Evolution....EVOLUTION!! (It is the big idea)

Evolution!

Evolution is a big subject. Full of controversy and “opinions”. Recently in our studies over evolution I have done some research on some different people who have contributed their theories to the subject of Evolution. Darwin is the philosopher that I had actually heard about...his name was familiar. Darwin had a theory that everything was related. And all life descended from a common ancestor. He believed that what an animal desired, like for example, longer trunks for an elephant to reach more food, or the changes a single organism experienced in its life had nothing to do with the evolution of the species. Darwin stated that all organisms are different, including organisms of the same species, and that those with variations in their traits that help them to survive have more offspring.  And when these “varied” organisms have their offspring, they are born with the parent’s variations. And as they reproduce, most of the population is made up of individuals who share that trait. The other individuals in the species, who are not as well adapted as the others, die off. Back to the elephants for example- Most elephants had short trunks. Then when food and water became out of reach with the shorter trunks, those elephants died off. But the elephants with longer trunks continued to reproduce and soon all existing elephants had long trunks. Darwin also had the belief that evolution follows no plan. Lamarck on the other hand did believe that changes were made according to what the organism needed or wanted. Using the elephants again, Lamarck said that all elephants were short trunked and when they could no longer reach food or water they stretched their trunks. And then their offspring inherited the new long trunks. Lamarck also had the belief that the human body parts that are not being used would eventually disappear, people would no longer be born with those parts. Lamarck believed that when it came to evolution it was all set out in a predetermined plan and that all results have already been decided. 



What is microevolution? Microevolution is evolution on a small scale. Basically evolution within a single species. Microevolution is focusing on one part of the tree of life basically. When I was looking through some websites I found that some of the keywords in microevolution are very important, they are the  Mutation is a word that is often seen or used in our society in different media sources, like movies or books. But really what role does it play in microevolution? “Mutations are the source of new alleles, through changes in the genetic material.”1  The most common changes in genetic material are single nucleotide substitutions and gene duplications. Mutations are a very important source of novelty in micorevolution. But  the observed rates of mutation are actually too low to be accounted for alone in the observed rates of microevolution in organisms. “Genetic drift is the random change of allele frequencies in small populations.”2  Genetic drift is the chance fluctuation in the frequency of the genes. Migration or gene flow also has an effect on microevolution. When organisms move to different places they take their genes with them, if their genes are different they change the evolution of the species in that area. Last but not least is Natural Selection. Natural Selection is when  the organisms with a certain gene escape predation and live to reproduce faster than the organisms with a different gene. Natural Selection over time gradually eliminates inferior species. Natural Selection is Darwin’s theory, which I described above when I talked about the differences between the theories of different evolution philosophers.  


Macroevolution on the other hand is evolution on a big scale. Macroevolution is what we see when we step back and look at the big picture. It focuses on the changes and stability of evolution as a whole over time. And it usually involves more than one species. It isn’t really easy to understand or see microevolutionary history or the effects considering we are looking at time spans that in some cases span billions of years. So evidence like geology, fossils, and living organisms are really helpful in seeing the history. Once we know what events concerning evolution happened we can look at how they happened. The basic evolutionary mechanisms like mutation, migration, genetic drift, and natural selection, which are also part of microevolution are present and at work in macroevolution and can help to show and explain the history of ever changing life. These mechanisms can create HUGE changes in evolution if given some time. That is what Macroevolution is, looking at those changes over time. 





Biochemistry reveals the similarities between organisms that aren't in the same species. There is additional evidence that all organisms developed from a common ancestor because there are certain blood proteins found in almost every organism.  Scientists have compared the universal blood proteins of some organisms. They have found evidence of the different levels of relatedness among different species. Embryology is the study of embryos, or unborn/unhatched animal or human young in the earliest phase. Embryos of many animals look quite similar. The traits found in the embryo of one organism are often found in the embryos of other organisms. One example is human and fish embryos. Both have gills. The difference is the gills on the fish continue to grow and develop, on the human being they disappear before birth. All of this shows that animals are similar and they develop similarly. This implies that they develop from a common ancestor and started out the same. Then they gradually started to develop new traits, but the basic plan for a creature's beginning stays exactly the same. Comparative Morphology involves the study of the external features of organisms. Analogous Structures and living fossils are the two evidences that Comparative Morphology reveal for evolution. Darwin used The Fossil Record to conclude that organisms just continue to get more complex. He noticed when he was studying fossils, that the older they get the less recognizable they became. They younger fossils were more like the organisms that exist today. Darwin used this as proof that organism's have not remained the same since the earth's beginning. From looking at the fossils he also found that new species arise and others go extinct.



