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...

Eugenics. Post (3 Pages? Psh....)

So, this week (ok maybe six weeks ago) we started a project on Eugenics (which was a minor factor in the delay of my last blog post). Eugenics is "the applied science or biosocial movement which advocates the use of practices aimed at improving the genetic composition of a population," at least according to wikipedia. In much simpler terms it's all about controlling the population's genetic makeup in order to ensure a "perfect" population. So, Lets look at the essential questions of this rather unsavory "biological science":


What were the social origins of eugenics?
 Eugenics developed in the wake of economic and social problems following the civil war. Depressions occurred every decade from 1876 to the beginnings of the 20th century. These depressions fueled a labor unrest, caused by militant labor unions and the rapid growth of american industry. Social Darwinism had attempted to explain the inequalities experienced by the lower class as "survival of the fittest", but by the the beginning of th 20th century that idea had been flipped.  Those people who sat at the top of the economy in the upper class had a declining birthrate. Meaning that they were in fact losing the struggle for existence. Not only were the working  class working and organizing against them, but they were also out-reproducing them. To solve all the new problems that came with industrialization, a new philosophy called progressivism emerged. Progressivism was all about managed capitalism- letting the government and planning have an increased role in the market. The biggest component of this was the idea of scientific management: long-term planning by specially trained university experts. This new "managerial" class would soon become important to the managerial process, science was seen as the new "cure-all" that would bring in a new era of control to nature and human society. Suddenly, the the idea that genetics explained the underlined causes of human social problems (feeble-mindedness, alcoholism, etc...) came about. These issues were said to be caused by "the inheritance of defective germ plasm", believers argued that society paid a very high price by allowing those people (who would eventually be cared for by the state) to be born. Their solution? Sterilize that "defective" adult. By doing this, eugenicists claimed that future generations could save thousands of dollars. Another problem that eugenics solved was the mutual antipathy, shared by eugenicists and their wealthy supporters, towards militant labor unions and political revolution. Both of which were seen to be caused by the large influx of immigrants from southern Europe. Eugenicists then claimed to have data that showed the problem was in their genes, effectively placing the blame in "germ plasm" and ethnic groups, rather than in the structure of society its self. In essence, they managed to use science as an excuse to blame victims for their own problems. Basically, eugenics offered the prospect of a smooth transition to a better future, and a method to attack social problems at their roots.

What were the scientific origins of eugenics?
In 1883 Francis Galton coined the term eugenics as a moral philosophy to encourage the healthiest, and most able people to have more children. His version is known as "positive eugenics". Negative eugenics supported the removal of the weakest members from a population. Needless to say the negative version was favored more...The idea of segregating people deemed unfit to reproduce dates back to antiquity. Concerns about environmental influences that could damage heredity were formalized in the 1700's as "degeneracy theory". It would maintain a strong following up until the 19th century. Onanism was presented as the first cause of degeneracy in medical schools. This fear of degeneracy through onanism prompted prison doctor Henry Clay Sharp to carry out vasectomies on prisoners beginning in 1899, later resulting a law that would make it mandatory in Indiana. Benedict Morel's work extended the causes of degeneracy to include poisoning by toxic substances. Richard Dugale believed that  good environments could turn a degenerate into a worthy citizen through three generations. He conducted a study (The Jukes, 1877) to prove this. In the 1880's August Wiseman's theory on germ plasm managed to convince most people that changes to the body tissues (the soma) had no effect on the reproductive tissues (the germ plasm). So, naturally this theory was favored by negative eugenics. Go figure..  Most basic scientists would shun eugenics as vulgar, but their contributions to the field of genetics would be absorbed by eugenicists. Eventually, Mendelian analysis would be part of most eugenicists backgrounds, as would agriculture where most eugenicists were present [like the american breeders ass. (ABA)]. Evolutionary models would also contribute to eugenic theory, with fears that the smarter families would have less kids than the degenerate families due to welfare supporting these people, which upset the role of natural selection. Soon even medicine hopped on the bandwagon, with doctors advocating medicine and programs to deal with degenerates. Most would argue that sterilization was the best plan for dealing with degenerates. With vasectomies and tubal litigation as the preferred methods because they did not alter the physical or psychological contributions of reproductive organs as well as saving the state money by not having to institutionalize them.

