Review Day

All we did in this class, as clear form the title was review.  We linked all the unit key ideas and learned the connections between everything we've learned.  I am currently reviewing all of these topics like a mad man, because it is almost 11 and I have my midterm tomorrow.  So I will keep this blog post short as well.  Not like there was a lot to talk about there anyways....

Your Inner Fish Chapter Six Summary

In this chapter of Your Inner Fish it talked all about embryology and how animals develop differently after their parental genes are combined.  That was basically the whole thing, and I am trying to study for the test...so this is my chapter 6 summary for Your Inner Fish, enjoy Mr. Quick.

Starting A New Unit: Mitosis and Meiosis (And A HUGE Project)

At the start of this class we had an opportunity to start working on our huge product that is due on Friday, the day of the test.  For this project we look at the inside of and animal, plant and bacteria cell to figure out how each organelle functions.  In theory, doing this project will not only let us understand how cells work in different forms, but why and how cells undergo mitosis.  After we had the short time to start the project, we got an introduction into using the microscopes, digital and optical.  We looked at a flea and some plant cells through both and figured out how to use the different parts of the microscope.  Next class
we will be using the microscopes again, so this was a good first attempt at using them.

Test Day: Genetics

In this class we took a test on our knowledge of genetics and everything else in this past unit.  I felt confident on every answer except for the Hardy Weinberg questions.  The formula is a concept that I am still struggling with but getting better at.  The prezi I turned in before the test helped me review a lot of the genetics and pedigrees.  If any questions from this test show up on the next one (excluding the Hardy Weinberg), I would be confident in answering.  I feel that I had a strong understanding of the concepts within this unit.

Even More Genetics! and Pedigrees

In this class we delved even further into the topic of genetics, this time looking at pedigree's and how dominant genes work together, such as AaBb.  So first of all, how they work together, is when in the genes their is too dominant alleles, like in AaBb, then their can be a co-dominance.  In pheontypic terms, it could be a brown cow with white spots.  Both of the dominant traits for color will show up.  If the genes were Aabb though, the cow would be all brown.  It only takes one dominant gene to over ride the recessive traits.  On to pedigrees, these are family trees that put into picture what punnett squares do for us in genetics.  Their is seperate symbols for male: carrier, deceased, etc., female: carrier, deceased, pregnant, etc., and even unspecified gender for pregnancy.  So with these you then have the ability to make a detailed family trees which show the traits being passed on through many generations of breeding.

Genetics and Meiosis

In this class we furthered our knowledge of genetics with alleles, as mentioned in the previous blog, and looked at the process of meiosis.  Meiosis is the process of your parents genes copying half of their traits and creating a new cell, a sex gamete.  These sex gametes are only supposed to have 23 traits each so that when they meet there is 46, the offspring's traits.  I say "supposed to have" because sometimes occasionally an extra trait will be coded in to the gamete and this can cause genetic disorders such as down syndrome.  The 23 traits that go into each of your parent's gametes are random, your mom and dad could give b recessive for blonde hair but they both might have brown hair.  This is where the punnett squares come in, if they are both carriers then there is that 1/4 chance you will be recessive-recessive.  But if they had four children, there would not necessarily be 1 BB, 2 Bb, and 1 bb.  This is because the process of selecting genes is randomized, yes the percentage outcome is still fairly accurate but, it will not be exact in this situation.  This is how meiosis works, and this is how your parents passed on their genes to you.

First Day of Unit 4: Alleles

In this class we started the fourth unit which involves genetics and how they work.  This is important to us because it is us.  Genetics are what determine anything that is living.  They are what distinguish each of us as different people down to our sex.  So for this class we specifically looked at how genes are passed down form parents to their offspring.  Traits get passed on from your parents, one from your dad and one from your mom.  Let's take hair color as a n example: Let's say B is the dominant gene for brown hair and b is the recessive trait for blonde hair.  Now your parents both have two genes for this trait because they got one from each of their parents.  Lets say your parents Bb and bb.  That means you have a 50% Chance of being Bb and 50% chance of being bb in other words you could be brown haired or blonde haired.  Recessive traits like blonde hair in the example only show up if both of your genes are that, if a dominant allele is present whether it is one or two, will show.  That is why it is called the dominant gene.  The first person to see these alleles and apply them was Mendel who bread pea plants and observed generations and how certain genes would show in them.  He would look at height, color, etc. and see how these traits would pass through in generations of pea plants.  This is how humans and all animals differ from one to another.

