Microscope Lab Day + Extra Credit + Your Inner Fish/ New World Example

Today in class, we did a lab using SUPER DUPER high tech microscopes.

First, we looked at a dead flea:

Note: not my picture. http://cdn.orkin.com/images/fleas/flea-exterior-interior_1162x1248.jpg. 

Then, we looked at some skin cells from James' cheek.

Next, we looked at a plant with a drop of water.

Finally, we looked at a slab of algae from saltwater.

The point of the lab was to get used to the microscopes and observe plant and skin cells.

Extra Credit:

This is the answer to the problem that was emailed to us.

Key:
BB = black Lab, no chocolate gene 
Bb = black Lab, carries chocolate gene 
bb = chocolate Lab, no black gene

Yellow is produced by the presence of a recessive epistatic gene which has the effect of masking the the black or chocolate genes.
EE = no yellow gene 
Ee = yellow carrier but apears either black or chocolate 
ee = yellow Lab

So....
EEBB =Basic Black (BB)
EEBb =Black that carries Choc. (Bc)
EeBB =Black that carries Yellow(By)
EeBb =Black that carries Yellow and chocolate (Byc)
eeBB =Yellow (Yy) [does not carry chocolate]
eeBb =Yellow that carries Chocolate (Yc)
eebb =chocolate pigmented yellow ~ No Black Pigment (NBP)
EEbb =Chocolate (CC) [does not carry yellow]
Eebb =Chocolate that carries yellow (Cy)

From: http://www.blueknightlabs.com/color/coatcolor.html

Because:

In the picture, it is about half of the puppies black, and half of the puppies chocolate, so the punned square above would make sense.

Embryology:

Embryology is the comparing of embryos. Species, such as salamanders, chickens, and fish, look completely different as adults, but look very similar as embryos.

http://www.nature.com/nrg/journal/v7/n11/images/nrg1918-f2.jpg 

Scientists use these embryos to discover the similarities within different species.

"Limbs as different as bird wings and frog legs looked very similar during their development" (99).

Embryology in Today's World

Embryology is used to help parents that cannot conceive naturally, conceive.

It previously had been a tedious and error-ridden job. However, new technology, called IVF Technology, has been created to make this job easier, faster, and more effective. 

Eeva (Early Embryo Viability Assessment test) is an example of this technology. The €100,000 Eeva is really new technology, as the first birth occurred today using its technology.

Here's a picture of the happy couple:

Embryology Manager Tony Price said of Eeva: “The main advantage of this technology is that we are able to identify embryos which have an extremely low chance of advanced development, and these can be excluded from use in treatment.”

IVF systems will continue to be used and make artificial conception a cheaper and more effective option in the future.

http://www.dailyecho.co.uk/news/10873585.Baby_is_first_to_be_born_in_Southampton_using_new_IVF_technology/

Genetics Test Day

The test went well... Yeah.

Final Day of Genetics

Today, we reviewed what we learned last class and took a short quiz on it.

Then, we learned a new concept called pedigrees.

Basically, pedigrees use symbols to determine who carries what gene for certain illnesses. Here is what a pedigree looks like:

After, we did some pedigree practice problems and that was it for this class.

Genetics Day 3

Today, we learned of different types of genetics, such as: Incomplete Dominance, Sex-Linked Crosses, and Medical Disease Inheritance.

Incomplete Dominance:

Incomplete Dominance is when one allele is not completely dominant over another allele. Here is an example: Yellow fur in guinea pigs is represented by: C^Y C^Y, White is represented by C^W C^W, and Cream is represented by C^Y C^W. Say a white guinea pig crosses with a white guinea pig, and produces all white guinea pigs. Cross a cream guinea pig with a cream guinea pig. Determine the phenotypic ratios.

Here's how you do it:

Simply use the foil method.

So then, you just convert the genotypes to phenotypes.

1 yellow : 2 cream : 1 white.

Sex-Linked crosses

Sex linked crosses are crosses that pass down traits through a sex chromosome.

Here is an example of a problem: 

Red  eyes is dominant over white eyes.

Red = R

White = r

Cross a homozygous red-eyed woman with a white eyed male.

Females are XX and Males are XY. Thus, because males don't have 2 X's, they can only have 1 half of an allele. Here is how you solve this problem:

So then you end up with 2 red-eyed females and 2 red-eyed males.

Medical Disease Inheritance

This has or so with blood types.

O, written as i, always is recessive.

A is written as I^A, AB is written as I^A I^B, and B  is written as I^B.

