Tuesday, May 13, 2014

Evolution Take-Home Essay

Organisms have changed over time due to environmental changes. They are many different beliefs that go around in why species change. Darwin believes that species change to fit their environment. As he traveled around the world he saw birds that looked alike but had a couple different physical features. After observing many animals, he realized that the animals change their appearances to help survive in their environment. He believed there was a variation of inheritable features that already existed. Darwin believed that environment selects features contributing to survival and tends to eliminate the others. The species that adapt to an environment live longer and produce more. Darwin was one of the leading intellectuals of the eighteenth century of England. He is a respected physician and a well known poet, philosopher, botanist and naturalist. Darwin often talked about how competition and sexual selection could cause changes in species. When other theories arose he would argue that complexity evolved simply as a result of life adapting to its local conditions from one generation to the next. 




 Lamarck believed in something different then Darwin. He believed that animals could sense a need and "passed" it on to their kids. Lamarck believed life had began through spontaneous generation. He claimed new primitive life forms sprained up throughout the history of life. Lamarck proposed that organisms were driven from simple to increasingly more complex forms. The proposing life took on its current form through matural process. Darwin relied on almost the same evidence for evolution (vestigial structures and artificial selection through breeding) but he made different arguements. Another early evolutionary phisospher is Georges Cuvier. He founded vertebrate paleontology as a scientific discipline and created comparitive method of organismal biology. He established the fact of the extinction of past landforms. Thomas Malthus was another early evolutionary philosopher who is widely known for his theories about change in population. He said that sooner or later the population will be checked by famine and disease, leading to what is known as a Malthusian catastrophe. He thought that the dangers of population growth precluded progress towards a utopian society. Thomas had said a decrease in population will cause a large amount of substince to grow and when there is less substince, a decrease of population will take place.  



Animals and insects do many things or change in many ways to be able to survive. The first thing I m going to talk about is mutation. Mutation is a change of the nucleotide sequence of the genome of an organism, virus or extrachromosomal genetic element. Mutations may or may not produce discernible changes in the observable characterists of an organism. For example, at a period in time we may see an decrease of green coloration  genes in a beetle population. It is possible that some"green genes" mutated to "brown genes." This is an exaqmple of mutation.


Migration also causes a change in an organism. For example, some beetles with brown genes immigrated from one population to another or some beetles carrying the green genes just emigrated. This causes two different colors or types of organisms to breed and produce a new color or new kind of organism.

Genetic drift causes a change in a population also. Genetic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining weather a given individual survives and reproduces.  Genetic drift may cause gene variants to disappear completely and thereby produce genetic variation. For example, when beetles reproduced there were more brown genes than green genes in the offspring. Brown genes occur slightly more frequent in the offspring than in the parents generation.


Natural selection is also another way organisms change. Natural selection is the gradual process by ewhich biological traits becomne either more or less common in a population as a function of the effect of inherited traits on the differential reproductive sucess of organisms interacting with their environment. This term was popularized by Charles Darwin. Throughout the individuals' lives, their genomes interact with their environments to cause variations in traits. Individuals with certain variants of the trait may survive and reproduce more than individuals with other vairants. Animals that are pretty may attract the opposit sex more but also at the same time they may stand out which makes it easier for predators to see them and kill them. An animal may escape predation more than another because they blend in and reproduce more, which causes that color of animal to reproduce more.





There are evidence for evolution in a lot of organisms to this day. DNA is an example of evolution. There are animals that are similar to those back in the day. The only explanation of this is DNA being passed down through generations. Serial structures are usually identical in the embryo, but specialized and diverged in the adult. Different species in the same class often have very similar embryos, even if the adult forms are quite deifferent. Variations in adult features are inherited at corresponding late stages. Darwin extrapolated this to larger groups, for example, the forelimbds might be legs in an ancestral species, but would be modified as flippers, arms, wings, etc at late stage in development; but the pattern in the embryonic stage would remain similar if not unchanged. Also the fossil record shows us evidence for evolution. Fossils are like snapshots of the past. Some fossils may missing pieces but we still can get a good look at an animal in the past. By comparing fossils to the bones in the present day, we can see how things have changed over time. We can see how animals from different locations adapted by looking at fossils. Comparative anatomy is also evidence of evolution. Buffon and Lamarck used comparative anatomy to determine relationships between species. There are common things foun in different species that show us they may be closely related. For example, bats, birds, and insects all have wings but we need to be careful when evalutating species this way. The wings of bats and birds are both derived from the forelimb of a common, probably wingless, ancestor. A difficulty in comparing traits between species rests on the fact that homologous structures not present in the adult organism often do sppear in some stage of embryonic development. For example, a humans embryo passes through a stage in which it has gill structures like a fish, and a tail like our close primat relatives. There is a lab that I did called DNA sequence comparison. I learned how things may be closely related to another thing more than another. I made a family tree with a chimp, human, mouse, chicken, wallaby, and goldfish. By making that tree I realized that some things may have the same physical feature but are not close to being related. Us humans are related more to mice than chickens and chickens are closely related to goldfish. The evolutionary distance between a mouse and a human is 75, between a wallaby and a human is 79, and between a chimp and a human is 99. There are a lot of different evidence that shows how evolution has took place.
 