What research methods were used to study eugenics and what were their flaws?
At the core of eugenics was the was a research effort to apply Mendel's laws to the inheritance of human traits. Eugenicists examined family pedigrees to determine the inheritance pattern of a trait, and then score family members for the presence or absence of that trait. They succeeded quite well on the first half, as large families were easy to spot patterns in, but scoring members was especially difficult due to the complexity of most traits. The main problem here was that researchers were lax in defining the traits they were studying. Most of the traits (mental and behavioral) they were looking for were subjective, so the diagnosis was often mishandled, corrupting their data. The second issue with their research was that they often treated large complex issues as if they were caused by one thing, and not multiple variables combining into one issue. Data was also affected by poor survey and statistical methods. Most researchers got their information from second had sources and heresy, due to to a lack of good medical records. Also, when presenting results, eugenicists were VERY biased, using their data to falsely exaggerate claims. False quantification also plagued researchers. For example IQ tests that were dependent on cultural knowledge were given to immigrants under a wide variety of conditions, and were counted as official evidence that immigrants were feeble minded.  To simplify it all, the research that was done was biased, not properly administrated, and to many variables were left open.

How did eugenics research impact American society?
Eugenics had a very large negative impact on American society. In a period of changing times, marked by industrial revolutions, and an influx of immigration. Eugenics promoted racial in equality, social inequality, and a sense of hatred against the lower class in America. Numerous rights of people were violated with the passing of marriage laws (preventing people from marrying outside their race), sterilization laws (forcibly sterilizing those with "bad" germ plasm), and the immigration restriction that would result from studies showing that they were bad for the population. The affects of American eugenics could also be felt across the world, with German leaders (on trial for war crimes Nuremberg) citing American eugenicists as the inspiration behind Hitlers purification laws, and the eventual genocide of the Holocaust.

DNA-My Model, and an gentle explanation

Recently in Biology we have been working on a rather fun concept: DeoxyRibonucleic Acid otherwise known as DNA. So, I made a model of it on Google Docs (*cough* tech savvy 4 *cough*) in order to study for the DNA quiz last week.  So here goes my explanation of DNA's structure, and what it all means...

Double Helix (Fig. 1)

At the base of DNA are little cornerstones known as nucleotides. A nucleotide is made up of three pieces a phosphate (the white circle), a five carbon sugar (deoxyribose, the black pentagon) and a nitrogenous base (one of the colorful weird pieces in the middle). Nucleotides first join together by connecting together the front pieces sugar with the second pieces phosphate creating a single chain. The second place that nucleotides link together, to create a double chain (Kiel's brand new descriptive word of the day) is in the middle linking two nitrogenous bases together. The only condition with nitrogenous bases connecting together is that A (Adenine) bases can only link with T (Thymine) bases and C (Cytosine) bases must link with G (Guanine) bases. It is that pattern of bases (read three at a time) that are the genetic instructions used in the development functioning of all living organisms. The flat structure shown above, in real life, is twisted into a double helix (fig. 1) and get wrapped around a protein in the cell (but, thats way above the scope of this post). (fig. 2).

DNA wrapped around a DNA-Binding Protein (Fig. 2)

Meiosis, Mitosis, Reproduction...and everything else I've been to lazy to post about.

If you couldn't tell by the title of this post, I've been slacking quote bad with my biology posts (Damn you stumble upon.) These past 2 (3?) (4?) weeks we've been covering Meiosis, Mitosis, Stemcells, Cloning, Reproduction, and Genetics. Which means it's time for another series of blog posts to cover all the information. So the official topic of this post will be "How Cells Reproduce" and "How a baby is made (ish)."

How Cells Reproduce, and Make Babies. Its Magical.