I think Darwin and his theories are really what swayed me here when I was writing this paper. I think that the way the puts his findings together and the way he backed up everything really made sense. I believe that species have changed over time from Darwin’s theories about how the organisms with variations continued to live and reproduce which made them in the end the only living “versions” of that species. It makes sense. Almost a survival of the fittest type thing. I really understand evolution because of what I read on Darwin and his findings and I really agree with his view of the topic. Obviously evolution is very controversial and there are so many different theories and new evidence is brought out in to the open everyday. But I believe there is indeed substantial evidence from Darwin and many other theorists that support evolution.






 All of the following websites helped me in completing this paper:

http://www.darwins-theory-of-evolution.com/

http://necsi.edu/projects/evolution/lamarck/lamarck_agreed.html

(1.)(2.)

http://science.jrank.org/pages/48618/Microevolution.html

http://evolution.berkeley.edu/evolibrary/article/evo_36

http://techcenter.davidson.k12.nc.us/spring026/biochem.htm

http://bioweb.cs.earlham.edu/9-12/evolution/HTML/live.html

http://necsi.edu/projects/evolution/evidence/embryos/evidence_embryo.html

http://www.tutorvista.com/content/biology/biology-ii/heredity-and-evolution/comparative-study.php

Some Stuff...

It is the day before the day before the last day of school and things are super busy and tiring...so tonight I put on some Maroon 5 and continued to work on some "stuff" for other classes and continued to finish my evolution paper. But my brain started to hurt and I decided I needed to do a blog about Biology Class because I can't skip over this...this class was too good...So here we go.
Biology this year has been so much fun. I really have learned a lot of new things about biology but also about technology and how it is affecting our world inside the classroom and out. Biology this year also taught me that I can do anything I want to do. That I can make things and think. If I want to learn about something I can do it. All on my own. I control my destiny. < WOW! that was cheesy haha. But on a serious note, I can be a part of society. I can contribute. I am a someone. I think I already knew this but Biology really taught me that I should use this power...I should contribute. I feel like I was fortunate enough to have a great teacher who really let me loose. He gave me a chance to prove myself, which is really nice, because I feel as human beings we all really want that chance and we rarely get it. Now I'm not just saying this because I know he is probably going to read this post, I am saying it because it is nothing but the plain truth. So huge thank you out to him :)
I think what I liked most about this class was the feeling that what I was learning actually mattered. I mean, How many times have you had a class and felt like the information you were getting from it was nothing but useless? What is the point in that? This class was so different. And I enjoyed that. I enjoyed being giving the choice to do my work or to not do it. There was a choice. Learn or Don't Learn. But if you choose to learn you can do it your way. I feel like that pushed me to try. It gave me extra incentive in my studies.
 Now, I'm not saying that this was all rainbows and butterflies all the time, there were plenty of late nights reviewing and studying, trying to connect my blog post to what I was learning about. But it was worth it. I feel now that I can apply what I learned to my life...

So to wrap it up, because I worry I will start to ramble soon...next year I will be a junior and I am not totally sure how I feel about that yet...but I figure it will be okay...I will just remember what I learned in Biology...and I should do fine ;)

Bacterial Transformation Popplet!

