total of their respective individual values".
Which is Evolutionary Theory? Is it a hypothesis or a well substantiated explanation?
Well, in scientific terms it is certainly a well substantiated explanation, but to doubters it is nothing more than a hypothesis. Arguments about Evolution often boil down to this. A new word perhaps is needed? This thread should perhaps be more correctly titled "Evolution - Theory or Theory?".
So that covers my second point, the first point is a little more complex.
Some parts of the religious right (the Intelligent Design supporters) are not happy about the prevelance of evolutionary theory because it appears to rule out the role of a creator or God. For the record I for one believe this is in fact true.
However putting that aside, lets address the issues.
They claim that evolution is impossible on two grounds; "Irreducible Complexity" (or "Irreversible Complexity") and "Mathematical Probability".
Evolution of life occurs through changes by means of random genetic mutations and Natural Selection (Survival of the Fittest); random mutations affect many many tiny changes, and Natural Selection ensures that the "best" most effective mutations go on to breed and reproduce. One outcome of this is that by looking at any organism you must be able to reverse the process and sustain a viable lifeform. So, if you could take away the previous mutation the lifeform must still function. In fact you must be able to continue "removing" mutations all the way back to the most primitive primordial cellular life forms. Darwin actually cited this in The Origin Of Species, as a well respected scientist he understood that it was necessary to highlight possible flaws in his theories in order that if it were to be disproved it would happen quickly. He wrote: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.".
Take a watch for example, you may be able to remove certain "design" elements, certain evolutionary changes to the style and design of watches added over time. But fundamentally you cannot remove the essential components that make it a watch, to do so would not allow it to function and so why would such a thing exist? It wouldn't, it couldn't. This presents a "gap" in the evolutionary chain, the only way to fill this gap, as with a watch is with a designer! Case proven! Or is it...?
What is needed is some hard evidence, Darwin the worlds most foremost biologist could not find such a case, but he certainly did not have access to todays microscopic technology.
The eye is a famous example of an "irreducibly complex" structure, due to its many elaborate and interlocking parts, seemingly all dependent upon one another. It is frequently cited by Intelligent Design advocates as an example of irreducible complexity. What use is an eye in a "reduced state"? How could an eye function with one component missing? How could all the components know to evolve in the "knowledge" that when they had "finished" they would fit perfectly with other simultaneously evolving components?
However, while difficult to imagine, (even Darwin stated that the eye proposed particular difficulties: "to suppose that the eye... could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree") there are plenty of plausible explainations for
eye evolution.
The Flagella is another favourite piece of evidence for the Intelligent Design proponents. The flagella is a long, whip like projection composed by microtubes. They help propel cells and organisms in a whip like motion. Requiring the interaction of about 40 complex protein parts, and the absence of any one of these proteins causes the flagella to fail to function. How could the 40 components all evolve together with the same "pre-planned" goal? Well again, it seems that there are plenty of
theories.
Put together is becomes obvious that the evidence for Intelligent Design, isn't evidence for anything at all, it is in fact just evidence of tiny less well explained components of Evolution. Most of which Darwin pointed out himself 150 years ago.
The second component of the Intelligent Design argument "Mathematical Probability" is not an argument for Intelligent Design at all but a badly constructed criticism of Evolution based on Mathematical Probability.
It goes something like this; the chances of complex life evolving are so remote that it should be considered impossible. If you try to calculate each step in reverse then the probability of this occurring is pretty much zero.
This argument however is flawed for this reason: If you enter a lottery, say you need to pick 6 correct numbers from a possible pool of 50 (as is the UK lottery) then your chances of getting it right are somewhere in the region of 14 million to 1. But at the end of the day you will always pull out 6 balls. You always end up with a set of 6 numbers. If you look at the draw in isolation you can say the odds are amazing, yet you always end up with a result.
Now if we were to draw all the balls, all 50, the odds of any particular order are staggering, but once you start, you indeed will end up with all the balls in a particular order. The odds of that order maybe 1 billion to 1 but the chance of you successfully drawing all the balls is pretty much a certainty.
Once you pull the first ball, you start the draw, once life starts, you have to end up somewhere, whatever the odds.
So, having dealt with the minuscule amount of "evidence", "against" evolution lets take a quick look at the basic evidence for evolution:
1) Survival of the fittest or more correctly "Natural Selection". The process by which individual organisms with favorable traits are more likely to survive and reproduce than those with unfavorable traits. Proven without doubt, millions of documented pieces of evidence, constantly peer-reviewed and accepted. Sometimes refereed to as a tautology - that is, it is so obvious that it does not need explanation, something along the lines of: "Out of the two options the best option is the best one". The strong survive the weaker do not. The strong pass on their genes the weaker do not. Lions catch and kill the weaker Wilderbeast, only the Peacocks with the finest plumes get to breed, only the strongest sperm reaches the egg.
2) Random Mutation or more correctly "Variation" is the process by which change happens. The AIDS virus is extremely difficult to kill because of its ability to mutate randomly and quickly. If you introduce and anti-viral AIDS drug into a patient it may kill off 99% of the virus but the 1% of the virus that contains mutations that make it less vulnerable to the drug will survive and multiply, again taking over the victim.
3) Replication or Reproduction. Replication occurs this isn't up for debate.
When thes three componets all work together: Selection, Variation, Replication you end up with evolution, its rather hard to draw any other conculsion!
All in all, I believe that "Evolutionary Theory" explains an awful lot of what we see. Not only that, but it is also elegant, succinct, beautiful and quite brilliant. A "Theory" perfectly fitting to describe the wonder of life.