• 1Aug 07

  Molecular Evidence for Evolution

  I would like to present, what I believe to be, a very compelling argument for evolutionary theory and the idea of common descent. First however, it will be necessary to define a few terms for those of you who have not taken biology, or did not do very well in biology.

  It is vital to understand what a gene is, so we'll start here. A gene is a unit of information on a DNA molecule that is used to determine the characteristics of an organism. The gene basically encodes proteins or regulates other genes inside a cell. Which genes get transcribed (or which genes are activated) determines what the cell will be like. A liver cell will encode differently than a skin cell, ect. Each cell in our body has a copy of our entire genetic code or genome, which is the entire set of DNA instructions.

  Now, cells are constantly dividing. Even as you sit right now, the cells inside your body are dividing. Each time they divide, your genome is replicated and becomes a part of the new cell. However, DNA does not always get copied exactly 100%. These mistakes in the replication process are called mutations and they can happen for a variety of reasons. There is a base rate of mutation that occurs randomly but at a measurable average rate. Now, if one of these mutations occurs and is transfered to the next generation then that mutation becomes part of the genome of the individual of that generation.

  This is a very important concept. Inheretience is the only known mechanism to transfer genetic information from one generation to the next. With this in mind, we can infer a genetic relationship based on the mutations seen in an individual.

  For example, suppose your Grandfather was the first person to have a particular mutation and that mutation was passed onto his offspring. This would include your Father and your Uncles. Suppose someone comes up to you and claims to be your long lost cousin. What could be used to determine if this was true? Well, if you were to compare your DNA to his, and they both had that same mutation, then that would be genetic proof that you both had the same Grandfather. Thus, shared genetic sequences imply shared ancestory.

  So we talked basically about how DNA worked and how DNA can mutate. Now I'm going to explain how we get proteins from DNA. DNA is divided up into two basic parts. Transcribed parts and non-transcribed parts. The transcribed parts are what genes are. Gene transcription is a process in which an RNA copy is made of a particular DNA sequence. RNA is very similar to DNA except that RNA can move around, whereas DNA stays inside the nucleus of the cell. To use the example from the podcast, it might be easier to think of RNA as a librarian who goes into the basement of a library, photocopies pages from a rare book, and then brings the photocopy of the book to the person who requested it. It is an exact copy of the original gene except it is made up of RNA nucleotides instead of DNA nucleotides. The RNA then travels out of the nucleus into the main part of the cell, where proteins are made.

  Now, a protein is made up of subunits called amino acids. There are twenty different amino acids that are incorporated into a protein, whereas there are only four nucleotides that make up a DNA molecule. Obviously a 1:1 ratio of nucleotides to amino acids is impossible. The solution is that each nucleotide strand is divided up into three units called codons. For example, suppose there was a gene that had the nucleotide strand of AGCCGCATCGCA. It would be read as AGC CGC ATC GCA. This creates the possibility of 64 different codons that can be used to create an amino acid ( Four nucleotides, three units: 4^3=64). This means that there are multiple codons that coorspond to the same amino acid. For those interested, here is a chart of codons to amino acids:

  

  Now, different amino acids behave differently. Some are electrically charged, some have no charge. Some associate well in water, others repel water. The behavior of each amino acid comes into play when determining the final product: a protein molecule. A protein will fold up into different configurations depending on the amino acids that are used to make it. All of this folding causes each protein to have a different appearence, or structure. It is this structure that determines what the function of that protein is going to be. This is important to remember, structure determines function.

  This piece of evidence is going to deal with what is called protein functional redundancy. Proteins are essential for life's functions. However, there are certain proteins that are more essential than others. These proteins perform very basic functions that are required for all organisms to live. These proteins are called "ubiquitous proteins". All organisms have these proteins, and they do the same thing no matter where they are found.

  As the protein post that I wrote earlier talked about, the function of a protein is determined by its structure. In much the same way that a pair of scissors cuts things because of the structure of two blades and a pivot point. Now, because the function and structure of a pair of scissors is so basic, it's not difficult to make modifications to the structure and have them still retain the function of cutting. You could made the blades out of iron, steel, or bronze. You could make the blades longer, shorter, sharper, or duller. Hopefully you get the point. You can make a wide variety of scissors and they all keep the same basic function of cutting things.