Test Day

In this class we had our unit 3 test.  Talking mainly about DNA replication and protein synthesis. There was also previous concepts brought up sporadically like osmosis.  The test was challenging for me though, and it has shown me that I really do not understand DNA replication and protein synthesis.  These are two things I greatly need to review as we go into the next unit of genetics.  I know it is all the background to what we are about to study, but I have trouble grasping exactly how to do the processes on paper.  The steps are simple enough in both, but it is difficult to take a short strand and go through these steps all on paper.  The Unit test let me see where I need a lot of improvement.

Snorkitty Snork Snork

In this class we looked at the process of translation.  Translation is where RNA is read by a ribosome and transformed into proteins based on the coding in the RNA.  In this labs these proteins then show up as traits in mythical beings known as snorks.  Lovable, but dangerous creatures indeed.  We looked at a small strand of RNA that would hypothetically represent 9 main traits.  Every group was given a different strand of RNA so that everyone's snork would look different in the end based on their physical traits.  This is how it works in real creatures cells as well, but on a much larger scale.  For the snorks though, mine came out as such:

SNORK

Sweet Jumpin' Genes He Has 8 Fingers

 This picture may only show a flower bursting with a lovely lilac color, but really there is 100's of jumping genes at play forming a mutation.The color gene in this flower, purple or white (you can't assume it is one or the other), has jumped around the DNA either cutting itself from one part and going into another or duplicating, and sending the copy to another segment. With the movement of this gene a mutation forms making the flower splash with vibrant colors. At one point in previous generations of this type of flower, it may have been all purple or white.

In this lil' curly devil's genes there was a duplication because of a movement in the Zone of Polarizing Activity (ZPA).  When shifted this can cause a duplication of certain structures.  In this case it was fingers, the ZPA must have moved multiple times and created many fingers on accident. This is why this child has so many excess phalanges.  

Chapter 3 Summary

In this chapter of Your Inner Fish, the author delves deeply into why organisms develop the way they do and what separates them form any other living organism.  The answer to the second part of that is within the DNA; organisms may have extremely similar DNA but the relatively small variations make huge differences. This is because of development also, when an organism is first created it is very small and has DNA that can only form so many cells.  Those cells though, then form more and more and eventually what started as a single cell organism is a self-functioning creature.  So this is why creatures with similar structures differ so greatly in the big picture.  The next question that is answered is why creatures have symmetrical structures.   A breakthrough in research at a Harvard research lab explained why pinky's formed different from thumbs and why hands formed symmetrically.  The zone of polarizing activity (ZPA), was where the development was happening that would make a the hands.  If moved, a may form two identical digits.  Another project where the ZPA was secluded to half of a cell showed that the half with the ZPA developed a hand while the other side did not.  In the final part of the reading it explained that because of the way certain parts of genes in DNA are active at only certain times to make different types of molecules, even humans and fly's have similar genes for hands/wings, but they develop differently.  It argues that the changes through evolution did not necessarily come from new DNA, but rather ancient DNA that was not active in other organisms during their developmental stages.

Reading Review

For homework we had to read chapter six of Survival of the Sickest.  This chapter talked about genes and how they develop and change over time.  The first idea that was brought up in this chapter was the old theory of evolution that has been disproved with more recent evidence.  Originally it was thought that DNA changed randomly and mutations were sporadic and extremely rare.  This could not be true though because it could not explain how far humans have changed in a relatively short amount of time.  Knowing that mutations must be intentional geneticists realized that mutation can be caused by virus', bacteria and radiation.  DNA can change when needed based on these outside sources and other genetic factors.  These other factors are things like genetic jumping, where genes can cut and paste elsewhere or copy and show up in another area.  This is where natural selection comes in.  Genes that vary in a beneficial way are passed on because the population will want that gene.  The opposite is true for harmful genes, they will eventually be eradicated from a population if they are not helpful to have.  Genes in everything are ever changing and they always will in any species that survives for multiple generations.

Blog Quizzical

1. Explain the significance of Mendel.
 He looked at how genes move through generations by breeding peas.  
2. Draw the structure of DNA and who discovered this structure. 
James D. Watson and Francis Crick proposed the structure of DNA in 1953: The Double Helix.