Blood type A can either be I^A or I^A i.

Blood type AB is the same as above.

Blood type B can either be I^B or I^B i.

Blood type O is I^O I^O or ii.

So here's a sample problem:

A mother has a blood type A, her daughter has blood type AB, and her son, blood type O.

What is the mother's blood?

Answer: I^A i, because without the i, then the son would never be able to have the blood type O.

That's it for this class.

Genetics Day 2

Today, we took a quiz on mono-hybrid crosses then went over di-hybrid crosses. This occurs when there are 2 genes involved in the cross. Here is an example of a di-hybrid cross problem. A heterozygous running, heterozygous white fur rabbit crosses with a homozygous running, homozygous brown fur rabbit. Determine the genotypic ratios. R = running r = waltzing. W = white w= brown. 

First, you can use Dr. Fitz's or Mr. Quick's way.

Here is Mr. Quick's way:

Then, you take each square from the left and combine them with all four from the right.

RRWw RRWw RRww RRww

RRWw RRWw RRww RRww

RrWw RrWw Rrww Rrww

RrWw RrWw Rrww Rrww

So the genotypic ratios would be:

4 RRWw : 4 RRww : 4 RrWw : 4 Rrww

Or 1:1:1:1

That was all for the di-hybrid cross class. 

Genetics Day 1!

Today, we were introduced to genetics and genetic crosses.

 

We only focused on monohybrid crosses today, as we will get to dyhybrid crosses next class. Basically, crosses are just methods of finding phenotypes and genotypes and determining which traits will show, which won't show, dominant and recessive traits, etc..., using a square.

 

Here's an example:

 

 

We worked on some practice problems then we took a quiz and that was it for the first class on genetics.

Lab Day

To start off class, we began by doing a white board based off of DNA structure. Mine looked as follows:

We then moved onto the lab.

Glow in the Dark Bacteria Lab

The purpose of the lab was to create bacteria with certain traits and to see which would display the glow of plasmid.

Here is out pGlo plus and minus tubes being heated. 

We found only one out of the four types to glow: LB with Amp. and Ara. 

Snork Day

Today we reviewed protein synthesis and took a quiz on DNA replication. 

After, we did a mini-lab where we determined the amino acids of complementary strands of RNA and were able to create features for our own snorks. 

My Snork looked like this

And here is a picture of the lab itself

Protein Synthesis Review Day

Today, we reviewed protein synthesis a took a quiz. The students taught the class, and went over the three categories: Transcription, RNA processing, and Translation. 

Here's what the board looked like when Mr. Quick explained the quiz answers:

We also looked at our pGLO labs and saw that most of the arabanose glow had gone out. 

That was it for the class before the test. 

DNA Structure Day

Today we took a quiz on the Journey of Man video, then we went over the structure of DNA.

Our white board looked like this by the end of class: 

As you can see, we drew the double helix  and labeled hydrogen bonds, nitrogen bonds, ATGC, and nucleotides.

Jump into the Gene Pool

Chapter 6 of Survival of the Sickest was about evolution that occurs inside our body, rather than the more popular view of outside evolution. 

It discussed how less than 3% of the DNA in our body is used to make proteins, and the rest (non coding DNA) comes from parasites that actually assist in shaping our evolution. 

Internal evolution is caused by slight mutations that, although most of the time are harmful, can sometimes result in beneficial adaptations for the body and then can be passed down through natural selection. Mutations are not random: they occur when the sequences of DNA change slightly, when the body is under stress. Jumping genes come in and delete or replicate genes to adapt to the stress, and this is when the sequences get changed and mutations occur. Our body changes its genes in hopes of beneficial mutations. Viruses, which make up some of the noncoding DNA, assist this mutations by grabbing onto areas in which the body believes are more likely for beneficial mutations. Once a beneficial mutation occurs, the body passes on the mutation through natural selection so that its offspring can have a higher survival and reproduction rate. 

Thus, through non-random mutations and the assistance of parasites, our body is able to evolve internally. 

Journey of Man Day 2

Today, we finished journey of man.

Just because the main guy totally looked like Luke Walton.

Homework:

1. The significance of Gregor Mendel is that he swept away the confusion of blending inheritance by breeding pea plants and seeing that both forms of a trait could reappear undiluted in future generations

And the alternative forms of the trait, though not appearing, were still not blended away in the offspring. Mendel gave us what we know about dominant and recessive genes.