So I am probably going out of order on posts...but I am getting things done, which is pretty good. So here you go! It is a Popplet!! On the Bacterial Transformation lab we did a little while back. So click on the link and check it out!


http://popplet.com/app/#/24034

Gattaca! (It's the future)

Recently we watched a movie in Biology to understand how important DNA can be. This movie told a story about one a man who lost opportunities to do what he really wanted to do because of a society where DNA was dominant. When he was born he was written off automatically because his DNA screamed out right away his defaults and his health problems. Vincent is our main character. And he dreams of going to Gattaca, the movie equivalent of NASA. His dream is to fly up in one of the ships and be among the stars. Now, because Vincent is an "invalid" he is kind of out of luck. His DNA from day one showed that he would have a 99% chance of heart disease and his estimated death was 30.2 years. What does this mean? No one wants to put the time and money into someone who is gonna drop dead any day now. Vincent's DNA causes all kinds of problems all throughout his life. So the important question here is...What does it mean if our world becomes dependent on our DNA? If EVERYTHING is determined by what your genetic code reveals. Would that be good for our world? Would it be helpful to the human race if we went that far?

Gattaca showed a world and shared a story of something that we are closer to than we think. One day very soon it might be one of us in the shoes of Vincent. Looking at a hard life just because our DNA is displayed all over. Available to EVERYONE. We would be judged, passed up because of what our DNA said. Is that fair? Obviously there are talented people who have rose above their "conditions" to have very successful lives, to better the world and human race. But if our DNA was cutting us down before we even had a chance to prove ourselves, wouldn't the world be missing out on a huge chance to better itself? So, alas! DNA and technological advance may not be so beneficial to us. It would definitely change the world...and how we view it.

I think when you watch this movie there is one character who really sums up what the movie is trying to point out. In the movie Jerome is the guy Vincent ends up turning to, the guy who gives Vincent his shot at the stars (literally). Jerome was the guy everyone wants to be. He was a magnificent swimmer, winning every medal he laid his hopes on. He was as healthy as a horse. His heart was in perfect condition and health. He had the ideal DNA. Then one accident put him in a wheel chair for the rest of his life. This character is important because he shows that even though he had the ideal DNA his life still didn't lead in the direction he thought it would. He ended up with a life he never expected. Now instead of living out the privileged life his DNA was promising to him, he is helping Vincent. Letting him borrow his ladder, or handing him his DNA. So that Vincent can pursue the life he never had a chance at. Jerome was my favorite character because his DNA didn't define him. His DNA meant nothing to his life now because of his injury, but he gave it away so Vincent could have something. I really admire that. It also shows that one day if our world is running on the information our DNA provides, we will still have people who mean something even though they are "invalid". And they will go against the grain with the help of others to make themselves into a "valid".

So obviously Gattaca shows a lot about what the world would be like if we took DNA and made it a determining factor in the way our lives are led. Below is a trailer for the movie. It will help to explain characters and meaning of this movie. Hopefully it will give you an idea of some of the ideas and questions I touched on here.

GTCAATC...etc.etc. Old School vs. New School

 DNA SEQUENCING

A couple weeks ago we started looking at DNA. And how it is sequenced. We learned about this in a couple different ways. First we did an activity with some nice old fashioned paper and pencil (It's wonderful to get back to the basics haha) This first activity was a simulation of a DNA sequencing gel. We had to read the DNA sequences for each patient. Then find the protein sequences. We would then compare those sequences to the sequences of the normal control. This would helps us to determine if a disease state was present in one of the patients. Abby, Bob and Carol were our three patients. And "Norm" was the normal DNA sequence we were looking at.

Sample of a DNA sequence.

 We first read the normal sequence and used a handy little chart to record the sequences. Norms read: ATG  GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC.  

Next we took a look at Abby's DNA sequence. Abby's read: ATG GTG CAC CTG ACT CCT GTG GAG AAG TCT GCC. 

Bob was next. His DNA Sequence read: ATG GTG CAC CTG ACT CCT GAG GAG TAG TCT GCC. 

Last was Carol's Sequence. Hers read: ATG GTG CAC CTG ACC CTG AGG AGA AGT CTG CCC.

