Evolutionary Essay

We've all talked about the study of life before, but have we take the time to really think about how it all flows together? Maybe your theory is different than mine, maybe they're not so different. Either way we all have our own way of thinking how the evolutionary process started, and how it was found out. While doing some research of my own I came across two causes; Comparative morphology and Macroevolution.

Comparative morphology is the systematic study of similarities and differences in body plans between major groups. Scientists started studying this in the 18th century.  By doing this they got a closer look at bone structures and physical appearances of life forms. A study performed to look at comparative morphology would be to compare the pelvic structure of a manatee, but there was no need for a pelvic structure because they don’t walk.  However, they did find out that sea manatees do in fact have a ghost socket where a pelvic structure would be found.  They found out that there was in fact intermediate fossils found that gave evidence to there being such a thing as a “land manatee.”  The fossils contained many of the same characteristics of sea manatees, but their pelvic structured showed that they were able to walk!

Charles Darwin, a great scientists, embarked on a voyage across the sea to South America in 1831 where he studied the diverse life on all the different islands. When Darwin went back to England, he noticed that he had discovered some fossils of extinct animals. It wasn't until he took a good look at them that he realized that some of the new species he examined resembled the extinct animals.  He looked through his drawings and notes and noticed that not all of the species were alike, but they did show variation in size, color, and many other characteristics.  Darwin was able to formulate a theory that included variation, a huge part of Darwin’s conclusion because variation would enable the species to survive and reproduce in certain environments.  

Darwin proposed that an environment would “select” specific characteristics for a species to possess.  This is known today as natural selection. Since then, variations in traits have been shown to be controlled by genes in DNA.  Microevolution occurs when little changes in allele frequencies are brought about by mutation of genes, genetic drift, migration, and natural selection. When mutation in genes occurs, the result is a change in the DNA structure, which is heritable.  This occurrence is the source for diversity in species and organisms.  Gene flow and genetic drift is also a contribution to the diversity of things. When alleles leave or enter a population, as a result of immigration or emigration, it is called gene flow.  This idea is much like genetic drift, however, genetic drift is brought about by chance only.  This size of a population affects the diversity of genetic drift because of the fact that small populations are more likely to loose alleles completely.

Macroevolution is large-scale patterns, trends, and rates at a broader view. Examples that fall under this are fossil records, comparative morphology, and biochemistry. Scientists use sedimentary rock sequences as geological time scales to define eras and eons.  Comparative morphology uses fossils as well as existing life to form similarities that show evolutionary relationships among groups. Scientists identify differences and similarities between species on a molecular level by doing this.  They can look at how one strand of DNA pairs with another from a different species, and form some kind of an idea of the evolutionary distance between the two tested. 

In my opinion, both of these are good studies to the keys to life and evolution.  You can see time and age first, then different structures of species and compare them to modern day species. We are all the same, just look at our DNA! We must have come from one common ancestor. I think that these studies show us a lot about the world, as well as ourselves!

Gel Trays! :)

A few weeks ago we learned how to color dyes into a gel tray. We used a 40 uls micropipet to put the dye into the trays to o see what the scientest used for the different DNA and how it worked is why we used the different color dye. 


In my group we put two red two blues and one green color dyes in. All of them were solid colors but once we plug it in, the electricity will helped us determine which ones are negative and positive energy. It looked really neat watching it happen! After each dye we had to take off the tip of the yellow top because we wanted to make sure you didn't mix up the colors. 


After waiting for 5 minutes the colors started going in different directions or going the same direction.  The dye that went to the right meant that it was negative DNA and the DNA going to the opposite direction ment that it was positive :) It was a pretty neat lab!

Transformation Lab!