There are many animals that have different features than those that live across the world. There are animals that I have seen pictures of that look very different than that species today. While watching the movie about Darwin traveling the world and seeing the same kind of bird with slightly different features made me realize that species have to adapt to their environment and those that cant eventually become extinct. I dont think Lamarck was correct because how can a Giraffe just be like "Oh those trees look good, let me just stretch my neck to reach them." That would be impossible and if that is the case, how would that physical feature get passed down to the next generation. Ive seen posters where monkeys turn into monkeys but they dont have me to convinced. People have talked about "cave men" walking on all four, similar to chimps, and now today us humans have evolved to walk on only two legs. Its crazy to think how closely related to them this makes us look. I am a very religious person and don't always agree but this subject has been quite interesting. Some time in life us humans evolved a lot. While doing an assignment I made a family tree with a few animals that I see no relationship with. This family tree showed me that we are closely related to mice somehow which I would have never guessed. Us humans talk and these animals have their own way of communicating. Its crazy to think that some point in life we looked similar to that and now somehow we are humans.  Learning about evolution has taught me a lot and gave me a whole new look on the world.



Work Cited















Friday, May 9, 2014

Did Darwin Do It All? Explanations of Evolution




EXPLORING THE ROOTS OF EVOLUTIONARY THEORY



Part 1.






Use the links in this section to learn about and briefly describe the background and scientific contribution of each of the following people:



1. Erasmus Darwin:
  • one of the leading intellectuals of eighteenth  century England
  • respected physician
  • well known poet, philosopher, botanist, and naturalist
  • talked about how competition and sexual selection could cause changes in species
    2. Jean Baptiste Lamarck
  • theory of heredity "inheritance of acquired traits"
  • acknowledge as a great zoologist
  • acknowledged as a forerunner of evolution
  • entered the Jesuit seminary at Amiens
  • studied medicine and botany
  • published a series of books
       
3. Georges Cuvier 


  • created the comparative method of organismal biology
  • established extinction of past lifeforms
  • contributed an immense amount of research in vertebrate and invertebrate zoology and paleontology
  • wrote&lectured on the history of science
  • studied at the Carolinian Academy in Stuttgart
  • did not believe in organic evolution



4. Thomas Malthus


  • theory of natural selection
  • political economist
  • worried about what he saw as the decline of living conditions
    • the overproduction of young
    • the inability of resources to keep up with the rising human population
    • the irresponsibility of the lower classes



Part 2.

http://whyfiles.org/125galapagos/index.html




Use the information from Sections 3 and 4 to answer the following questions:



1. What interesting evidence of geological change did Darwin observe while visiting the Galapagos?


  • South America was rising from the ocean
  • realized quakes come from the raised beaches he had seen in Patagonia
  • ancient shorelines



2. What did Darwin learn about the Galapagos finches when he returned to England? What vital information had he neglected to record when he collected them?

Darwin learned that the finches in which the Galapagos finches were not of the same ancestors. He did not think of the geologic site and saw there could be a difference.

3. Describe the distribution pattern of Galapagos mockingbirds. What question did this raise in Darwin's mind?


Darwin saw many differences that happened in the finches. He thought to himself what and how could this happen? This was one of his first and most important thoughts that would help him improve his science of evolution.

