E-V-O-L-U-T-I-O-N

While discussing evolution, Terry Pratchett said “Most species do their own evolving, making it up as they go along, which is the way Nature intended. And this is all very natural and organic and in tune with mysterious cycles of the cosmos, which believes that there’s nothing like millions of years of really frustrating trial and error to give a species moral fiber and, in some cases, backbone.” This quote is a humorous way of basically breaking evolution into very simple terms. Evolution is a controversial and touchy subject in schools, but can be researched from different points of view.


There are a few people who have made dramatic contributions to the world of evolution and what evolution entails. Jean Baptiste Lamarack thought that organisms inherited the traits that had acquired during their parents’ lifetimes. “‘Lamarckism’ or ‘Lamarckianism’ is now often used in a rather derogatory sense to refer to the theory that acquired traits can be inherited.” Lamarack believed that a change in the environment caused needed changes in the organisms in that environment, which could cause changes in their behavior. He fully believed that organisms altered their behavior in response to the changes in the environment. This in turn modified the organism’s organs, which their offspring inherited, becoming evolution. For most people, this made the most sense at the time; if the parents had it, why couldn’t the babies? Unlike Charles Darwin, Lamarack believed that all living things evolved in a continuously upward direction through simple or more complex forms, eventually working toward “human perfection.” Lamarack also believed that species never become extinct, but instead changed into animals, such as a land dinosaur into a whale or a bird.

Charles Darwin, on the other hand, presumed the development of life from non-life forms and stressed a purely naturalistic and undirected “descent with modification”. Darwin believed strongly in natural selection and a “slowly but surely” change when it came to organisms. He popularized the theory of humans being animals and deriving from apes, which upset many church nations and numerous people as most British occupants were strong believers in the Bible. While on a journey on the HMS Beagle, Darwin had his major breakthrough in the Galapagos Islands. He noticed that each island had their own forms of a bird: finches. They were extremely closely related but diverse in many important ways. He theorized that as a random genetic mutation occurs within an organism’s genetic code, only the beneficial mutations remain because those mutations aid survival. This process is widely known as natural selection. Darwin’s theory is now in turmoil due to tremendous advances in molecular biology.

Karl Popper, a popular philosopher of science, was known for being extremely logical and was also very beneficial to the Evolution theories. Popper focused on separating science from pseudo-science. Psuedo-science is defined by Webster’s Medical Dictionary as a system of theories, assumptions, and methods erroneously regarded as scientific. Popper accepted psuedo-science but denied that they were any part of general science. He also did not believe that Darwinism was a testable theory. He was widely accepted in Europe, particularly England. Popper was really critical of attempts to turn evolution theory into a fact. He said, "The idea of a law which determines the direction and character of evolution is a typical 19th century mistake arising out of the general tendency to ascribe to the natural law the functions traditionally ascribed to God."

These scientists not only contributed ideas and ways of thinking to the evolution theory, but also added a face to all of the research and hard work that has been put into this topic.

Although these scientists had altering views of evolution, there are some things that a wide variety of scientists agree on. Mutation, migration, genetic drift, and natural selection are all major factors that affect the conclusions of biology. During mutation, genes “randomly” mutate to other genes. This process is extremely rare because the process alone can’t account for a major change in the allele frequency over one generation. Certain mutations can either be beneficial, neutral, or harmful to the single organism. Mutations do not attempt to supply what the organism needs, because they are random. Whether a particular mutation happens or not, it’s not related to how useful that certain mutation could be. Migration, also known as gene flow, is when organisms with certain genes immigrate or emigrate to another region, carrying those genes with them. A number of different species have migratory instincts which develop in different species for many different reasons. Most of the time migration is a response to population pressure (which also can cause evolution) such as the “leave somewhere cold for somewhere warm, then return” pattern. Things such as climate changes may have had an affect in forming or shaping different migratory patterns, which can also be described as evolution. Birds commonly follow this pattern, therefore migrating not only themselves, but also the genes that they carry. These genes can then remain in a different area. Genetic drift, or allelic drift, is when certain individuals may by chance, leave behind more descendents and genes than some other individuals. Then, the genes of the next generation are the genes of the “lucky“ individuals but not really the healthier or better individuals. Unlike natural selection, genetic drift occurs completely at random. Even though it’s a mechanism for evolution, it has no part in an animal’s adaptation. The changes that occur are not driven by environmental or adaptive pressures. The changes can be beneficial, neutral, or very detrimental to the animal that the changes have occurred to. Genetic drift happens to all populations. Now, natural selection is a pretty simple concept but can become extremely complex. For example, if there were two worms in a toy Barney doll bin and a predator was hungry, these two worms could be in trouble! One of the worms is the same color of Barney (purple) while the other is, well, we can say White. Now, the bird is more likely to see the white worm than he is the purple colored one. This causes the white worm population to decrease, while the purple worm population can rapidly increase. In this case their color saves them from predation and allows them to survive in order to produce their color more frequently.