This lab was pretty neat! We went through a step-by-step process to figure out a different transformed version of bacteria. For instance we found out if they were more similar to the original non-transformed E. coli colonies. The genetically transformed bacterial cells were transformed after we did these steps (some pictures shown above):

1. Label one closed micro test tube +pGLO and another -pGLO
2. Open tubes and use transfer pipet to transfer 250 ul of CaC12
3. Place tubes on ice
4. Pick up colony of bacteria with sterile loop
5. Spin loop in +pGLO tube until colony is dispersed
6. Place back in ice
7. Repeat with -pGLO tube
8. Examine pGLO plasmid DNA solution with UV lamp
9. Immerse new sterile loop into the plasmid DNA stock tube and withdraw a loopful
10. Mix loopful into the cell suspension of +pGLO tube
11. Close and return to ice
12. Close -pGLO tube but DO NOT add plasmid DNA
13. Incubate tubes on ice for 10 minutes!
14. Put both tubes in water bath at 42 degrees C for 50 seconds
15. Place back in ice for 2 minutes
16. Remove and open a tube and use new sterile pipet to add 250 ul of LB nutrient broth
17. Reclose it and repeat with other tube
18. Incubate tubes for 10 minutes
19. Pipet 100 ul of the transformation and control suspension onto the plates
20. Spread suspensions evenly around surface
21. Stack plates and tape together
22. Stack and place upside down in 37 degrees C incubator until next day

When we were all done the results were pretty cool! It came out glowing all purple and what not! :) I was surprised because I didn't really think it would look all that cool, but I guess all those steps paid off! It looked awesome! :)

GATTACA Review :)

1. The following terms were used in the movie. How do they relate to the words we use: degenerate and invalid?

         De-gene-erate: Thought less of because of background.

         In-valid: Not acceptable.

         Borrowed Ladder: 

2. Why do you think Vincent left his family, tearing his picture out of the family photo, after winning the swimming race against his brother?

-I think that Vincent found strength in himself and realized his family never had any in him. He didn't want to be part of a family that never really accepted him and cherished him like his brother even though he proved (by swimming) that he could be just as good as him.

3. Describe the relationship between Vincent and Anton.

-Vincent and Anton we're always competing against each other even though Anton was genetically born with far greater DNA. Vincent was always trying to prove that he could "keep up" with Anton by playing chicken by swimming. 

4. When Jerome Morrow said to Vincent/Jerome, “They’re not looking for you. When they look at you, they only see me,” what did he mean? Can you find any parallels to this type of situation in real life?

-He was literally saying they're looking at him because he had taken his identity. They didn't want someone like Vincent to work for them because of his genetic background, but Jerome was perfect!

-You could relate this in real life as to when like NFL people are drafted. They base people on their skills and strengths.

5. Choose your favorite character from the film. Explain why you choose that person. Would you want to be that person? Why? Why not?

-My favorite person was probably Jerome. He was funny and witty, although his life wasn't so much.

- I wouldn't want to be that person based on he couldn't walk, or really have a life since Vincent took it, but I would like to have a funny friend like him around :)

6. At the end of the film, you are told that the Doctor knew about Vincent all along. Why did the Doctor go along with the fraud? What would you have done if you were the Doctor?

-I think that the doctor went along with it because he didn't discriminate Vincent because of his background. He saw that he had proved that he could be just as good as anyone when it came to the job.

-If I was the doctor I would of done the same thing.

7. The technology to do what was done in the movie is definitely possible within the next fifty years. Do you think that Vincent’s world could eventually happen in America? Why?

-Yes, it is always possible for something for this to happen when the technology is available. It would give people new opportunities, like picking your baby, and stuff like that so I think people would be open to the idea of it. 

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?

-It was wrong for society to judge and determine people's jobs based on their genetic background. Society is nothing but disgust when it discriminates. 

Sadly, it was not right, but if something like that was to ever happen, it'd most likely be accurate. 

 

9. What were the screenwriters trying to tell us through the episode of the 12-fingered pianist? Is anything wrong with engineering children to have 12 fingers if, as a result, they will be able to make extraordinarily beautiful music?

-They were trying to show us that although something as beautiful as music could be created from engineering children to have 12 fingers, it wouldn't be ultimately right to genetically transform the human structure for something so petty. Sure, 12 fingers would help, but an alternation really be necessary just for perfection? Some things are better off as is, and more beautiful natural.  

