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Crash Course in Evolution and What It Is

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Shane for Wax:
A/N: This was originally posted by Vene. As such all credit goes to him. I am simply bringing it over here.

So, we all know that a big part of biology is evolution. We also know that a big part of apologetics is creationism. Seeing as I have an interest in the science, I thought I might as well write up a post giving an overview of the evidence for it and explain some of the concepts. After all, I know some of the members here get into debates about it with fundies and more information is always helpful.

To start with, I might as well define a few terms so that we're all talking about the same thing. I am talking about biological evolution. The definition being the change in allele frequencies of a population of organisms over successive generations. Essentially, that the genes and traits of a form of life will change over time. There is nothing about it going for something better. As long as it changes, it's evolution. Deletion or gain of genes, it doesn't matter one bit. When I say macroevolution, I mean evolution at or above the level of species, microevolution is evolution within a species. Abiogenesis is the natural explanation for how life came to exist on Earth. Evolution explains why life is as diverse as it is, abiogenesis explains where the first life came from. Refuting one doesn't mean the other is automatically wrong.

Let's go with something easy, macroevolution. Speciation events have been observed in nature. One simple one is the evolution of the London Underground mosquito and the common mosquito. It has been shown both that they have difference overall genetic composition along with reproductive isolation (source). This is an entirely artificial environment, there is not way the mosquito could have been there to start with and it has changed to the point where even if a male and a female mate, they don't have offspring. But, the underground mosquitoes do mate successfully with other mosquitoes in the underground and common mosquitoes do mate successfully with those above ground. Even if the populations become mixed at this point, they are separate and distinct.

Macroevolution has also been shown to occur with bacterial. One of the defining traits of the bacteria E. coli is that it cannot digest citrate. Bacterial species have to be separated due to metabolism as they don't exactly reproduce sexually. What was done was that scientists took pure colonies of E. Coli, like the ones that currently live in our intestines, and grew them on petri dishes with high citrate levels, but with low levels of the nutrients they can digest. What happened is that over tens of thousands of generations (31,500 actually) a strain emerged from all of the bacteria that could digest citrate (source). Remember, this is a trait that microbiologists use to tell if a mystery bacteria is E. coli and this organism, from a colony of pure E. Coli, had an enzyme that could use it for energy. So, this enzyme is entirely new and had never existed before this experiment. Entirely new function and entirely new information.

I suppose now is as good of time as to talk about mutations and how new genes and proteins evolve. There are multiple ways that DNA can mutate. But, I think I should give a basic explanation of what DNA actually is and how it works.

DNA is a long chain of nucleotides. Different combinations of nucleotides lead to different shapes of proteins. The shape of a protein is what gives it an unique function. I know that's a very basic, but there is more to it. DNA is transcribed to make a complimentary RNA strand. DNA is a double stranded molecule, each nucleotide has a corresponding nucleotide it form a weak bond to, when it is used as a template for the synthesis of RNA. From the RNA a set of three nucleotides are called codons. Each codon corresponds to one amino acid. Amino acids are the basic unit of proteins, so altering the order of them and the ones used will drastically change the shape of the protein. So, a change to the DNA leads to changing the protein. This is the central dogma of biology (or molecular biology, or biochemistry, or genetics, it depends on who you ask). A diagram outlining the process is below.

The mutations occur whenever a cell undergoes mitosis and divides. The DNA has to be copied. During this process, errors can occur. Nucleotides are deleted, inserted, copied, and altered. One example of how this happens is with the globin proteins. The one dominate in humans is hemoglobin. Hemoglobin evolved due to DNA duplication. Hemoglobin itself it actually made out of four different domains, or strings of amino acids. The are two types that compose it, alpha and beta. A picture showing the molecular structure is below.

Hemoglobin's function is to carry oxygen through the bloodstream, but the is another protein that can do the same thing, myoglobin (pictured below). Myoglobin has a structure that is nearly identical to that of a single domain of hemoglobin. What happened was that the myoglobin gene was duplicated. This lead to the rise of both alpha and beta hemoglobin (source). These two distinct domains were then used to form the hemoglobin protein. The duplication of a single gene is also what leads to many protein families. One of them is preserved and the other can mutate without harming the organism.

