Evolution: In 30 minutes or less (ok 53 if you want to be precise..)

Due to the fact that it's the end of the quarter, and I've been procrastinating the hell out of doing any sort of constructive work in my science classes (thank you 20 page English paper, and my addiction to stumbleupon), it is finally time for me to throw  up a post that covers evolution, and standard 4 (Hypothetical Experiment Design, and trust me...my experiment is very hypothetical.) So, sit back, enjoy my ramblings, and hope I get a 4.


A friend of mine recently wrote a post about evolution. (He says "Go read it" so go..) He starts off by mentioning #Evolution. And indeed as he says, there is a long running debate going on all the time between people of differing religions and beliefs. Today however, I am not going to get into that particular debat, I am merely planning to discuss Lamarck, Darwin, Micro, Macro evolution, and how (hypothetically) we could prove it.


In 1801, when John-Baptiste Lamarck published his Theory of Inheritance of Acquired Characteristics. Right away, anyone who knows anything about evolution thinks about one thing, what Lamarck got wrong. Lamarck thought that organisms could inherit acquired characteristics. For example, if a Giraffe, throughout the course of its life, develops an extra long neck (see fig. 1) like 15 feet long, to reach super tall trees in his environment,  Lamarck thought (for whatever reason) that it would pass that overdeveloped neck directly on to its offspring.

Fig. 1
Giraffe's got long necks.

Simply put, he was wrong. You don't pass acquired characteristics, instead you pass on mutations.  That was the basis of Darwins theory. (Which has not been proven wrong yet, as Mr. Ludwig put it, the examples were crap but the theory was sound)  Because organisms pass on mutations, if those mutations give an organism a certain competitive advantage against their peers, they have a better chance of producing more offspring. Those offspring may then may have the same mutation, which gives them the same advantage over other organisms, giving them a better chance of producing more offspring (again). These offspring carry the mutation, which gives them an advantage...and the cycle continues, over and over again.

Basically that's the theory of evolution which is also called natural selection. 

The classic, case of evidence for natural selection is the story of the peppered moths (much better than salted moths) in Britain. There are two main varieties (Mrees would say Phenotypes) for this type of moth: light and dark. Before 1848, dark moths made up less than 2% of the total population. However, by 1898, over 95% of moths in industrialized areas were dark. 

The mid-1800s was the time of the Industrial Revolution in Britain. All of those factories were emitting a "crap-ton" of pollution (also called soot), so the landscape itself became somewhat darker. This meant that birds could see the lighter moths more frequently, and so the lighter moths were the ones that were eaten. The darker moths were able to reproduce, which produced more dark moths. Over a period of fifty years, the gene pool of the population changed, which simply put, is evolution.That is a perfect example of microevolution (defined as a change within a species) and there are many other ways in which this can occur.

One other way that microevolution can occur is Gene Flow. Gene Flow states that the migration of organisms has an effect on the gene pool. If two populations share an general boundary, there's nothing to stop them from interbreeding, introducing genes into the gene pool of both populations.

Now, all of the "anti-evolutionists" (see angry people on the internet) will claim that "*whine* *whine* There is no evidence for evolution, *nag* *nag*, etc..."
It turns out though that there is quite a lot of it. 


My favorite example to prove evolution is Homologies. Homologous structures are structures that are shared across many species. For example, even though a aspen tree and a daisy have very different structures that work as leaves, they both preform the same basic function. Another example of this is ears among mammals. Even though, say, a rabbit and a human are clearly quite different, their ears are built along the same basic design.

Homologies can also be found at the cellular and molecular levels, as a significant percentage of genes are shared across species. Just look at a grasshopper and a human. Although we are two very different species/creatures, almost 22% of the genes we have are the same. And that goes across the entire taxidermic chart (at least under animalia.)




Quite frankly, Mrees offers the best example of "proof" I hase seen yet: 


"First off, let's look at the fossil record. I've often been told that there simply aren't any intermediary fossils (fossils of animals that were "in between" species--they have features of both). And the more I research that claim, it's simply not true. For example, look at these fossils:

In these fossils, over a period of 50 million years, we can watch the nostrils move from the front of the skull to their current location at the top of the skull." 