10. You and your spouse are having a child and are at the Genetic Clinic pictured in the movie. What characteristics would you want for your child and what would you ask to be excluded? Why would you make those choices?

-If I had to chose I'd of course want my child to be as healthy as possible, but besides that I don't really know what I would choose. I'd just worry about the kid's health at the moment and any other benefits he or she could have.

-I'd make those decions because bases on how society would be, it'd be best for me kid if I wanted him or her to have a bright future.

 

11. Picture yourself as either Vincent, Jerome, or Anton. Would you have acted the same or done things differently if you were in the same world as them?

-No, society made them the way they are and I most likely would of acted the same as all of them.

12. How does the society in GATTACA resemble the type of society America was during the height of the eugenics movement?

I don't really know what the eugenics movement went, so I'm not really sure :)

DNA Sequencing Activity

For Biology we did a DNA Sequencing Activity. We sequenced three different patient's DNA (Norm, Abby, Bob and Carol) in order to determine if they had any diseases. Above were my results after "cracking the code" as you might say. It displays each patient's DNA sequence as well as the proteins currently located in their bodies.


I used a Condon Usage Table to figure out how the DNA structure went from that to proteins. There were simple steps to take. For example:


To find "AUG":

1. The first base is A. Find A in the first column. Put your figure on it.
2. The second base is U. Find U in the center columns. Move your finger on this group.
3. The third base is G. Look at the last letters. Look for a G at the end.

Codon Usage Table

Here were my results after everything:

From the graph you can see that Abby had only one base change or Point Mutation. She does not have the disease because her percentile is very high and it very close to the "Norm" bases. Like Abby, Bob has the same percentage. He has one point of mutation but his is in a different base. So, instead of the potion being LYS it is STOP. This is called Truncation Mutation. Obviously Bob does not have a disease because his bases are very similar to the "Norm" bases as well.

Now, unlike Abby and Bob, Carol has more than half of her bases different from everybody. On the graph it shows that she is a 78%. She has to be the only diseased because she is the only one with a different sequence then the rest of the group! :)

All and all like I said it was a pretty simple activity, but I still learned how to do something off it. I found out that Norm and Bob have the DNA and protein sequence of the normal control, while Abby and Carol did not. All I really had to do was see if any matched Norm's for normal control because Norm's sequence was already listed as normal control. Like I said, this was a simple activity, but i still learned something :)

Its a Boy! :)

So while in the process of learning about genetics and what not, Bri and I made a baby! We decided to name him Damien Ryan Gonzales (Gonzalez 'cause Bri was the male in this project ha!) Bri and I had a really good time doing this. It was really simple to do, but anticipating the results was the more curious side of this lab. We flipped a coin to see what parts of Bri and I would be genetically given to our kid- it was tails for me and heads for her. Since I played the female in this lab and Bri played the male my symbols were XX while Bri's was  XY.

First we flipped our coin to see what gender our baby was going to be, and it came out to be Xy, which was a boy. As we continued with the list, flipping the coins back and forth, we came up with how he was going to look taking parts from both parents. A lot of Bri's and my features were the same so it was pretty easy to figure out how things would turn out. I think his features came out looking pretty good! :) Our drawings came out the same, which was good 'cause it just showed that we pictured the same kind of kid in mind. I had fun doing this project, it taught me a lot about DNA structures and how you never know how your kid is going to turn out! Just pray it isn't a ugly kid! :)

Above is a photo of the structure of DNA that Bri and myself made. The Phosphate is the white tubes and the sugar is the black in-between that connects them. The bases are:

 A= orange

 T= green

 G= blue

 C= yellow.

 And all together... 

Phosphate, sugar, base all = nucleotide!

Cloning Mimi!