2. Francis Crick and James D. Watson created the structure for DNA.

It looks like this:

3. The five different types of DNA mutation are substitution of one letter for another, deletion of a letter, duplication of a letter, insertion of a letter, and inversion or translocation of a letter (letter is in different order). An example of substitution would be instead of the sequence ATAGCA it would instead be CTAGCA. An example of deletion would be instead of ATAGCA it would be ATAGC. An example of duplication would be instead of ATAGCA, it would instead be ATAGGCA. an example of insertion would be instead of ATAGCA, it would be ATAGCAG. An example of inversion or translocation would be instead of ATAGCA, it would be ATACGA. 

4. Evo-devo is a subspecialty within evolutionary biology that concentrates on studying the effects of changes in important developmental genes and their roles in evolution.

5. A connection between human migration and lactose tolerance is that East Africa contains a strong percentage of people who are lactose tolerant, while in the rest of the world it is a minority. This means that early humans in East Africa were lactose tolerant because they were a milk-dominated society, but as they migrated to different parts of the world less became lactose tolerant because the trait was unneeded in less milk based societies.

Journey of Man Day

Today, we reviewed our test and what we learned from the homework assignment the night before, then we watched a video regarding the "Journey of Man," and how we got to where we are today.

Response to Article 1, "Does Race Exist?"

Nowadays, it is often preached that race should be ignored because we are all humans at heart, that just because our skin color is different doesn't mean we don't function the same way. Recent findings have supported this theory and have given it meaning in the biological world. 

Upon reading "Does Race Exist," I have learned that the concept of race is invalid in comparing humans and our ancestors. When we think of race, we think of physical appearance such as dark skin, or light skin, curly hair, or straight hair, brown eyes, or blue eyes. Although race does sometimes account for different resistants to disease, these physical differences are essentially meaningless in providing evidence for where we came from. People are affected by numerous variations and mutations and although two people may have similar appearances, they could come from completely different environments and have completely different ancestors. Because people look similar does not mean that they are genetically similar. Also, in contrast, people may seem genetically dissimilar because natural selection has exaggerated the differences in appearance, making them more similar underneath than on the surface. Thus, scientists must look at genetic makeup to determine where we came from.

As explained in "Journey of Man," evolution is created through variations of genes that  are then passed down from generation to generation and then those genes are then variated some more down the line. Some variations do not occur within genes, and do not directly affect a particular trait. These variations, known as polymorphisms, are variations in the building blocks of DNA, which scientists study to show individual variations in traits and genetic diseases. Upon studying polymorphisms, scientists are able to see the these variations come from natural selection. As variations that allow species to survive and reproduce better are passed on, the DNA strands of the next generations differ from their ancestors and thus make the search for our ancestors more difficult.

Another tool of polymorphisms that scientists use are Alus, or similar pieces of DNA. Once an Alu is placed, it remains there for eons and is passed onto the following generations, giving scientists another tool to track down our ancestors. For example, if two people have the same Alu then they are descendants of a common ancestor. Scientists have been able to break the myth of race using Alus. By comparing Alus from different populations and sorting people off of their Alu similarity, there was little parallel between Alu similarity and race. When scientists studied different populations based on their Alu differences, they were able to draw connections from all the populations to two places, thus proving that genetic differences can be studied to discover geographical origin, or at least obtain a small sense of it.

Genetic variations account for different defenses against diseases. For example, people that lack the CCR5 polymorphism are less susceptible to HIV-1 because it hooks onto the CCR5 in order to enter our system. We have been able to see that polymorphisms affect different populations differently. For example, a common polymorphism found in Europeans delays a certain type of disease while the same polymorphism accelerates the disease in Africans. Therefore, but studying different details of genetic differences, scientists have been able to separate different populations into different classifications and are that much closer to discovering our human origin. 

Test Day

The test was fairly straightforward, and it was graded very quickly along with our Paleo projects.

Yeah...

Allele Frequency Lab Day

Today, we learned how to find allele frequencies and do Hardy-Weinberg Problems, like the one below:

Hardy-Weinberg problems are all about the equation, p^2 + 2pq + q^2. In this equation, p^2 is the homozygous dominant gene, meaning the same dominant gene twice, 2pq is the heterozygous gene, meaning one dominant one recessive gene, and q^2 is the homozygous recessive gene, meaning 2 recessive genes. Homozygous dominant and heterozygous genes will always show the dominant trait. The only way the recessive gene can appear is through the homozygous recessive gene. This is why the recessive gene always stayed alive in the tiger lab, but couldn't appear often enough to drastically affect the tiger population. 