Wednesday, May 7, 2014

DNA Sequence Comparisons Between Species


EXPLORING MOLECULAR EVOLUTION

STUDENT WORKSHEET



Results of your pairwise alignment comparing the beta globin gene in humans and in chimps:
  1. Data about the alignment can be found below the blue/black alignment chart. How many base pairs (bp) are there in the beta globin gene for:
    1. The chimp?
  • 600
    1. The human?
  • 626
  1. A blue asterisk indicates that the nucleotides (bp) in both sequences are the same, we say they are conserved. What percentage of the beta globin sequence is conserved in chimps and humans? (Don’t include the insertion at the beginning of the human gene). This percentage is often reported as a similarity “score” below the alignment.
  • 99
  1. Would you expect the protein structure to be highly similar or markedly different in the chimp and the human? Explain.

I would expect the protein structure to be highly similar because there is so much DNA that is similar.


RETURN TO BIOLOGY WORKBENCH INSTRUCTIONS


Results of your pairwise alignment comparing the beta globin gene in humans and in chickens:
  1. What is the percentage of sequence conservation between the beta globin gene in chickens and humans?

Chickens: 601
Humans: 626
  1. Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or that found in chimps? Explain.

I would expect the beta globin protein found in humans to be similar to that found in chimps because their DNA is more similar to humans than the DNA found in chickens.


  1. Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology (similarities)? Explain.  
The results achieved by running these alignments does support the results on evolutionary relationships determined by scientists using anatomical homology because they are similar in ancestry.

Results of your multiple sequence alignment comparing the beta globin gene in a variety of animal species:


1. Examine the Unrooted Tree produced.  
Record the species at the end of each branch on the unrooted tree shown below.





                                   





2. Based on the information in the unrooted tree:


    1. Which two species appear to be most closely related to each other? Explain your choice.
The human and the chimp are the two species that appear to be the close.


    1. Which two species seem to be the least closely related to each other? Explain your choice.
The chicken and the mouse seem the be the least close because they are the farthest from each other on the tree.
3. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give the comparative evolutionary distance (by percentage similarity “score”) between:
    1. The mouse and human
  • 75
    1. The wallaby and the human
  • 79
    1. The chimp and the human
  • 99
Comment on the significance of these results given your knowledge of mammalian groups.







Results of your Rooted Phylogenetic Tree:
  1. Examine your Rooted Phylogenetic Tree and record the species at the end of each branch.  








  1. Based on this tree diagram, which species is/are most closely related to:


    1. The goldfish: Chickens


    1. The mouse: Humans


  1. Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species. Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology. Which two species in the tree above share greatest homology with respect to the beta globin gene?
Chimps and humans



  1. A node is a branch point representing a divergence event from a common ancestor. Which two species have the most ancestral nodes (divergence events) in the tree above? Explain your answer giving the number of nodes leading to these species.
Chimps and humans have four nodes.




  1. Looking at the phylogenetic tree above, which two organisms:


    1. Diverged from their common ancestor most recently?
  • Chimps and chickens 


    1. Diverged from their common ancestor least recently?
  • Chimps and humans



  1. Draw a modified phylogenetic tree to show how the tree above might change if the beta globin gene for a kangaroo was added to the multiple sequence alignment. 























  1. It is important to understand that the phylogenetic trees you generated using bioinformatics tools are based on sequence data alone. While sequence relatedness can be very powerful as a predictor of the relatedness of species, other methods must be used in addition to sequence homology, to determine evolutionary relationships. Briefly describe 3 other methods that you think might be used to determine evolutionary relationships.

Embryology

Anatomy

Fossil Evidence

Monday, May 5, 2014

Microevolution: Changes in Populations


Microevolution


PART 1: EVOLUTION 101



1. How do the authors of this page define microevolution?
The authors of this page define microevolution as evolution on a small scale.
2. How do they define a population?
They define a population as a group of organisms that are interbred with each other.

3. Summarize each of the 4 mechanisms of microevolutionary change that are discussed.
Mutation: a change in a gene

Migration: when one type of organism migrates on way and another type goes a different way

Natural Selection: when a species adapts to their surrounding for easier survival

4.  Summarize the 3 examples of microevolution on this page.
Size of Sparrow: due to different situations and climates the birds have changed size and shape that way they could adapt to their surrounding where they live
Coping with Global Warming: mosquitoes have became familiar with the day length for the time of year and now know a shorter day means to be dormant

Building Resistance: when plants or bacterias grow resistance to a certain poisonous gas/liquid/solution.

5. Summarize the results of the two different experiments (with and without predators).
Without predators there is a huge population of spotted guppies, which females are more attracted to; with predators guppies adapt to blend in and hide, which makes them not as attractive.
6. What types of selection were demonstrated in each experiment?  Are these experiments truly cases of artificial selection? Explain your answer.