  A protein is the same way. You can change the way a protein is made up without giving up its basic function. Remember, proteins are made up of a chain of amino acids. This is the important part, you can create separate proteins that have the same basic structure, but have a completely different set of amino acids strung together. So, for any given protein, there are many different amino acid sequences that are functionally redundant.

  So what does all of this have to do with the evidence for evolution and common decent? Well, as I said before, there are proteins that are so essential to the basic functions of life that they can be found in every living organism. Their function is absolutely necessary, and as previously mentioned a functional protein can be made up of many different chains of amino acids strung together. Ubiquitous proteins are also functionally redundant in terms of amino acid sequences.

  Cytochrome C is one such ubiquitous gene ( which are what create proteins ). It is found in all organisms, and is essential for cellular metabolism. Many different amino acid sequences have been shown to fold up into the basic structure required for Cytochrome C function. Experiments in yeast show that if you remove the yeast's own Cytochrome C protein and replace it with another organisms Cytochrome C that it works just fine. A study was published that there are in fact 10^93 different possible amino acid sequences for Cytochrome C. To put that number into perspective, there are more combinations of amino acid sequences for Cytochrome C than there are atoms in the universe. Needless to say, it would be possible for every single organism alive today to have a completely different amino acid sequence.

  However, this is not what the evidence shows. Comparing the human genome with the chimpanzee genome we find that the amino acid sequence for Cytochrome C is exactly the same. When the human genome is compared to that of other mammals, you find that there is only a difference of about 10 amino acids. The chances of this happening without shared heredity are about 1 in 10^29. Compared to organisms that are the least related to us, outside of bacteria, you find that there's only about a 51 amino acid difference. The chance of this happening without shared heredity is about 1 in 10^25.

  This evidence shows that the amino acid sequence of a ubiquitous protein has a greater sequency similarity than would be expected by chance, thus it supports the idea of evolution and common decent.

  Sources

  Evolution 101 Podcast

  Evidence for Evolution

  • Posted Aug 1, 2007 2:54 pm PT
  • Category: Science
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• 1May 07

  Thread Topics

  Something that occurs on the forums that gets kind of annoying are people who tend to complain about a particular thread topic.  This is especially prevelant with religious topics.  The people that I'm referring to are those who feel the need to post a comment that is nothing more than whining about why the topic even exists in the first place.  The main thing that I wonder is, if you are not interested in the topic, why bother clicking into the thread in the first place.  Below is a screen shot of the off-topic forum as of the time of this blog entry.

  

  It seems to me that there are a wide variety of topics that one can choose from.  So, really, what point is there in going into a thread you clearly do not like and making a post that has absolutely nothing to do with what the topic is about.  Even if there was no off-topic thread currently available that peaked your interest, you always have the option of creating your own thread.  I just don't get it, and more than likely I never will. 

  • Posted May 1, 2007 8:33 pm PT
  • Category: Rant
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• 13Sep 06

  Free Will?

  Cause and effect. It is this very simple concept that is one of the foundations of the universe as we know it. Causality is a relationship that exists between events. All events have a cause, and all events create an effect. A cue ball has the effect of putting the eight ball into a pocket, and it was caused by someone hitting it with a cue stick. It is this relationship between cause and effect that has me questioning the validity of free will.

  A wanderer is traveling through the woods and he come to a fork in the road. He can either go left, or he can go right. According to the idea of free will, he could choose one direction just as easily as he could choose the other direction. In other words, the original cause begins inside the mind of the wanderer and is not the result of any preceding effect. If one is to believe in free will, then one has to abandon the idea that the universe is governed completely by a cause and effect relationship.

  If, on the other hand, one believes in cause and effect then it seems very difficult to reconcile that belief with free will. If the choices that we make every day are the result of preceding events, then can we really say that we have free will? After all, prior events made it impossible for any other decision to be made.

  Free will and causality. Is it possible for these two concepts to be compatible with each other, or are they mutually exclusive?

  • Posted Sep 13, 2006 8:23 pm PT
  • Category: Other
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