Since I'm speaking about mutations, I might as well talk about junk DNA. Junk DNA is DNA that has absolutely no function. Only about 2% of the human genome actually codes for proteins and even if there are non-coding regulatory regions, over half of it is completely useless (source). There's even been studies done where sections of DNA have been removed from mice in order to see if it's detrimental (source) and it has been shown that large chunks of the genome can be safely removed. This is important for evolution because not only does evolution explain where it comes from, such as duplication events that don't grab the entire gene, it also provides raw materials for evolution to work with. Junk DNA can be drastically altered without any harm coming to the organism and novel genes can evolve from it. The odds of any given gene are low, yes, but with so many organisms and with so many generations occurring, it can and does happen. And, like the E. coli experiment showed, a successful change can lead to the new trait permeating through the entire population very quickly.

Since we know how genes arise and how they can change, it is possible to map them out backwards. And since we also know the DNA directly leads to the protein, we can do it with just proteins instead of having to look at the gene itself. This is what is done with phylogenetic maps. A protein that is common to multiple forms of life is sequenced so we know the amino acids it's composed of along with their order. The differences between different organisms can then be compared, base by base, and organized with the changes shown in sequential order. The greater the difference between the protein, the further apart the organisms are and the less the difference, the closer they are. This also has the side effect of showing that there is more than one way to accomplish a task as different organisms have different chemicals accomplish the same function. Anyways, one of the best examples of phylogenetics in action is cytochrome c. Cytochrome c is an essential part of metabolism and is present in a wide variety of organisms. The sequence of it is shown below (each letter just represent a different amino acid, don't worry about which one it means) (source).

From this data it is possible to chart out the information in an actual tree, like below.

This is one of the most powerful techniques for mapping out evolutionary pasts and trees can be confirmed by looking at different proteins. If special creation was true, we would expect different proteins to make different trees, instead proteins create phylogenetic trees that match up with each other.

I think I'll end this post with a little bit on abiogenesis, because even if it's not evolution, it's important for this subject as it leads into evolution. The science on this is still in the early stages, there hasn't been a single theory that unifies all the data. But, it has been shown that biologically important molecules can form in conditions close to early Earth. There's the Miller-Urey experiment which started showing the plausibility of the concept by making some amino acids from methane, ammonia, hydrogen, and water (source). So, the formation of amino acids is plausible at the least. Lipids, another major group of biomolecules, have also been shown to form abiotically or outside of a cell (source). Finally, the sugars and nucleotides needed for DNA and RNA have been synthesized in conditions the same as early Earth (source). There is no doubt the ingredients needed for life were present, the question at this point is only how they formed the first protocell and evolution started to occur.

This is only a small overview of some of the lines of evidence for evolution. Hopefully it wasn't too terribly long and hopefully it has some useful information for somebody. And if there's a creationist reading this by some chance, please, I dare you to refute this.

D Laurier:
Evolution: An ongoing process of imperfect genetic replication leading to ever increasing genetic diversification.
Evolution was recognized by neolithic farmers, but was not understood untill the 19th century when several researchers figured it out independantly of eachother.
Alfred Wallace, Charles Darwin, and Thomas Huxley all figured out sexual selection... And Gregor Mendel discovered genes.

You and Vene +1

I've heard this one theistic evolutionist say that Evolution is impossible with a guiding force, and cited analogous structures, such as bat's and whale's Prestin evolving in an extremely similar fashion for echolocation as a reason. I don't think it is really evidence against natural selection, but it is interesting.

The guiding forces would be the laws of physics & the situations of the environment.

The Right Honourable Mlle Ant├ęchrist:
Someone should really buy Vene a drink for writing this. Or a particle collider, which he'd probably enjoy more. Buy the man something, though, 'cause this is awesome.


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