Okay so I took advantage of the technological ability to change the text color to show you the differences between the Normal sequence and the sequences of the three patients. The normal sequence is in all red. Where the other sequences matched the normal sequence I kept in red. The blue parts are where the sequence differs from the normal sequence. As you can see the Abby and Bob's sequences stayed pretty much the same with the normal sequence. Only differing in one part. Carol's sequence on the other hand is pretty different. Carol is missing a base. A T to be exact. This is called a Frame Shift Mutation. The sequence is off by that one T. There is a C where the T was. But it isn't because the T was traded out for a C. The T is completely missing, causing the "shift".

Codon Usage Table

The next step was to find the protein sequences. We used the sequences I showed above in red and blue and this table to find the Protein Sequences.
 For example Norms Protein Sequence: MET VAL HIS VAL SER SER GLU GLU LYS SER ALA.
After we found the DNA and Protein sequences for Norm and the three patients we could see if and what mutations were present. Abby's sequence showed a point mutation. And there was truncation mutation in Bob's protein sequence. It traded out a Lysine for a Stop in the sequence. The sequence was three amino acids short. And Carol's sequence as mentioned before had a Frame Shift Mutation present.

Graph showing the similarity between Norm and the three patients.

 So after we finished up our "old-school" DNA sequencing, Mr. Ludwig had us take a look at a website that did a virtual lab of DNA sequencing. The new-school way! We basically set up a whole experiment to find the DNA sequence of a patient and see if they had a disease present. The website for this experiment is:
http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html

I personally like doing the "old-school" way better. In the virtual experiment version it was cool to watch and make it happen but I really did enjoy looking at the sequences and writing it all out. Then again, I only did about three inches worth of a DNA sequence...it would probably get old after a while. So feel free to take a look at the "new-school" way of DNA sequencing. And see what you think. NEW SCHOOL or OLD SCHOOL?

Protein Code Chart found at : http://www.nbii.gov/portal/server.pt/community/basic_genetics___cell_biology/401/genetic_blueprints/559

DNA Sequencing Sample found at: http://www.biology.fourcroy.org/chapters/09dna/handouts/dna_seq_activity.htm

DNA Extraction Lab

Below is the slide show Sidney and I made on Google Docs. It just briefly goes over what we did.
Check it out :)

Genetics...phenotype...genotype...

More than recently ago, we did an activity in class. We made babies. (Nonexistent babies of course.) Each of us had a partner and we conducted an activity to create a child. Later, we drew pictures of our "children" and they were proudly posted on the wall of Mr. Ludwig's classroom. This activity, I believe was done to teach us about genotype and phenotype. Both very important key words when talking about genetics. I'll start off by telling you a little bit about the activity we conducted in class...
          After we had been paired up in partners Alii and I got right down to making our baby. The way the activity worked was we had a list of different features...eyes, mouth, nose, ears, freckles, no freckles, hair color, etc. etc. We flipped coins and used pencil and paper to decide what our baby's genotype would be. I was the daddy (haha) and Alii was the mother. After the genotype was decided this helped us to know what our baby was gonna look like. Which is the phenotype.

         So these traits-eyes, mouth, hair color, etc... is controlled by two alleles. There is the dominant allele and the recessive allele. The dominant allele is referred to this way because of its ability to mask the expression of the other allele. A dominant allele is expressed with a capital letter. The recessive allele is identified with the same letter but in a lower case form. Two identical alleles, for example- TT. (Which is two alleles for tallness in plants.) are homozygous. This means that if there were two parent plants that were homozygous all the gametes produced by these parents would contain alleles for tallness (T). And all of the gametes produced by shorter plant parents would contain alleles for shortness (t). So let's say there was cross-pollination between two plants. Then this new generation would have one allele for tallness and one for shortness (Tt) Because they had two different alleles they are considered heterozygous. Even though these plants had one of each type of allele, they were all tall because (T) was the expressed allele. This makes it dominant.
         This brings us back to genotype and phenotype. Genotype refers to the alleles an individual receives at fertilization. Phenotype refers to the physical appearance of the individual. For example- a person with Genotype TT (homozygous dominant) would have the phenotype of being tall. A person with the genotype tt (homozygous recessive) would have the phenotype of being short.
           In the activity we flipped the coins to decide which allele we would give to the child...it works sort of differently in real life...but you get the point. :)
So there you go! A kind of brief overview on genetics. And how genotype and phenotype fit into all of it.