Scientists often look to biochemical information to learn more about evolution. Biochemistry is the universality of a genetic code. For example, the human versus ape chromosome. Humans have 23 pairs of chromosomes while apes have 24 pairs. The human Y chromosome also has huge affects as the Y chromosome is passed mostly unchanged from the father to the son with occasional mutations or differences. These mutations are said to be the basis of human origin from apes. Embryology is also commonly looked to. This means that different species who may be in the same class (ex: mammals) often have extremely similar embryos. This case is true even if the adult forms are quite different from the adolescent forms, such as in the case of a caterpillar and a butterfly. Fossils, from my understanding, are the largest pieces of evidence of evolution. These include the evolution of vertebrate legs, birds from dinosaurs, mammals evolving from egg laying creatures, and whales that have evolved from land bearing animals to sea depending mammals. Apart from fossils, comparative anatomy is also discussed and analyzed when looking at evolution. Comparative anatomy is when anything similar is “evidence for evolution.” In simple terms, this can basically mean that completely unrelated species that happen to live in similar environments have evolved from similar forms. This may be possible in the case of a cat and a dog, because they have the same body shape.

Microevolution and Macroevolution cover the same topics, but have very diverse “specialties”. Microevolution is on a small scale, such as in a single population. It’s defined as a change in gene frequency in a population and that population has a group of organisms that share a common gene pool. For example, all of the individuals of one beetle species living on a particular mountaintop. Macroevolution is on a bigger scale. It refers to evolution about the species level. A macroevolutionary lense would focus on the tree that a beetle lives on, rather than it’s opposite, the microevolutionary lense, which would focus on the beetle species itself.

Although there are a lot of people who fully believe in the theory of evolution, I believe it is what it’s called: a theory. We don’t have any legitimate solid proof that that’s actually what happened. We claim to have come from apes, but how do we really know? Even after looking at the anatomy, genes, and fossils of apes, there are a number of scientists who still aren’t sure. I grew up in a very Christian home, and believe strongly in the Bible. The Bible claims that God created us in one day, man first, than the woman from the man’s ribs. I also believe that God made the animals. Now, in regard to all of the evidence that I, and many other scientists, have discovered and researched, I do believe in adaptation. Animals need to continually adapt to their environment. But adaptation and evolution are two very different concepts that seem to have commonly been crossed. The fossils and genes that are always looked to for evidence of evolution, is actually, in my opinion, evidence for adaptation. Now, regarding the theory that humans have derived from apes; this I do not believe at all. Apes and humans are too diverse, and throughout my research, I have found no physical evidence that this “evolution” is possible. Researching evolution and the theories behind it has really been an interesting topic, but I can understand why it is so controversial.

Works Cited

Charles Darwin (1809-1882). (n.d.). BBC. Retrieved May 9, 2011, from http://www.bbc.co.uk/history/historic_figures/darwin_charles.shtml



Cline, A. (n.d.). Karl Popper and Evolution. About.com. Retrieved May 9, 2011, from http://atheism.about.com/b/2006/06/20/karl-popper-and-evolution-is-evolutionary-theory-based-on-a-tautology.htm



Darwin's Theory of Evolution. (n.d.). All About Science. Retrieved May 9, 2011, from www.darwins-theory-of-evolution.com/



Evidence for Evolution--Embryology. (n.d.). New York University. Retrieved May 11, 2011, from http://www.nyu.edu/projects/fitch/courses/evolution/html/embryology.html



Genetic Drift.(n.d.). Evolution 101. Retrieved May 9, 2011, from http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml



Genetic Drift as a Mechanism of Evolution: Random Genetic Changes Help Drive Evolution
Suite101.com. (n.d.). Suite101.com: Online Magazine and Writers' Network. Retrieved May 11, 2011, from http://www.suite101.com/content/genetic-drift-a124881



Grabianowski, E. (n.d.). How Animal Migration Works. How Stuff Works. Retrieved May 9, 2011, from animals.howstuffworks.com/animal-facts/animal-migration3.htm



Jean-Baptiste Lamarck (1744-1829). (n.d.). UCMP - University of California Museum of Paleontology. Retrieved May 9, 2011, from http://www.ucmp.berkeley.edu/history/lamarck.html



Migration.(n.d.). Evolution 101. Retrieved May 9, 2011, from http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml



Mutations. (n.d.). Evolution 101. Retrieved May 9, 2011, from http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml



Natural Selection. (n.d.). Evolution 101. Retrieved May 9, 2011, from http://evolution.berkeley.edu/evosite/evo101/IIIC1Mutations.shtml



Sonleitner, F. J. (n.d.). What Did Karl Popper Really Say About Evolution?
NCSE. NCSE
National Center for Science Education - Defending the Teaching of Evolution in Public Schools.. Retrieved May 9, 2011, from http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution

Animal Indexing

So, a while ago we had this dude that came into our class to talk about the growing problem of animal overpopulation in the Valley. He showed us that after only a few generations of cats, 2 cats will soon become over 300 cats!! That's insane. So, to include us in his research, we have to do an indexing project. It's the easiest homework I've ever gotten in my life. Basically, we take a 30 minute walk, and count the animals. We were asked to count all feral dogs, owned dogs, and any cats, as well as any other animals we encounter. The company will then collect this data and use the information to determine if spaying and neutering animals helps the abandoned animals numbers. This is actually a pretty cool and effective way to count these animals.
I have two walks down and two walks to go. On my first walk I only saw a few animals but on my second walk I saw a lot more dogs, cats, and SQUIRRELS!!!
This activity is probably the easiest homework assignment I've gotten in a long long time, and it forces me to get my exercise. (:

Transformation Lab

Our group was amazing! It included me, Sierra, and Tyler. We worked really hard to focus and learn something about the pGLO gene(also known as jellyfish gene!!) By the way, jellyfish hurt, a lot!!

The PROCESS!!
1. label one closed test tube +pGLO and another -pGLO. Place in the foamy tubey thingy..
2. open tubes and use pipet to transfer 250ul of the CaCl2. Place on ice.
4. Use loop to pick up a single colony of bacteria from the starter plate. Get the +pGLO tube and immerse the loop into the transformation solution at the bottom of the tube. Spin the loop "washing machine" until the entire colony is dispersed. Place the tube back in the ice. Repeat with -pGLO with a new sterile loop.
5. Examine plasmid DNA with the UV lamp. Immerse new into plasmid DNA stocktube. Withdraw a loopful. Should be a film of plasmid across the ring, like you're about to blow a bubble. Mix loopful into the cell suspension of the +pGLO tube. Return it to the ice. Don't add plasmid DNA to the -pGLO tube.
6. Incubate tubes on ice for 10 minutes. Bottom of tubes should make contact with the ice.
7.Label four agar plates on the bottom as follows: one LB/amp plate label +pGLO; LB/amp/ara plate label -pGLO; LB/amp label -pGLO; and the LB plate -pGLO.
8. HEAT SHOCK!! Transfer both tubes into the water bath that's set at 42 degrees Celsius for exactly 50 seconds. (Push the tubes all the way down in the rack so the bottom of the tubes make contact with the water. Replace both tubes on ice immediately. Incubate in ice for 2 minutes.
9. Take off ice and open a tube. Use a new pipet to add 250 ul of LB nutrient broth to the tube and reclose it. Repeat with a new pipet to the other tube. Incubate at room temp for 10 minutes.
10. Tap closed tubes with finger to mix(or flick it). Use new sterile pipet for each tube, pipet 100ul of the transformationa nd control suspensions to appropriate plates.
11. Spread suspensions evenly with a sterile loop.
12. Stack of plates and tape them together, upside down. Put it in the Biology rooms' incubator overnight which is set at 37 degrees Celsius.

