Garrett+Roell+Your+Inner+Fish

Post 1...

“Our world is so organized that we can walk through a zoo to predict the kinds of fossils that lie in the different layers of rocks around the world” (Shubin 27).

This excerpt delves deep into many different scientific concepts. For one, it can’t be understood, without first having an understanding of phylogeny. Phylogeny is the study of the relationships between species. Phylogeny can all be traced back to a single common ancestor. From there, many mutations have created the biodiversity that we see on earth today. This can be explained using Charles Darwin’s Theory of Evolution. This theory states that when an animal has favorable traits it has the ability to live until reproduction, and thus pass its traits on to the next generation. However, if the new traits are a disadvantage to the organism, it will not live to reproduce. This is where the phrase ‘survival of the fittest’ comes from. But how to these new traits come about. Traits are introduced into a gene pool through mutations. During DNA replication every so often, mistakes are made. This happen once in about every 10 billion base pairs. This is so uncommon because DNA polymerase rarely makes mistakes, about once every 10 thousand base pairs. These mistakes are very commonly corrected by ‘proof reading’ enzymes, which finish the job. The mistakes are also uncommon because the base pairs are complements. This means that the adenine atoms mirror the thymine atoms, and guanine atoms mirror the cytosine atoms. These pairs create hydrogen bonds, and ensure that mutations don’t happen. However, sometimes they do. When this happens enough the species branch into two different species that are sexually incompatible. This is divergent evolution. This is how all of the very different creatures in the zoo developed from a single organism. The animals in the zoo can be ordered according to complexity. The animals with the highest levels of complexity can be assumed to have developed the most recently of all the animals. This is because they have gone through the most mutation. These most advanced species will be found closest to the surface. This is because the most recent earth layers are near the surface. It would only make sense for them to be there. Using this technique, we can figure out when different animal species inhabited the earth. I didn’t find this section to be too difficult. I mean, it is pretty basic evolution. However, I understand that Shubin wants to build a foundation in evolution before expanding on it. I am hopeful that in the upcoming chapters Shubin will bring up more enlightening topics. Works Cited Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

-GR

Post 2...

"All our cells contain the same DNA; what differs is which bits of DNA are active.The genes involved in the sense of smell are present in all of our cells, however they are only active in the nasal area (Shubin 140)."

It is critical that the information in this passage is known for one to have a proper understanding in how multicellular organisms are organized. In the beginning, at conception, the organism consisted of only a single cell. From there, many cellular divisions take place. Eventually the cells become differentiated, meaning they become specialized to do a certain task. The first cells to differentiate in humans are the cells that make up the placenta. How does differentiation occur? How do cells that contain the same DNA become different? The answer lies in the protiens that are translated from the DNA.

In a cell protiens do almost everything. They do tasks from supporting the cell to catalyzing reactions to letting molecules flow in and out of the cell the cell membrane. The protiens get their primary structure, or sequence of amino acids from DNA. DNA contains the code from which protiens are made. Certain segments code for different protiens, and with the presence of introns and exons, a single segment can code for many different protiens. These segments can be blocked by inhibitor protiens. These protiens bind to the promoter before the gene along the DNA strand, this impedes DNA polimerase from attaching to the DNA and transcribing RNA which would be then translated into protein at the ribosome. These operons can be found in almost any living cell. They regulate which proteins are found in each cell. This in turn regulates which function the cell will take. This is a prime example of regulation.

When certain genes are turned on, they create different proteins. This is because the primary structure of the protein changes. This means that the amino acid sequences are different, this will affect the secondary structure of the protein. The secondary structure describes the shape the individual segments create. There can be alpha helices or beta sheets. These formations are determined by the R-groups of the amino acids, and how they form weak bonds with each other. These bonds include hydrogen bond, Van der Waal Interactions, and hydrophobic bonds. This is the part that doesn't remain consistent among all amino acids. Amino acids are the building blocks of proteins. The secondary structure lends itself to the tertiary structure. This is the overall structure of the protein, which comes from interactions between the alpha helices and beta sheets. The quatrenary structure is how the protein bonds with other protiens.

The structure of protiens is very important to their function. For example, enzymes, such as Phosofructokinase, have pockets called active sites. These active site allow substrates to enter into a suitable environment for which to carry out their reaction. Also, protein structure is important in integral proteins which span the gap between inside and outside the cell membrane. These proteins must have a hydrophilic and hydrophobic portions in order to do their jobs. This job is to channel molecules in and out of the cell.