To simplify everything that he said, the picture of skulls that he shows, offers an example of an intermediate species. The middle skull has features of both the original species, and the species that it would eventually evolve into (50 million years later...* Napoleon dynamite style "gosh" *)



Now for the fun part...Over the course of this post I have made mention of a lot of theories and proofs, but what does it all mean in the end to me? Its wonderful that I can sit here, and throw all of these facts and examples out into a blog, but I don't know where I stand on the issue (#evolution) what good does it really do me? 
It is my personal opinion, based on all of the facts and evidence that I have seen, that evolution does in fact exist. The only problem however is that It is impossible to prove evolution through a controlled experiment due to 
1) the enormous time span that evolution occurs over, and 
2) there are too may variables involved. 
So, I came up with a (very) hypothetical solution/experiment.


Here goes: If we lived in the book "The Hitchhikers Guide to the Galaxy" 

proving that evolution exists (or doesn't, what ever you believe) would be quite simple. If you remember, in the book, in order to find the question to life, a group of "hyper-intelligent" and "pan-dimensional" beings commissioned an entire planet (Earth) to be built. The same basic plan would apply to proving evolution. All we would have to do is:

1) Get a custom planet built on Magrathea for some lab mice (say 20 million ish)
2) Introduce a large number of lab mice to the planet (a 98/2 mix of light and dark mice) 3) Get large laser cannons that act as predators 
4) Recreate the Peppered moth example on that plannet 


The Hypothesis would be: Because the cannons kill light moths only, in order to survive, the entire population would become black over 8-10 generations in order to ensure survival. Of course, as this is a custom planet, the only natural predators would be the laser cannons, ensuring that all variables are completely controlled. In the long term, the plannet could be set up to fill with water over 50 million years, and see if the lab mice adapt to swimming over that time. The only downside that I can see is that, the dead mice  bodies could eventually affect the environment, and become an uncontrolled variable.   


Not a bad experiment right? So yeah, thats evolution, in 53 minutes. Never again will I procrastinate this much.... 

The ABC's of DNA sequencing...(ish)

Want to hear a (anti) joke?   Ok, here goes: "Abby, Bob, and Carol walk into a hospital.......and get their DNA tested for a horrible disease." Because the hospital that they walked into a hospital stuck in the 1980's they are using the Sanger method of sequencing to examine the DNA. To make a complex process rather simple, the Sanger method takes a sample of DNA from a subject, each base (A,T,G, C) is radioactively labeled (for detection later in a sequencing machine) and synthesized (copied). The newly synthesized DNA is then put through gel electrophoresis, which uses electricity and gel to sort the DNA Molecules by size and creates a visual representation on X-Ray fil, or the gel itself. (Figure 1)

(Fig. 1)

So, Abby, Bob, and Carol all had their DNA run through the Sanger process. The next step to get their results was for a "skilled" technician to write out the DNA sequence out. To write out the sequence you start at the bottom and write down the the letter that each mark represents. (the above sequence would be CGA GAT ATA etc...) Each letter represents a base, and he three letter sorting is important later on to determine the proteins that the sequence represents.

Abby's Sequence went:  ATG GTG CAC CTG ACT CCT GTG GAG AAG TCT GCC

Bob's Sequence went:    ATG GTG CAC CTG ACT CCT GTG GAG TAG TCT GCC

Carol's Sequence went:  ATG GTG CAC CTG ACC CTG AGG AGA AGT CTG CCC

In order to determine if they had the "life ending disease" their DNA sequences were compared to that a control subject (Norm) who did not have the disease.

Norm's Sequence was:   ATG GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC

To determine the likely hood of having the disease the hospital needs to create a quantitative representation of what all those letters mean, so the create a number called the percent similarity. To do this the put the number of bases that are simular to "Norms" over the total number of bases in the sequence. I took the liberty of putting the results into a pretty little graph to show how each of the patients compares to the control (Norm.).

As you can very clearly see, Bob and Abby have a very simular (96.45%) DNA sequence to the control, which would lead me to assume that they would not have the horrible disease. Carol on the other hand was not that simular to Norm, therefore I would assume that she has the disease. 

One Last Note: (for content stuffs) 

The reason that DNA is sequenced in chunks of three (called codons) because the proteins that are formed based on the DNA are created from the three letter sequences. Each set of three letters, in other words, represents a protein. To determine what proteins are made by what sequence, one has to look at a magical "decoder table." The nice thing about proteins and DNA sequences, is that the same protein can usually be made a number of different sequences, so long as the first and second letters of the sequence are the same. For example, the sequences CCU CCC CCA and CCG all make "pro" (Proline.) Which means that if a sequence is off, the proteins won't always be off. Which is the important part...