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I was contemplating all night whether I should get involved in this topic or not; but I feel like there is a small amount of misunderstanding of what the current Evolutionary theory states (contrary to popular belief the theory has changed a great deal since Darwin first proposed the theory), and so I thought I'd chime in. I apologize in advance for the length, but there are a few things I'd like to explain thoroughly. If you're serious about this debate, I hope you'll take the time to read some of my comment here. Thanks in advance for your attention.

As a Bioinformaticist, my main background is in genetics and molecular Biology. And so, for that reason, I see a lot of evidence supporting evolution every day, whether it be in comparative genetics (essentially using computer programs to compare genomes that are now sequenced to one another), or the study of microbial strains of bacteria.

One only needs to watch the development of a strain of bacteria when under selective pressures (that is, put in an environment that allows for the selection of some characteristic which is beneficial to survival in that environment) to see the underlying mechanism of evolution at play and see how the strain's characteristics will change very quickly. Because Bacteria reproduce at a very fast rate, it is much easier to follow these changes. A good example of this can be seen when a strain of bacteria that is not resistant to an antibiotic can over time develop a resistance. This will only occur when this strain is put under selective pressure (that is, put in an environment where this antibiotic is present). Over time, any bacterium that have acquired the gene for resistance (either through conjugation (sharing genetic material), or genetic mutation) will be selected for, and these will be the individual organisms that propagate and divide. Therefore, over many generations, this strain will go from a non-resistant strain to a resistant strain. This will occur very rapidly (that is, in our sense of rapid), and as a result is a serious problem in Hospitals due to the heavy over-prescribing of antibiotics. If you want to learn further about this, type in MRSA (Methicillin-resistant Staphylococcus aureus) into a search engine, and you'll get plenty of results back talking about this topic.

Although this example I described occurs in bacteria, the underlying mechanism is exactly the same for every single living organism on Earth. Everything that is alive has some form genetic molecule that stores the information for life (DNA for most all organisms, RNA for viruses (although they aren't technically considered alive, they do propagate and share many similar characteristics with living organisms)). When placed in situations that favor certain features that an organism, or group of organisms, possess, these organisms will survive to reproduce.

Underneath all of this, however, is the actual mechanism: the mutation of the genetic code (in single-celled organisms, it's the mutation of the chromosome(s), and in multi-celled organisms that reproduce sexually, it's in the mutation of the germ cells (that is to say, if you get cancer in the liver due to a mutation in that cell causing for uncontrolled division, you won't actually pass on this mutation to your offspring; but if you get a mutation in your sperm or egg cells, this mutation will be passed on to the next generation). Sometimes these mutations are deadly, while other times these mutations may be beneficial and may code for some new protein that may have some effect on survival (often times, when people think of mutation, it has a bad connotation associated with it, but in evolution, "good" mutations are the driving force). Given enough time, these mutations accumulate, and when these mutations code for new phenotypes that are beneficial to survival, these organisms are more likely to survive to reproduce and propagate their genes. When you realize that the Earth is over 4 billion years old, and life itself is over a billion years old, one can see that given this amount of time, life can evolve to pretty much any form.

However, it should be noted that not every organism evolves at the same rate. This rate at which evolution occurs depends on a great deal of factors. I'll cover two factors briefly:

1) There are distinct differences between the way DNA is replicated in prokaryotes (bacteria) and eukaryotes (basically everything else alive), and this has a distinct effect on the rate of mutation. Because Bacteria are not as good at checking for mistakes in their genetic code as Eukaryotes (that is, us, humans), bacteria replication is more likely to produce mistakes (mutations). For this reason, there will be more mutations over time in bacteria, and they will undergo evolution at a faster rate (rate being over each generation, not literal time as bacteria reproduce very fast).

2) Evolution occurs at different rates for each species depending on the environment. Using the strain of bacteria that was not resistant to a certain antibiotic above again as an example, when this strain is placed in an environment where no selective pressures exist (that is, there is no antibiotics present), then there will be nothing that causes bacteria with resistant genes to reproduce more than the bacteria that do not contain the resistant genes. In other words, both types of bacteria, resistant and non-resistant will survive and reproduce at the same rate. And as a result, the overall percieved rate of evolution will not be as fast as the situation where a selective force exists. However, when this strain of bacteria is placed in an environment where there is an antibiotic, the bacteria that have the gene for resistance will survive and reproduce. Therefore, the rate of evolution will be higher here. This helps explain why certain organisms exist over millions of years with little changes (sharks, or alligators for example), while other organisms undergo evolution at a much faster rate (differences in the shape of the tortoise, or the shape of the beak of finches on the Galapagos Islands for example). The organism that have little evolution over time have little evolution because there is little in the way of selective forces being applied. On the other hand, the organisms that evolve at a faster rate into new species do so because of changes in the environment that select for more beneficial genes.

I'm using the idea of evolution of bacteria here because it illustrates the mechanisms of Evolution very well and in a time frame where humanity can witness the changes (after all, these changes take thousands of generations often...and thousands of human (or any animal) generations is a very long time). I'm sure some people will dismiss this evidence because it's happening in bacteria; but they're ignoring the fact that evolution occurs by the same exact mechanism in humans as it does in any other organism on this planet. Therefore this "micro-evolution" (as people sometimes refer to it) is occurring by the same mechanism that humans evolved.