Works Cited Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

"Functions of Protein in the Human Body." //Find Health, Education, Science & Technology Articles, Reviews, How-To and Tech Tips At Bright Hub - Apply To Be A Writer Today!//27 Mar. 2003. Web. 01 June 2010. .

Post 3...

"Our bodies are not put together at random. Here, I use the word "random" in a very specific sense; I mean that the structures of our bodies is definitely not random with respect to the other animals that walk, fly, swim, or crawl across this Earth (Shubin 178)."

What Shubin is getting at in this except is speciation, or divergent evolution. Divergent evolution is when one species, becomes separated into two groups. These two groups don't breed together and eventually the gene pools between the two populations will become so great that individuals from different populations will be unable to reproduce with each other. A good example of this is the kit fox and the red fox. At one point they had a common ancestor. However they somehow became separated. The red fox, of course, received the red color, and small ears. The kits fox got large ears, and a sandy color. Just as Shubin asserts in the quote, these changes aren't random. The mechanism determining the differences between these differences in these here species, is natural selection.

These two species live in different ecosystems. The Kit fox lives in the desert. The sandy coat helps her to evade predators, and the ears help to regulate temperature. The Red Fox lives in forests and farm lands. This species has the red fur for camouflage. Both of these animals are best suited for their habitat. This didn't just happen randomly. It was evolution by way of natural selection. This process works because individuals that reach the age of sexual maturity have the best genes for survival in their population on average. These individuals are the ones whose DNA will be present in the next generation. In each generation, animals with unfavorable traits are killed off, and their genes are removed from the gene pool. Eventually the entire gene pool will have the favorable trait. Tis a prime example of Continuity and Change a main principal of biology.

Convergent Evolution is when two species that start off very different, but the become more similar due to environmental factors. An example of this is when native african plants develop into cactuses that resemble the completely different cactuses in North American Deserts. This happens because the same kind of genes prevail in both environments. Since natural selection would choose shiny pines over large leaves in a warm, dry environment, both species ended up the same way.

Both of these are excellent physical examples that all organism are constantly changing. It would be difficult to look at this information and say,' meh, I think that the creator determined all species and set them to be fixed, and unchanging.' One of the important concepts in Biology is continuity and change.

This theme of Biology is very closely related to another theme, Evolution. The species in the two aforementioned examples all underwent evolution. This is change in the species over time. A wise man once said, ' Biology makes no sense unless analyzed under the lens of evolution.' This helps to answer the 'why?' in biology. Why do some animals walk, fly, swim, or crawl? The answer is evolution. All of the animal shared a common ancestor at some point. Then they underwent massive divergent evolution to develop their mode of travel on what would best suit them in their own environment.

Works Cited

1. "Patterns of Evolution." //BioWeb//. Web. 07 June 2010. . (wow. !!!!great site!!!!!) 2. Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

Post 4..

"In 1962 the anthropologist James Neel addressed this notion from the perspective of our diet. Formulating what became known as the "thrifty genotype" hypothesis, Neel suggested that our human ancestors were adapted for a boom-bust existence. As hunter-gatherers, early humans would have experienced periods of bounty, when prey was common and hunting successful. These periods of plenty would be punctuated by times of scarcity, when our ancestors had considerably less to eat (Shubin 187)."

This quote pertains to both science as a process and energy transfer.

The quote talks about James Neel's hypothesis of the "thrifty genotype". This basically says that humans have gene that when the body has lots of energy, such as right after eating, it would save the energy in the form of fat. This fat energy could later be used to fuel the body when there wasn't anything to eat. To come up with this hypothesis Neel and his fellow scientists went through a long process. First they made observations. They probably analyzed fossils and rocks of the time period to determine what the climate was like for early humans. Then they most likely studied the bones of these ancient humans, and the types of substances on them. From there they made the inference that these humans were hunter-gatherers. From that inference, Neel made the hypothesis that humans had a gene that regulated this fat storage. After its conception his hypothesis was going to have to be tested. The book doesn't explain the outcome of the experiment, but it can be assumed that humans do have this gene, as some of the energy from food is used right away, while other energy is stored, for example as fat.