3. Explain each of the five examples of variations that occur to DNA and give an example of each. 
Point mutation, insertion, gene copy number, deletion, and inversion.  Point Mutation is a single base pair change.  Insertion is the addition of another base pair.  Gene copy number is duplication of certain genes that happen during cell division.  Deletion is the absence of a base pair in genes.  Inversion is when a chromosome is flipped around.  
4. What is evo-devo? 
It is a sub-study of evolutionary biology where developmental genes are more closely examined and how they play a role in evolution.
5. Make a connection between human migration and the mutation of lactose intolerance.
Humans in America, Africa, and Europe were the only ones who after they grew up continued to use animal's milk for sustenance.  This is why people in other parts of the world are more likely to be lactose intolerant.  

Option 3: Traces of A Distant Past

I got option 3 assigned to me from Mr. Quick in this class and read the article: Traces of A Distant Past.  In class we watched a movie that discussed everything that was discussed in this paper.  The first main subject was the migration patterns of humans over millions of years.  Evidence shows that humans started in Africa and expanded to other parts of the world through slow migrations.  The evidence that proves this lies within human DNA.  By looking at the DNA strands of people in the Sans tribe in Africa, scientists can observe the y chromosomes of males and see the changes over time.  Scientists are creating a family tree of everyone in the world just because of there slight differences in DNA over long periods of time.

The article and movie have conclusive evidence of how humans got all over the planet over a relatively short period of time.  A lot of the movement was sparked by environmental changes in their environment so they moved on looking for means of survival.  Evolution was possible in humans because of this and it is why everyone is different today.  

Unit 2 Test Day

We took the unit 2 test today and I felt confident in my answers for 99% of the questions.  The genetic standards we are currently looking at are logical and easy to comprehend so it is not too complicated.  Everything is logical because it makes sense that genes will get passed down through generations, and as more branches form there is going to be more mutations/variations. UPDATE: I did well ont eh test and got a 93% giving me an A- for the quarter.  I understand what my mistakes were on the few satandards I missed and corrected them.

Dominant & Recessive Genes...NOT JEANS

In this class we looked at dominant and recessive genes and how they act over generations in a given population.  To do this everyone in the population (our class) was a Aa and they randomly selected one of someone else's genes and one of their own to show that their offspring would be that.  Although AA and Aa will show the same phenotype, we took a count of AA, Aa, and aa to find how genes change after 5 generations.  In the end of our first experiment we found that AA was 10, Aa was 3, and aa was 3.  Using the Hardy Weinberg formula we found that A showed up 57 % of the time while a showed up 43% of the time.  In the next step we took two separate populations, one of 6 and one of 10.  In the 6 population 3 were AA and 3 were Aa.  this showed us again using the formula, that A showed up 50% of the time and a showed up the other 50% of the time.  Recessive genes may rarely show on the phenotype because there has to be two present for a phenotype to show.  In Aa, only the dominant gene shows because it dominates the recessive gene.  This is is how genes work and do not confuse them with jeans this took me about an hour to figure out....

Brine Shrimp Lab

In this lab we looked at how certain brine shrimp in a given population are evolved to survive in different salinity's of water.  We placed Brine shrimp in 0, .5, 1, 1.5, and 2% concentrations of salt water.  A different amount survived in each salinity because not all brine shrimp are mutated to survive in one specific concentration.  The majority did show .5% was the most ideal environment to survive in.  It is impossible for the brine shrimp to all adapt to one salinity in as they are put in water because they are not able to adapt immediately to their situation like humans.  This would take them many generations.

Natural Selection --> Evolution

In this class we looked at natural selection and how mutations that are not good for the environment do not survive through the generations.  We did this by using 25 beads each of two colors to show how hairless Bengal tigers got wiped out.  The two green beads represented hairless tigers.  These hairless tigers were put in the killed section because they did not survive in the wild without hair.  After ten generations there was no more possibility for hairless tigers because that mutation was down to one bead which when put with a red one was no different than two red beads.  This shows how a mutation that does not survive the conditions of a creatures environment get wiped out after enough generations pass by.  This is one more point that further proves evolution.  It displays why and how species change over time and eventually evolve with mutations that let them survive, a.k.a.: adaptations.

Parents Day: Survival of The Fittest (sexiest)

On parents day we looked at what features humans look for in other humans based on attractiveness.  In men, the majority, looking at males, chose less masculine features because they saw the one of the two that was less threatening.  This leads to the decision to take on the weaker rather then the stronger. The men who chose more masculine features did this because they were more confident that they were better then the manly of the two faces.  In women men picked the less masculine faces because they were, to the male eye, more attractive mates.  In women, they picked men masculine or feminine based on what time of the month it was.  If they were going through ovulation they wanted a more manly face for mating.  If they were menstruating they wanted a more feminine face to be a care taker.  In women, they picked the more feminine faces every time because they all thought that they were more beautiful.