Even so, this is just one small example of Evolution in action. There are literally mountains of evidence supporting Evolution out there, and I suggest people who discount the theory for whatever reasons look into recent research that is being done (be recent, I mean in the last 10 years for comparative genomics for example). The theory has evolved quite a bit since Darwin proposed it (by the way, if anyone has any interest in going to the Galapagos Islands, I highly recommend it; it's a truly amazing experience), and in many ways he wasn't completely right (for instance, the underlying mechanism alluded him his entire life...if only he had met a man named Mendell). We now know this mechanism to be the crossing over and mutation of our DNA in our germ cells.

Also, almost every week, a new organism's complete genome is sequenced and cataloged in a gigantic database (well, it's probably many databases, although I'm not sure). Using this information, it's now very easy (thanks to brilliant programmers) compare similarities of genomic data, and create trees showing how closely related species, or groups of species, are to one another. When these trees are created, it's very remarkable that these trees align very closely with the phylogenetic trees that were already in place previous to genomic data being known. This is just one small field of biology that is helping to further prove the theory. There are many other fields, that I'm not an expert in, such as comparative biology (comparing the features of organisms to one another (whale to other mammals, for example)) or the effects geographical isolation (when organisms that are the same species are split by some barrier, such as a new sea, become different species over time due to their new environments) that further help provide evidence for the theory.

Yes it's a theory; but if you're not intelligent enough to know what the word "theory" means in scientific terms (after all, I'm sure you'd be surprised to know that Gravity, the orbit of our planet around the Sun, and Electricity are all "merely theories"), then you have no right taking place in this argument. The theory is constantly evolving changing with each new discovery. However, that is not to say that the theory is not accepted, and it certainly is not grounds to prove that it shouldn't be taught.

Having said all of that, I'm not in any position to say whether there is a God or not, although there is nothing in science that contradicts the existence of God. I personally believe in God, but I also agree with evolution and its underlying mechanisms, and I agree with the scientific theories of the beginning of our known universe (often called the Big Bang theory). The Earth is billions of years old, and even though this an amount of time that is almost impossible for my little mind to comprehend, I do see that given that much time life could go from a pool of amino acids, nucleic acids surrounded by micelles to all the organisms that exist on our beautiful planet.

And so, at least to me, this in no way contradicts an existence of God. In my mind, there is nothing to say that he didn't set forth the Big Bang and create the universe, which eventually led to the creation of our solar system and eventually to us humans. I believe that the Universe is so large and complex that we know very little about anything; but I do feel what we know about evolution is true and supported by sound Science; and none of that sound Science contradicts the existence of God (Darwin even himself never stated in his works whether evolution meant there was a God or not).

I do not agree with Intelligent Design, for I feel it's merely creationism in disguise. If you want to believe in it, than more power to you. To be honest, I don't really care what you believe because it's a "free country" and you can believe what ever you want to believe. However, don't plan on it ever being taken too seriously in the field of Biology. Maybe if some sound proof supported by sound science that shows that Intelligent Design is true comes out, it might start getting taken more seriously, but until then I don't consider it any form of science.

I suppose a major issue I have with the theory is that for whatever reason when this topic comes up, the integrity of science always comes into question. People say "oh there's no evidenc for Evolution" or "it's just a theory" or "we haven't found the missing link, therefore it's not true" (this shows a somewhat misunderstanding of the theory because evolution is a gradual process and our point of view now is only a snapshot of the evolutionary journey...there aren't distinct jumps from species A to species B...it's gradual, and so finding the "missing link" is not really realistic). But, like I said, I don't have a problem with people believing what they want to believe, but when the overall integrity of science is put into question, I have serious qualms. I have the same issue with the Global Warming skeptics (do people really believe that scientists aren't pretty much unified in the idea that the Earth is indeed warming?) who claim that science is faulty; and if everything seems ok today, then of course everything is ok. Believe what you want, just don't question the validity of science. After all, without, we wouldn't have all these wonderful gadgets; and we certainly wouldn't be able to drive to work every day.

With that off my chest, back to what I was saying: In my opinion, the underlying mechanism behind evolution is based on random mutations (see bacteria evolving due to random mutations over time due to the presence of an antibiotic), but that doesn't mean there is no God. In fact, evolution doesn't set out to prove or disprove God...it really has nothing to do with God, and makes no mention of whether a higher power exists or doesn't exist...I think people misunderstand this often, and this leads to trouble...like I was saying before, there seems to be a lot of misinformation just in general. And I saw some here, so I chose to comment on it.

But, in the end after years spent of my own life learning about the complexities of life and evolution, I still believe in God (after all, as was quoted above, odds are you're better off believing in God, haha); and most importantly, I feel that Science and Religion can co-exist without contradiction. I hope people welcome my point of view and, I hope this comment has helped some people better understand the current theory of evolution. Thanks for reading.