Review Answers:

• I would expect to find bacteria on the LB plate because I never saw any plasmid.
• Genetically transformed bacterial cells would be located on the LB/amp/ara and LB+ plate. Because the antibiotic is selecting.
• LB/amp plates should be compared to determine any genetic transformation because it can be used as a control.
• The controls were: same bacteria, same temperature, and the same amount of bacteria. In this case the LB was the control.

Observations:
+pGLO; LB/amp: has the gene but it isn't "turned on". It has a medium to heavy population which is white and yellow. Our estimated count was 130. Transformation plates
+pGLO; LB/amp/ara: has the protein that is turned on, which makes it glow. It has a medium to heavy population that's yellow then a light white. Our estimated count is 149. Transformation plates
-pGLO; LB/amp: has no population and no bacteria!! Control Plates
-pGLO; LB: has a HEAVY bacterial lawn!!! Control Plates

Analysis:
Plasmid doesn't make a difference to the health.
Our goal is to see if it glows or doesn't glow
The amp kills unless a gene from the plasmid is LB/amp +/-

Definitions:
amp = antibiotic
ara = arabinose sugar (activates some genes)

GATTACA

Questions about GATTACA!

(I wasn't here for the second part of the movie. :[ )

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

         De-gene-erate 

         In-valid -  an invalid in the movie meant that a person wasn't "perfect" They weren't created artificially through the country's program to make the perfect child.

         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 he finally proved his point to his brother that he could do what he wanted even though he was an invalid, but after he accomplished that he felt that he could move on with his life and pursue the things he wanted to pursue, without his family.

3. Describe the relationship between Vincent and Anton.

Vincent and his brother, Anton were very competitive in the beginning of the movie, always trying to beat the other one in a competition or race. Anton was then the detective investigating Vincent's case.

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 meant that Vincent technically didn't exist anymore because Vincent became Jerome. The government didn't realize that Vincent was even around because he was pretending to be Jerome. 

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 the real Jerome, oddly. I wouldn't want to be that person, but it seemed throughout the movie he became friends with Vincent, instead of using him for his money. I know Jerome had a rough life but he was still there for Vincent. I wouldn't want to be Jerome because he was stuck in a wheelchair and had a lot of drinking and smoking problems, eventually ruining his life. 

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?

 I do think this is possible because we are already so close to this. Manipulated babies are becoming more accepted. Throughout the years this will become more common, possibly eventually making manipulated babies the only population. Also, our personal information is becoming more and more publicized, just like their health records and everything were publicized.

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

 I don't think anything was right in that movie. I think the fact that the parents got to choose the baby was extremely wrong. The fact that they discriminated against the "invalid" or the unhealthy ones, in order to get a perfectly normal job was wrong. It seemed that if you weren't "valid" and had perfect health, history, etc you were basically an outcast because you could possibly have a .1% possibility of having a heart problem or something.

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?

I wouldn't choose to have my child chosen from the Genetic Clinic. Basically because of my religion and believes that's not okay with me in any way. It's basically determining the 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?

 I probably would've acted the same as them. All of them. I think they all handled the situation the way that they thought best, especially because they couldn't do anything extremely beneficial in order to change the growing problem. 

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

People were going crazy with "making their own personalized babies" just like in GATTACA. In GATTACA the clinic babies were the only babies thought acceptable, which was probably what some people thought during the eugenics movement.

I really enjoyed this movie. It taught me a lot about how America could possibly turn out if we keep digging for information or going against our beliefs to make our lives perfect. It's scary how close we could be to a world like this. 

PCR!!

If only it was PBR right? (: (Professional Bull Riding) but no. This is almost as interesting, without the screaming fans, angry animals, and cowboys.


I did an online Bacterial ID Lab that was intended to identify the bacterial sample given.

First of all you have to prepare the DNA sample that is to be used. This involves placing the bacterial colony in a microcentrifuge tube and inserting the digestive buffer. The tube has to sit for several hours until the sample is ready. Following that you have to heat-inactivate the digestive enzymes which will denature and inactivate them. Add counterbalance and spin down cellular debris for removal from the sample. Then the wanted DNA is supernatant. Transfer the supernatant to the PCR tube and the sample prep is complete!!