In class we did an online activity having to do with cloning. The activity took us step-by-step showing how to clone a mouse called Mimi. Here's what we used and did:

Materials:

Mimi (Mouse we clone), Megdo (Egg cell donor), Momi (Surrogate mother to grow Mimi clone), Microscope, Petri dishes, Sharp pipette, Blunt pipette, Chemical to cell division

Procedures:

1. Isolate donor cells from Mimi and Megdo
2. Remove and discard the nucleus from the egg cell
3. Transfer the somatic cell nucleus into the encleated egg cell
4. Stimulate cell division
5. Implant the embryo into Momi, the surrogate mother
6. Deliver the baby mouse clone of Mimi

All the steps for this were really simple, but they taught me a lot. After isolating the donor cells from Mimi and Megdo, then removing and discarding the nucleus from the egg cell I moved on to step 3. During this time it told me that the new DNA and the egg cell need some time to adjust with one another. Basically this is supposed to take a couple hours for the DNA to "re-boot" or "reprogram" so that it behaves like the DNA of an egg cells, but thankfully they speed up the time to a couple seconds.

Then I got to do some technology based mitosis and stimulated the egg cell. I got to use this real interesting liquid chemical called "Divided-a-Lot". (I know, they're so creative!) Now, usually after doing so the cell divides, creating a ball of 16 cells. Once again which naturally takes up to several hours took the program no more than several seconds.  So then I put the embryo in the womb of Momi, and the embryo continued to increase. It began to differentiate its cells into various tissue types which went on for 19 more days. Then a baby was born! :) It looked just like Mimi because its genetic material came from Mimi. It was called Mini Mimi -aha!-

When the activity was done it showed that the testing worked obviously. The most interesting thing about this activity was that it was actually based on scientists who did the actual experiment in 1998, at the University of Hawaii. This procedure was based on the research protocol that was used as a giant landmark in experiments involving cloning. This was a totally cool experiment. I didn't really understand the whole cloning thing until I went step-by-step and did it. I would encourage anyone go do this activity! :)

Class of 2011! :)

So recently I read this article (located at http://www.paulgraham.com/hs.html) talking about things that High School students WISH they'd known while in school. I was kind of blown away. Most of the time all you hear from adults is the typical speech about school. You'll never go anywhere without graduating high school and college is all that parents like to shove into our tiny little heads. As if they weren't filled with the paranoia of failing already! The honesty is this author's paper has opened up my mind a little. Here I was already trying to choose a job that would help me be "set for life" instead of trying to figure out what I really want out of life.

Yes, I completely understand that if I want to be financial stable and don't have the natural talents of "Shakespeare", as the author would say,  then I have to do good in school. Now-a-days, with our nation in a horrible economical situation as is, you really can't get a job without having some kind of education. My parents have already rammed me about how if my grades continue the way the are I'm not going to go as far as flipping burgers, or working at Wal-Mart for the rest of my life. It never really bothered me as much as it does right now though. Maybe that'll be all I want out of life, who knows? Who are they to tell me what I should and should not do for the rest of my life? This article has inspired me to go after I want, really want, not just what others "believe" is right for me. Maybe working at Wal-Mart is all I'll ever want (Seriously doubt it, but still) I want to do what I want, and be happy. Honestly, I can understand why my parents push me so much at time, I get it. Parents always want their kids to do better then they have in their life. I guess, I just wish they would lighten up on me a little and let me figure things out on my own. How am I supposed to figure out what I want out of life if all I'm ever taught is to go by what everyone is telling me?

Now, I'm not saying that this article has like, changed my life or anything. In fact, considering that I'm one of the biggest procrastinators you'll ever meet, didn't really help my whole "I do what I want" speech. That's kind of a big disaster in the making.

"I do what I want" + procrastination = ONE LAZY DESI GETTING BUTT CHEWED :P

I've seen my parents struggle with a whole lot financial problems, and I don't want to ever be in their situation. I already know I want to go to college, and major in something I really enjoy. I was really paranoid about what to do after High School before this article. I was worried about making the wrong decisions for my life, and choosing something based on financial growth instead of what my heart was telling me. That's all I've ever known because that's all I've ever really been told. I'm just glad someone had the pleasure of writing such a honest article. I was starting to believe that my fate was already set for me. Now, I think I might actually take the time to sit back and ENJOY High School. I might live a little more, hang out with friends, and just find out who I really am. You know what they say, these are the best times of our lives! :)