This trait was helpful to early humans. As hunter-gatherers they lived a very active lifestyle. When they ate they would need to store their energy, as they wouldn't get more energy for a good while after eating. This energy is most times stored as glycogen, but when the glycogen reserves are full, the body turns the food into fat molecules. These fat molecules have large hydrocarbon chains. These chains are capable of storing immense amounts of energy in their bonds. They get the energy to form these bonds from the breakdown of the food. The exergonic breakdown of food releases energy, and this energy is coupled with fatty acid synthesis to endergonically create covalent bonds between the hydrogens and carbons. This whole process is overall exergonic meaning energy was lost from the substrate (food) to the products (fatty acids). This energy is lost to the environment as heat. When the person needs to call on their fat reserves for energy the molecule of fat gets broken up. When these chemical bonds are broken, energy is released. This energy can be used to phosphorlate ADP to become ATP. ATP is very commonly used throughout the cell to perform all kinds of cellular work. Everything from protein synthesis to flagella movement.

I feel that this except is a very important to know if you are trying to keep people healthy. These days, with technology and all, people are lazier than ever, and food is more accessible than every. They aren't active like their hunter-gatherer ancestors. Yet they have very similar genes. This is not a good combination. These people frequently, and rarely get any exercise. The result of this is a very large obese population. Our inner hunter-gatherers are hurting ourselves. With added fat, that never gets expended, people are lining themselves up for some serious health issues. Such as, diabetes, stroke, atherosclerosis.

Works Cited. Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

Post 5...

"One theory about this is extremely simple: Perhaps bodies arose when microbes developed new ways to eat each other or avoid being eaten? Having a body with many cells allows creatures to get big. Getting big is often a good way to avoid being eaten. Bodies may have arisen as just that kind of defense."

The quote pertains to in creasing body sizes. When life was only microbes, that is, all living things were single celled, some developed the ability to consume other organisms. This relates to the endosymbiotic theory discussed on Nick's page. To paraphrase, one time a predator organism engulfed another smaller organism, probably by way of phagocytosis. The smaller organism wasn't digested though. The aerobic organism had a double membrane, which allowed chemiosmosis to occur. This resulted in the larger cell to have a continuous supply of ATP which could preform work. Also, the smaller cell got protection from predators, and a constant supply of nutrients from the cell. This event was significant because it allowed the larger cell to perform oxidative phosphoralation, meaning the cell could get 36-38 ATP from a Glucose molecules, as opposed to the 2-3 it could get from glycolosis in the past. This was a major **change** in the biological world, and it has **continued** to be prevalent even today. The cells in this environment would want to grow larger, because you can't be consumed through endocytosis if you are larger than the predator. This was able to happen with the advent of the eurkuryotic cell. This type of cell would preform aerobic respiration, and thus could preform lots of cellular work. This added work could be used to support a larger body, a multicellular body.

A multicellular organism would need more energy per cell than a single celled organism because it would have to replicated DNA more often, signal in between cells, and have some cells provide energy for other cells. All of these tasks would require more energy. So, the advent of eurkyrotic cells gave the cells the ability to have multicellular bodies. This path was successful for many reasons. For one, as the quote says, larger organisms often avoid getting eaten. Also, a multicellular organism has the ability to have specialized cells, as the name suggests these cells, have special roles. Each cell has a certain role, and they are all reliant on each other. It's kind of beautiful, every cell has their purpose in life, and it helps out other cells that don't have the ability they do. At the same time, they are being supplemented with the products of other cells that can do the tasks that it is unable to do. A body is capable of being more productive this way.

Bodies may also have arisen for mobility, a single cell, even with cilia or flagellum, can't move as fast as a multicellular organism, this relates back to the specialized cells. This added mobility could be used to seek out new food sources, or mates..i don't know about that. Further experiments on ancestors of these primitive multicellular organisms that still resemble them will have to be conducted.

Endosymbiosis animation- [] Works Cited.

Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

Commentary on Avery's Post 1...

Avery- You did a very good job describing the breathing organs in fish as opposed to land animals. Also, your connection between the FASTA lab and the quote is good. However, I feel that you are looking at the quote with "tunnel vision". The quote holds great potential for debate, and you are correct when you said that the excerpt could act as "a stepping stone for further conversation on this topic." I feel that I would be remiss if I didn't continue the discussion.