Once upon a time, you were a cell. As a cell you couldn't move, breathe, talk or hear, but the one thing that you could do is reproduce, and reproduce you did. Starting as one cell and then doubling exponentially until you ended up as a body with 50-75 trillion cells. The processes that control how that original cell is made, and how a person is made from that cell are some of the most important and intricate process in biology.

Disclaimer: 

Now the first thing that I should explain is how the cell cycle and Mitosis work, as these will be necessary to understand how Meiosis (slightly more complicated than Mitosis) works, and how the baby duplicates its cells to grow in the womb. 

Mitosis & The Cell Cycle:

Since Mitosis is a circular cycle (seems redundant right?) Which means the new cycle starts right after the last cycle ended. Now that the last cell cycle has ended our newly created (cloned would be a more accurate term?) cell (let's call it Joe) enters the magical phase of G1 (not G6, G1, that song is just stupid). The G1 phase is all about...you guessed it, Growth! All that the cell does during G1 is get nice and big to prepare to duplicate its chromosomes. This happens in the next stage, aptly named Synthesis. All that happens in this stage is the chromosomes make clones of themselves going from 23 pairs of chromosomes (2 sets of 23) to 46 pairs (4 sets of 23.) From here Joe then enters phase G2, also known as.......wait for it.......wait for it.......wait......GROWTH PHASE TWO!!!!!!! During this phase the cell gets to a large enough size that it cannot efficiently remove waste from the insides, and get "food" in. Which, of course, means it's time to end interphase (the last three phases/stages) and enter...Duh Duh Duh......the Mitotic cycle!!!  

The Cell Cycle. Obviously.

This is where the action starts. The mitotic cycle consists of four separate phases: Prophase, Metaphase, Anaphase and Telophase. Prophase, the first phase, is when the chromosomes become visible (under a microscope) and the nucleolus magically dissolves. During this phase the pairs of chromosomes, due to their cloning, are in an "X" shape, where the original, and duplicate are crossed over each other. These pairs are joined to the cells by spindles attached to "Centromere's" 

"X" shape.

Then comes metaphase, where the chromosomes lined up across the center of the cell, across what as known as the metaphase plate, by the spindles attached to the centromeres. In anaphase this lining up pays off because, the pairs are then pulled apart by the centromeres to the opposite sides of the cells. In telophase the spindles disappear and the cell membrane starts to split apart into daughter cells.  When the cell enters the final stage of mitosis, and the cell cycle, cytokinesis, the cell splits into two daughter cells, each with 23 pairs of chromosomes. 

Mitosis-ness....In image form!

Meiosis & The Beginning of a Baby

When a mommy and a daddy love each other very much, (or 16 year old's want to get popular, yes I do hate MTV's programing) a baby is made. Ok, I'm joking. It's a lot more complicated than that. The process of cellular reproduction starts back when parents are just babies themselves. Creating a sort of never ending cycle of "which came first?" In order to create the cell that replicates into a baby, the parents must have sex cells (called gametes) to produce the sperm and the egg that join up and become a baby. Now, most people know that each cell has 46 chromosomes, organized into 23 pairs. But for a baby to be formed the sperm and egg have to have half that number (23 unpaired chromosomes) this happens through a process called meiosis. As Michael Rees, in his blog post "Cell's: They Reproduce." said:

  "First off, the goal of meiosis is to produce a cell with only twenty-three chromosomes so that it can share its chromosomes with another cell in order to produce a cell with unique genes that is then 

capable of developing into a baby of the species."  

Simply put, Meiosis is Mitosis with an extra division added on to the end, allowing you to get 23 individual chromosomes rather than the 23 pairs normally produced in Mitosis. Meiosis follow's the basic pattern of mitosis, but at the end, it adds in an extra division of the daughter cells. By adding that extra division at the end of the mitotic cycle,  the daughter cells of "Joe" do not get to go into synthesis, which then means that they don't double their number of chromosomes, which allows each daughter cell to get split into cells that each contain 23 individual chromosomes. Because sex cells each have 23 chromosomes they are able to combine into one cell with 23 pairs of chromosomes, which then divides by mitosis into more cells, which then create a baby. Simple right?