Evidence of Evolution Quiz

1. Explain the following picture in terms evidence for evolution.

A: This picture shows how, this land animal adapted over millions of years and generations so it would be better suited for it's environment.  

2. Which of the following continents did marsupials begin from?
1. Europe
2. Africa
3. Australia
4. South America
5. North America
   
   
   A:  e, North America

3. Comparing a dragonfly, bird, bats - explain the type of evolution that these organisms show.

A:  They evolved bones, got bigger and eventually back down to a smaller size once again.

4. Explain how the Common Descent Lab shows DNA evidence and ancestry as evidence for evolution. Include examples of Primates.

A: This lab showed how over generations species changed slowly to adapt to their environment   This slow evolution is visible due to homologous structures and similarities in Hemoglobin DNA strands.  Chimpanzees show a 97% similarity to human DNA.

5. Explain homology using some examples from your readings.
   
   
   A: Homology is the use of comparing similar structures in species. In the reading we looked a the tiktaalik which was similar to the land-fish that were before and after it's time. This is one of the key points in proving evolution.

Eleventh Class: More Transition Fossils

In this class we brought em' back.  Oh yea baby, Transition fossils.  Only this time, Adam and I got to choose which fossils we would like to look at.  The obvious choice, and the one we chose, was to examine platypus fossils and now we must create, from our IMAGINATIONS a fossil that would show transition between two already known genii of platypus.  This fossil needs to show characteristics of both genii and clearly be a step up form the last while not quite being the newer genus.  We are going to make a full research webpage for our "discovery" which will be linked in the blog later.

What does the platypus say?

Tenth Class: Tiktaalik and Evolution

In this class we looked at the extinct creature the tiktaalik.  This is a transitional fossil that adds one more important link in the long chain of evolution.  The change from fish to animals was a slow one with many holes along the way, but the tiktaalik was an important step in the process.  There is still fossils between the tiktaalik and those around it, but it did fill a gap.  This is what finding any new species does, it fills gaps so that we can explain why animals are very different from their ancestors.  For example by finding ancient horse fossils we can see how at one point, a long time ago, horses used to have three toes.  Over thousands of generations they lost two because they did not need them anymore.  Evolution like this can be seen in any animals around today.  Fossil hunting and identifying explains to humans why we are the way we are.

Tiktaalik display -- We have one in the museum!

Ninth Class: DNA Strands and Cladograms

In this class, as you can tell form the title, it was all fun and games as we examined hemoglobin DNA strands of humans, chimps, apes, and a mystery common ancestor.  looking at all the similarities between very short strands of all 4 of these DNA samples, we were able to form a cladogram showing evolution between these animals.  The common ancestor was at the very start because, it is in the name...ANCESTOR of the other three.  Next on the cladogram, branching off, was the ape because between the three remaining species it was the most similar to the common ancestor, and was the first to evolve.  After the ape were the chimps on their own branch as well, because they did not directly evolve from apes.  Finally humans fall onto the cladogram also coming off the main branch because they are very similar to chimps, but not directly down on the evolutionary chain form them.  You can see all of this in the HOMEMADE cladogram below.

Eighth Class: Test Day

In this class we took the first unit test that covered water, osmosis/diffusion, cell structure, and micro/macro-molecules.  Knowing that all these concepts are connected it is easy to figure out logical reasoning for the way one works by knowing another.  For Example, knowing that the cell wall only lets through certain molecules and wants to have equilibrium on both sides, we can figure out why osmosis and diffusion occurs.  Having connected concepts that overlap made the test a whole lot easier than memorizing a bunch of random concepts and formulas we are never going to see in our lives again.  Thanks for not making us read all of these and "memorize the material" Mr. Quick!

Seventh Class: Ye Olde Tale Of The Theft Of Young Jerell's Ipod

In this class we figured out who stole Jerell's iPod based on the food sample they left behind.  We tested the foods: pretzels, butter, jelly, fat-free yogurt, beans, and a wet and dry sample of food the thief left behind.  From this we found which of these foods contains glucose, starch, protein, and/or lipids.  Knowing which foods had each, we then looked at what Jerell's co-workers ate for lunch.  The only food that matched the mystery substance was Jose's bean and cheese burrito.  Thus the culprit was Jose, the new guy around the joint.  Finding this out was only possible by using iodine, biuret, benedicts and sudan to test for basic elements within everyday food.

Wasn't me e se...