The Bengal tiger lab: 

We then took home a cladogram and evolution quiz:

Parents Day

Today, we first gave parents a taste of the labs we do in class by collecting data for 48 hours for the brine shrimp lab. 

Brine shrimp after they hatch.

Next, we did an experiment with masculine and feminine faces. Morphed faces were shown on the board and it was our job to put which we thought was more attractive.

We found that masculine faces were chosen because a strong, work-horse mate was desired and feminine faces were chosen because a caring, nurturing mate was desired.

I got half and half for my male category and mostly feminine for my female category, meaning that I like a mix for male and I want a very nurturing and good parent female for a mate.

Left feminine right masculine.

Shrimp Egg Lab

In class today, we started by sorting snail shells and discussing various differences we saw between the shells, such as shape, size, or design. We concurred that these differences happen due to mutations and different species. Lastly, we hypothesized why some shells had 2 shells and it turns out the second hole is from predators sticking their tongue in and eating the snail. 

We then moved onto a natural selection lab.

Shrimp Egg Lab

First, we filled 5 beakers with different percentages of NaCl dissolved into each. Next, we placed double sided tape on 5 microscopic viewing slates. 

Then, we placed mini shrimp eggs on each (around 20) and placed the slates into each beaker. 

Lastly, we placed the solutions from each beaker into a separate container, and close the lid shut. We now have to wait 24 hours to test the results...

Paleo Project Announcement Day

Today, we reviewed evolution in relation to plants and disease, particularly in fava beans.

Then, we took a short quiz.

The majority of the class was spent picking and working on our Paleo Project.

PROJECT

James and I chose to research early kangaroos.

We have learned that early kangaroos were more like dogs, with 4 legs, claws, and sharp teeth. Here is a picture of a Nambaroo gillespieae:

We also discovered that these kangaroos evolved from possum-like tree-dwelling marsupials in Australia, similar to the one in these pictures:

This is what our research has consisted of so far.

We are continuing to discover new clues regarding kangaroo evolution every day.

Evidence for Evolution Quiz

1. The picture shows evidence for land to water evolution. It shows that the land animal evolved into a whale by first, his feet becoming webbed and losing his fur. Then, his limbs begin forming into fins and his tail is now the tail of a whale, and his body is now covered in scales. Lastly, his arms and legs fully transform into fins, and his head becomes longer and more like that of a whale's, as his entire body is now whale-like after adapting to the conditions of the ocean.

2. E, North America.

3. These organisms show convergent evolution because although they all have wings with similar functions, they have analogous structures because the bone structures are completely different. They show convergent evolution because they are all completely different species, but have evolved to have wings that have the same functions.

4. The Common Descent Lab shows DNA evidence and ancestry as evidence for evolution because in it we compared the DNA strands of gorillas, humans, chimpanzees, and the common ancestor, and we were then able to discover that chimps and humans share a common ancestor and that gorillas were the most similar to the common ancestor of the three species. We could then use this evidence to determine which species evolved from the ones that we studied.

5. Homology is the similarity of the bone structures of certain limbs that organisms share with a common ancestor. For example, pterodactyls, humans, and tiktaaliks all share the same "one bone, two bone, blob" in the arm and wrist area. Homology is used to determine transitions in the fossil record, for instance the evolution from water to land. Tiktaaliks share many homologies land animals, showing that although it lived in the water and looked similar to a fish, it also had the same bones to allow it to move onto land and thus supports the evolution of water to land animals.

Blog Day 9

Today, we covered DNA aspect of evolution. We divided up into small groups and worked on different projects. James and I found the similarities between monkeys, gorillas, and humans by creating DNA strands for each like these below:

Here's what the chimpanzee DNA strand looks like:

And the positioning:

Here is the positioning for the gorilla DNA strand:

And the positioning for the human:

Upon analyzing the strands, we found the chimpanzee and the human strand to be very closely related. Upon studying the gorilla strand, we found it very close to the common ancestor strand:

Thus, we came up with this common descent model:

This model shows gorillas, chimps, and humans all having a common ancestor, chimps and humans having a common ancestor, and gorillas being the closest to the common ancestor that they all share. 

Blog Day 8

Today, we began our introduction to evolution. We studied tiktaalik and went up to the museum to study the transitional features that tiktaalik has. It was really interesting to piece together the transition from water to land as tiktaalik contains features of both.

Here is tiktaalik half in, half out of the water. The bones in its wrists allow for it to do push-ups, or push the bottom of tiktaalik quickly through shallow water and away from predators.

We finished the class by taking a short quiz.