In Sickness and in Health...Case Study/Greg & Olga

This is the Pedigree that Sidney and I created for Greg and Olga. Greg and Olga are labeled. And you can see their families history.

So Im taking a risk here...the way I understand it, as long as I can prove I understood this whole "assignment" we won't have a problem. Well, obviously the easy way to do it would be to answer the questions provided on the site and show that I was indeed paying attention to what I was reading. BUT as much as I love to answer questions, I am going to just write. And describe what the heck genetic counseling is and how it applies to our friends Greg and Olga. So here we go! :)

          Let's start off with why Greg and Olga came to a genetic counselor in the first place. Greg and Olga are concerned. They want to start a family but each of them have some worries about their families medical histories. Hemophilia A is present in both of their histories and they knew it could be inherited, and they were concerned about passing it on if they had children of their own. Also, several of Greg's relatives suffered from (MD) Myotonic Dystrophy. Knowing that MD runs in families, G & O also had some concerns that they could pass that on as well.

          First we will address the worries over the possibility of Greg being an MD carrier. MD is an autosomal dominant disease. MD does not skip generations. Greg's mother has two siblings that have MD. But there is no chance that his mother has the disease. Neither Greg or his mother could not be carriers of the gene because if they were they would be sufferers of the disease. The possibility of G& O's kids inheriting MD is ZERO. Because neither of Greg's or Olga's parents had the disease, G & O can't be carriers of the gene themselves. That means they can't pass it on to their kids themselves.

        Now when G & O came into the office they also had a couple concerns about diseases that aren't as easy to weed out, Cystic Fibrosis for example. Now CF is one common RECESSIVE TRAIT. A recessive trait can skip generations. Recessive traits (this is very important) are equally likely top affect both males and females. Consanguinity is also included in here somewhere. Consanguinity is the matings between two related individuals. Consanguinity is important when talking about Recessive traits because two people who are consanguineous they have a very good chance of having similar genotype...example, recessive traits.


             If you look at G & O's pedigree we can see that Hemophilia A, Greg & Olga's main concern, is only present in males and it appears rarely. This is a very good indication that Hemophilia A is an X-linked gene. X-linked genes mostly appear in males because the mutated gene is on the X-chromosome. Males only have one X-chromosome. Unlike girls, who have two X-chromosomes. This means if a girl had a mutated gene on the X-chromosome her second "good" X-chromosome could cover it up. If G & O were to have a boy there isn't any chance that Greg could ever pass on the disease at all. For G & O to have a son Greg would have to pass on a Y-chromosome which is not affected by the disease. Because the disease effects the X-chromosome and Greg does not suffer from it there is no possibility that he has the disease. This means he could not pass it on through the X-chromosome he would give a daughter. Looking back at Olga's family history we can see that her mother and grandmother were both carriers. This means there is a chance that she would pass the mutated gene on to her child (male). OR the child could be a carrier as well (male or female)

            This an example of a case that could be brought in to a Genetic Counselor. Genetic Counseling can be very helpful if you have concerns about the child or children you hope to bring into the world.

Here is the website I used to help complete this post:
http://www.sciencecases.org/sickness_and_health/sickness_and_health6.asp

It is very late...but here it is.

I have been a very bad blogger lately! I have been working on so many projects for Biology they all kind of just take turns getting worked on. The good news is that I have made progress and finished some stuff on Mitosis and Meiosis. The following is a link to a glog I did on Mitosis:
http://sierra3.edu.glogster.com/glog-6479-4769/