--Click on the quick quiz link to go to the quiz.  


7. Pick your three favorite questions from the quiz and write how you would answer them if you were teaching this class.

If I picked guppies that had colorful fins, can I get them to change?
-No it would be impossible to get them to change unless there was a predator and they were trying to hide that way they can survive.

Is microevolution the evolution of small things?
-No this is not true, microevolution is small changes in a species.

PART 2: SEX AND THE SINGLE GUPPY


  1. Why do some guppies tend to be drabber than others?
Some guppies tend to be drabber than others that way they can blend in to hide.
  1. Why do some guppies tend to be more colorful?
Some guppies tend to be more colorful to attract the opposite sex.
  1. What role does color play in guppy survival?
The role that color plays in a guppy for survival is either they are a certain color to attract the opposite sex or they are a certain color to blend in from predators to survive.
4. Explain the push and pull that the environment (including predators) has on the coloration of guppies in Endler’s pools.
Guppies want to find another guppy for sexual reproduction so they are a pretty color to attract other guppies, but the push is they are more obvious for predators and they cannot blend in making it harder to survive.

Thursday, May 1, 2014

Endless Forms Most Beautiful Notes

Charles Darwin

  • Wanted to go to medical program until he saw surgery
  • Took up his passions
  • Started at age 16
  • Father thought he was amounting to nothing and wanted him to join the clergy
  • He was able to travel w/ the British ships and left what his father wanted
    • His father didn't approve
  • At age 22 set off on a 2 year voyage ended being 5 years
    • experienced all weather
    • experienced sea sickness
  • Lyell's principles of Gology and the bible 2 most important books
    • Found out all landforms change
  • First great theory about coral reefs
  • Voyage took him many places
    • Deep jungles of S. America
      • saw flightless birds
      • found fossils (giant sloth fossils)
    • Galapagos Islands
      • swimming lizards
      • giant turtles
      • seals
      • fenches
  • Not only land forms change, so do species
  • species changing was dangerous at the time
    • knew it was a risk
    • kept to himself
      • wrote in secret books
  • married his first cousin
  • became a pigeon reader
  • finches he collected were all different
    • decided came from the same ancestor
  • life is connected in a family
  • he had a theory
    • no one would hear of 20 years
  • fathered 10 children, worked at home (home body)
  • Anne Darwin was threatened by another scientist that was proposing the same thing for awhile now
  • completed the origin of species
    • supports evidence and arguments
  • wallace did not become as known as Darwin
  • Darwin's books inspired more people than Wa;;ace
  • let his wife read the theories and told her to put in drawer till he dies, but he lived much longer than he thought
  • fossil record was the best proof of evolution
  • 13210 feet up sea level you can see fossils
  • Burgee Shale; Trilobites over 500 years old
  • Bone Fossils fount 150 million years ago
  • Fossil Butte national park
    • fossil fish due to lake there
  • palm trees (climate related to Florida)
  • La Brea Tar Pits
    • thick, goey petroleum
    • dead center of L.A.
    • piles of bones due to animals becoming trapped and feeding on each other 


Key Facts From the Fossil Record

  • animal and plant forma have changed over time
  • the timespan of evolution is immense
  • extinction is the fate of most species that ever existed 
  • How?
    • variation
    • time 
    • selection
  • Example
    • lava flow
      • pocket mice live there
      • sandy mouse/dark rock
      • dark mouse/ light rock
      • all same species
      • MCIR gene determine color variates
Color of Mouse Depends on:

  • mutation rate
  • population rate
  •  reproduction rate
    • 1 in 25 million will have dark coat
    • at least 5 babes a year 5000 females
    • every thousand years a black mouse in born to a sandy colored mouse

Wednesday, April 23, 2014

Personalized Genomics

The future holds so much information about DNA that some people may want to know and some may have no interest in knowing. In the future we may be able to tell if we have a disease and how to prevent it based on the genetic information. By getting a DNA sequencing scan you may be able to prevent a disease from happening before it is to late.Genes reveal your risk of diseases one letter after another. Just by having one letter out of place or one misspelling in your DNA, can cause you to have a disease. There is a lot of hope for gene based drugs in the future. Cancer genomes tell us how to prevent a cancer from happening. I as a person would love to know what my genes say and what my health is. Many people find it wrong but wouldn't you want to know what your future holds? I would love to know what is going to happen in my future that way I can plan ahead and know what to be prepared for. If my genes show a disease, I can plan on how to save money and what to do when it comes to the doctors. Also I can figure out how much time I have or what needs to be done to cure the disease. I would definitely submit samples to have genetic screening done on my body. I'm the kind of person that prepares for the future, I am always planning ahead.