Next step is to use PCR to make copies of DNA sequences. To do this you have to add a PCR master mix solution to all of the tubes. To set up a positive control reaction, you have to add control dna to one tube. For negative reactions you must add de-ionized water to one tube. Then insert both of them into the PCR machine. The short strands are desired DNA strands from PCR thermal cycling process.



NEXT: Purify the PCR product. To do this you have to set up the microconcentrator column and add a buffer solution to the column, then add the PCR product to the column. Put the positive and negative controls on ice until needed again. Add counterbalance to the tube and put it in the centrifuge. After a while DNA is trapped into the column and you need to loosen it into a new tube. Invert the column into the new tube (turn it upside down) and add a buffer. Now put centrifuge assembly to collect DNA into a collection and wait patiently.



PCR sequencing prep is next. First you have to dillute the PCR product to increase the volume. Add distilled water to purify the PCR product. The green and blue strip tubes contain PCR reaction mixtures, so now you can add purifed PCR product to them. They are now ready for PCR amplification so put it in the PCR machine. The Sequencing prep is complete!



Second to last step is DNA Sequencing. You must load the auto sequencer and insert the tubes. In my case the first tube read tacggtagcgtaatgcc. And that completes the DNA sequencing event.



The last step is to analyze the sequence. Copy the output from the DNA sequencer and past it on the ncbi website. The ncbi website searches through it's massive database and eventually comes up with results. The bacteria was identified as bartonella henselae.

DNA Sequencing Activity

This graph represents how alike Abby, Bob, and Carol are alike to Norm, or the Normal DNA.

• Abby only had one difference from Norm. Norm had GAG, but Abby had GTG, otherwise known as a point mutation. This also changed the protein from Glu to Val. This could lead to disease, or other problems because of this change. 
• Bob also only had on difference from Norm. Norm had AAG, but Bob had TAG, another point mutation. This also changed the protein from Lys, to the signal that the protein stops, also read as "stop!" Clever huh? This change causes the protein to become too short, otherwise known as truncation mutation.The stop causes Bob's protein to become three amino acids short because the DNA stops. This could cause some major problems for Bob in the future.
• Carol is the most different from Norm. She has 14 differences, creating the lowest percent of similarity. Her DNA is actually really similar to Norm, except that with the fact that she's missing a base, it made everything shift over, creating new codons within the frames. The frame shift has huge consequences on Carol because all of the proteins are different than Norm. This can cause drastic consequences for Carol and her health. 

Interesting Fact: 99% of DNA changes, do not cause problems for the person!

This is pretty interesting actually, I didn't understand that this is how DNA and diseases, etc can play out. I thought it was a lot more complex, but on the surface it doesn't look that difficult. It's crazy how all three of them have a disease risk, just because they're DNA is different. 

Pedigree Analysis

A while ago, we became "genetic counselors" for Greg and Olga, a couple who wanted to have kids, but was terrified of the fact that they're children could be born with a genetic disease. They were concerned because they had the Factor VIII deficiency disease throughout both sides of their families.

This particular post taught me that autosomal recessive diseases skip generations, while autosomal dominant diseases don't skip generations. Autosomal recessive disease is when there is one mutated allele and one normal gene. It has a 50% chance of being transmitted. All children of the infected people will be carriers no matter what. The disease is either transmitted by either the father or the mother. Both sexes have an equal chance of getting the disease, unless it is a sex-linked disease. Recessive diseases are never inherited directly because recessive diseases are only inherited by the y. Women can't display sex-linked genes, but they can be carriers. Greg and Olga could be a carrier for this disease because people in their family have the disease. In this activity Greg has a high chance of being a carrier, he can pass it to his sons, and his daughters could become carriers. His daughters could also have children that could possibly get the disease. Consanguineous means relating to or denoting people descended from the same ancestor. The advancement of technology can really harm the future of the kids with these genetically inherited disease. If a parent finds out that their unborn child has a disease, they are less likely to carry through with the pregnancy in order to "try again." Also, insurance companies would have to be forced to accept all children, no matter of their health because every disease could be "pre-exsisting."

The world of genetics is definitely a complicated one, that could cause a lot of problems, or great advancements in the future.