-Jose

Sixth Class: Cell Wall Structure

In this class we examined how diffusion and osmosis work at a cellular level. Molecules trying to get through the call wall must either be non-polar and pass through the bi lipid layer, or get "ferried" across by a protein.  Polar molecules such as H2O cannot slip all the way through the bi-lipid layer because when they reach the second layer the polarities repel and it is shot back out.  For non polar molecules that are not too large, this is no problem and they slip through without going through a protein.  For the polar molecules to get into cells, this is what they must do.  Certain proteins will accept certain molecules while others will let any molecules of the correct size pass through easily.  These proteins are scattered all over the cell wall to pick up molecules as they come in.  They serve as the GATEKEEPERS  for the cell.  The carbohydrates on cells reach out and grab connect with other cells.  Messages such as pain, are sent through the body by these connections chemically.  Thus a body of cells works together by connecting cell membranes.

Fifth Class: Diffusion Lab

In the fifth class of biology, we conducted a lab to find the effects and rules of diffusion in molecules.  As previously explained in the last blog, diffusion is the ability molecules have to move through semi-permeable surfaces.  This lab showed us that molecules can diffuse based on their size and take longer to move through thicker surfaces. In the picture on the left we placed starch in dialysis tubing and let it soak in Iodine.  The starch turned dark blue form the iodine diffusing in.  We than took some of the remaining iodine out and mixed it with benadicts, while heating it, to see that no starch escaped the tubing and the chemicals bonded to form a brown solution. The middle and rightmost pictures show how far through NaOH can soak through a "cell" of that size in 15 minutes. The last picture is simply for your enjoyment, enjoy.

Yeaaa Baby! -Adam

Fourth Class: Diffusion and Osmosis

In our fourth class we looked at the processes of Diffusion and Osmosis. Diffusion is the way molecules will exit or enter a semipermeable surface to balance the pressure on either side of the surface.  For example, when a bottle of perfume is opened, the molecules will slowly shoot out as they are bouncing all over the place.  In balloons, after a while they shrink and no longer float on their own.  This happens as helium molecules rush out of the thin material and it becomes heavier than the air around it.  Osmosis is a similar process, but is only used to describe water molecules.  In cells water molecules can move in and out through the cell wall because it is semi-permeable.  This is important especially to human life, because it is the reason we drink water.  The water enters our blood system and hydrates the blood cells.  Water can move like this due to its size and it's innate ability to balance the pressure on either side or a membrane.  Osmosis and diffusion are important in life because of their significance in the movement of molecules.

Third Class: Water -- Cohesion vs. Adhesion

In class three we looked at the properties of water: cohesion and adhesion.

Cohesion:
         Cohesion is the ability that water has to "climb" up objects like straws.  This is possible because of the way the molecules bond together they will appear to climb up the sides of glasses or straws.  The water can only go to a certain point before having to stop because it cannot support any more molecules on top.
Adhesion:
         Adhesion is the ability that water has to hold together and form a bubble shape with high surface tension.  In the lab we would drop as many droplets of water onto a penny before the surface tension would grow to great and the water would spill off the penny.  The bonds within the water lets it retain it's shape on top of the penny.
          These properties of water allow trees to get water to their leaves, let water striders run across water, and water to form symmetrical droplets in nature.

Second Class: Co-valent And Ionic Bonding

In this class we looked at the basic part of basic chemistry: bonding of atoms.  The first two that we study are: Co-valent and Ionic bonding.  Co-valent bonding is where valence electrons are shared between the two molecules that are bonded share the electrons to complete each others outer shells.  In ionic bonding some of the molecules will give up their valence electrons to drop down to a complete electron shell and become stable.

Co-valent
                                               Ionic





These different types of bonds dictate what atoms can bond with other atoms and in what way they will do it.

First Class: Dancing Milk

In the first class of Honors Biology we created an experiment to explain why milk with food coloring "dances" with a drop of soap.

First, Eddie and I hypothesized that the intensity of the reaction was based off of the amount of fat in the milk.  To test our theory we made the milk a variable and tested different types while keeping the soaps a constant.  The different milks we used were whole, 2%, and skim.  Using the same soaps in these three different milks we found that whole milk had the fastest and longest lasting reaction while skim had the least.  To make sure that this result was caused from the difference in milk we used Dawn, Sun, Ajax (bleach), and Palmolive Orange dish soap in all 3 and found that the different soaps made little to no difference in reaction.  From this we concluded that the amount of fat in the milk did affect to what extremity the food coloring would "dance."