   After watching a couple videos over people that have dealt with a disease due to a mutation has made me think. I learned about a little boy that was having trouble with multiple things. This boy got a genetic screening to help and try to see what went wrong and if there is a cure. Unfortunately a cure could not be found at the time being due to the fact that the one of the mutations has only been seen one other time and the other mutation has NEVER been seen before. There was also a man who was diagnosed with the screen cancer called melanoma. This cancer has no symptoms and you usually feel perfectly fine. He was told patients with this usually only have a year or less to live and by time he found out he had it, he only had a month or two to live. He took action and tried to cure it. After awhile he returned to work feeling better. Even though it started to regrow in places, it disappeared fully in a lot of other places. After watching these videos I think genetic screening would be a big help to our future. Imagine being told before it's to late that you carry or have a disease but you don't need to worry because there is a cure for it. Being warned before your world changes can make you a lot happier. These videos were pretty interesting, I recommend everyone to watch them to create their own opinion on genetic screening.




Tuesday, April 22, 2014

Genetic Engineering: Bacterial Transformation Lab

In this lab we are see in if any genetic transformation is taking place when we place bacteria into different situations. We left them to sit overnight to get a result in the morning. My group found this lab to be very interesting. Down below are the instructions, data collections and a few pictures of the after results.

INSTRUCTIONS:

  1. Label one closed micro test tube +pGLO and another -pGLO. Label both tubes with your group's name. Place them in the foam tube rack.
  2. Open the tubed and using a sterile transfer pipet, transfer 250 ul of transformation solution (CaC12).
  3. Place the tubes on ice.
  4. Use  sterile loop to pick up a single colony of bacteria from your starter plate. Pick up the +pGLO tube and immerse the loop into the transformation solution at the bottom of the tube. Spin the loop between your index finger and thumb until the entire colony is dispersed in the transformation solution (with no floating chunks). Place the tube back in the tube rack in the ice. Using a new sterile loop, repeat for the -pGLO tube.
  5. Examine the pGLO plasmid DNA solution with the UV lamp. Note your observations. Immerse a new sterile loop into the plasmid DNA stock tube. Withdraw a lapful. There should be a film of plasmid solution across the ring. This is similar to seeing a soapy film across a ring for blowing soap bubbles. Mix the lapful into the cell suspension of the =pGLO tube. Close the tube and return it to the rack on ice. Also close the -pGLO tube. Do not add plasmid DNA to the -pGLO tube.
  6. Incubate the tubes on ice for 10 minutes. Make sure to push the tubes all the way down in the rack so the bottom of the tubes stick out and make contact with the ice.
  7. While the tubes are sitting on ice, label your 4 agar plates on the bottom (not the lid) as follows: LB/amp plate: =pGLO; LB/amp/ara plate: +pGLO; LB/amp plate: -pGLO; Label the LB plate: -pGLO
  8. Heat shock. Using the foam rack as a holder, transfer both the (+) pGLO and (-)pGLO tubes into the water bath, set at 42C, for exactly 50 seconds. When the 50 seconds are done, place both tubes back on ice.
  9. Remove the rack containing the tubes from the ice and place on the bench top. Open a tube and using a new sterile pipet, add 250 ul of LB nutrient broth to the tube recluse it. Repeat with a new sterile pipet for the other tube. Incubate the tubes for 10 minutes at room temperature.
  10. Tap the closed tubes with your finger to mix. Using a new sterile pipet 100 ul of the transformation and control suspensions onto the appropriate plates.
  11. Use a new sterile loop for each plate. Spread the suspensions evenly around the surface of the afar by quickly skating the flat surface of a new sterile loop back and forth across the plate surface.

DATA COLLECTION:

  1. Carefully draw and observe what you see on each of the four plate.    (Pictures are listed below)
  2. How much bacterial growth do you see on each plate, relatively speaking?  There is a lot of growth. It looks like there are thousands of tiny spots.
  3. What color are the bacteria?  The bacteria is a tannish, whitish-yellow color.
  4. How many bacterial colonies are on each plate (count the spots you see).  To many to count.