I decided since I do Glogs for EVERYTHING! I would take a break and do an "old fashion blog post" and just tell you a little bit of what I learned on Meiosis.
       First of all, what is Meiosis? Meiosis is the type of nuclear division that reduces the chromosome number from the diploid number to the haploid number, in sexually reproducing organisms. The total number of chromosomes is referred to as the diploid number. The haploid number still refers to chromosomes. But the haploid number of chromosomes is half of the diploid number. For example, in humans, the diploid number is 46. In the haploid number, you end up with 23. Gametes are the reproductive cells, often times this refers to the sperm and egg. Gametes usually have the haploid number of the chromosomes. When these gametes form and fuse they make a cell called a zygote. This is all part of the integral parts of sexual reproduction. A zygote always has the full number of chromosomes, the diploid number. In meiosis there are two unique cell divisions. Meiosis I and Meiosis II. Prophase, Metaphase, Anaphase, and Telophase are the phases of both Meiosis I and II. Crossing over occurs in Prophase I. Crossing over is very important. It is the exchange of genetic material between NONSISTER chromatids of a bivalent. Due to this swapping of material, the chromatids held together by the centromere are no longer identical. That means that when those chromatids during Meiosis II, separate, some of those daughter cells will receive chromosomes with recombined genes. The offspring will have a different sequence of alleles, due to genetic recombination. What does that mean? It means that they will have different genes than their parents. Making them, their own person. At the end of Meiosis I the two daughter cells will have one chromosome from each homologous pair. The chromosomes still consist of two chromatids. In Meiosis II, the chromosomes align at the metaphase plate and then the sister chromatids separate and become DAUGHTER chromosomes. In Telophase II spindle disappears, nuclei form. And then cytokinesis takes place. At the end of Meiosis we have four haploid daughter cells. After Meiosis II, the haploid cells become gametes in animal cells and spores in plants. And you know the rest already, those gametes form and fuse to make the zygote! For humans, Meiosis occurs only in the reproductive organs to make the gametes.
So there you go! A little bit of information on Meiosis. Very soon, I will be posting blogs on the things we have been working on more recently. Chapin, Sidney, and I are all working on our Eugenics post and it should be up soon! I will also have a blog on a case study very soon :)

The Cell Cycle Glog!! :)

Being Reflective...

        Christmas Break has recently ended and myself like many other kids all over the country are getting back to walking through halls, reading books, writing reports, typing things up, and learning all kinds of good new "stuff".  On the first day back I was presented with an opportunity to read this article. It was called What You'll Wish You'd Known. I love to read and I really love to write. This article was so enjoyable. And it presented a lot of things to the think about. It wasn't an article on biology at all but it really helped me in that class and all of my other classes, from Choir to Math. The article was in fact a speech directed at high school students. It was something unlike anything I had read before in a good way. I enjoyed it because it addressed things that I have been hearing about for a while now. Things that are important at the moment but also have a direct connection to you later. It made a shout out to something that all American high schoolers struggle with. I guess what you would call it is our placement in the world at the moment. And what our placement will be in 5, 10, 20 years. Among many other things it discussed how we as high school students shouldn't be defined as high school students. Because yes, we do have to go to school 7 hours everyday, and it could be considered a "job". But the author of this article suggested something very smart. Treating high school as a DAY job. Going and doing what you have to do at school but also working on hard problems. Pursuing things that matter. Things that will make a difference to your own life and the lives of others. Learning things that will have a real impact on your life. Putting some of the focus that we so generously give over to t.v. or Facebook into things that will be beneficial to our lives. This article made a very big impression on me. Because it had a message that meant something. It was giving anyone who read it a head start on something that some people never grasp in their lifetime. This article is beneficial to anyone who reads it. Even people who are "old".  I believe that all of us can make a difference when we focus on the hard problems. And use our own talents to "make a difference". This article gave me a big realization that all of the things I am interested in and take an opinion on are part of my future and the future of the world. This article has helped me in this past week back from break, a week that focus appears few and far between. It inspired me. It inspired me to not waste time. To make an effort in everything I do. Whether it be a blog post for bio or a poem for english class...or maybe my own personal creation I have been working on lately. It helped me to look at myself, and see if I was really being true to this world and my "placement" in it. So I have decided to make this the best semester ever. The best summer ever. The best year ever. The best lifetime ever, by getting to work to get things done.


Here is the link to the article incase you are now inspired to read it and become inspired yourself :)


http://www.paulgraham.com/hs.html