As I stated above your breathing connection is fantastic, but what about the other activities; feeding and moving about. (I didn't exclude excretion because that wasn't part of our ap bio curriculum). For feeding, land animals have learned to develop new teeth structures. Upon leaving the water, the animals evolved new types of teeth to help them eat terrestrial plant matter. To help better mechanically digest their food, the creatures developed specialized teeth. These teeth didn't show up in the marine animals, because under water plants don't have the same kind of cell structures as their dry land brethren. Plants that live in water get lots of support from the water molecules that surrounds them. this is because of the density and pressure of the water. On land, though the plants only have air surrounding them. This offers very little for support. As a result the land plants became stronger. To do this they developed larger cells walls and different types of cells. Sclernchema and collenchema cells were developed to fight the force of of gravity and get the plants leaves closer to the sun. As a result animals coevolved. They developed specialized teeth, as mentioned before. Also some animal gained a symbiotic relationship with microbes to help to digest cellulose. An example of this would be the bovine (cow).

Moving about also changed in animals when they left the comfort of the water. To move around on land you must have a strongly supported body. This is also tied to the density concept. In water, animals don't need as much support because they get support from the water. (Think jellyfish). A creature like the jelly fish could never move about on land. So in order to live on land creatures had to develop strong structures to support their bodies. Examples of this are the arthropod's exoskeleton, and the larger members of the phylum cordata's bones. From their the animals would also have to be able to move their bodies. For this most animals have muscles. Muscles are found in almost every phylum. And they are surprisingly similar in form. I.E both insects and mammals have smooth and striated muscles.

I don't really disagree with anything that you said, that is with one exception. The quote is very general, and that most people people already would know it. I feel that the "billions of years" that life has been around part is baffling. I can even begin to wrap my head around that number, I don't think that this is common knowledge. But what ever, i mean if this is what I'm critiquing you for, you probably had one h*ll of a post!!!

-GR

Commentary on Nick's Post 1...

First of all... Wow what a nice page you made..can you make me a website for a small fee if I ever need one?

Back to your post. In your post you constantly link the simularities of almost all animals...everything from the "one bone-two bones-lotsa blobs- digits pattern" to the hox gene box. You attribute these simularities to the fact the all of the animals you mentioned shares a common ancestor. I feel that this is the case, but I would like to present a counter arguement.

You are assuming that life only popped up once, the common ancestor of all living things. But what's to say that this didn't happen twice, three times, or millions of times for that matter? If it has happened once it might have happened many different times. Now I am not advocating for creationism, I am only saying that maybe not all animals are related. Your discussion constantly stresses that the similarities in animals come from the same ancestor.

Instead I propose that in at least two places life was created completely independent of each other. From there they took similar form (DNA, phospholipid membrane,...ect.) because that's what works. They must have formed in similar climates because both favored very similar traits. After that both evolved evolved into multicellular animals. Then this pattern of "one bone, two bones, lotsa blobs, digits" formed in unrelated animals because it is simply the best pattern for life. I also feel that the frog connection is stretch. I mean by "fusing several bones together" you are no longer in the presence in the pattern that the rest of the animals follows. Perhaps amphibians are unrelated to the rest of the majority of animals.

The same argument is relevant in the DNA discussion. You again assume the origin of all animals was a single organism. This is what accounts for the similar genetic material. All living organisms on Earth share DNA as their genetic material (retroviruses aren't "living"), some use this as proof that all organisms share a singular common ancestor. However, this is only proof that DNA is the best genetic material. With the pairings of molecules, A to T, and C to G, connected by only hydrogen bonds, the molecule lends itself to replication. The phosphate backbone is strong this allows the DNA to stay strong, even when separated for transcription, or replication.

This is just a possible counter argument to your post, I'm not saying that I support it, or that I don't.

-GR

Commentary on Phil's Post 3...

To start...nice connection between the relationship of structure to function in arteries, capillaries, and veins. I thought this piece was well done, however I feel your quote also lends itself to other themes in biology. For one, it strongly relates to interdependence in nature. Each part of the circulatory system is dependent on the other parts. After all, it is the CIRCulatory system, it creates a circle, if one part is missing, all the rest are going to be impaired. The arteries, veins, and capillaries all need each other to be successful. The arteries, with the exception of the pulmonary artery, carry oxygenated blood away from the heart. This oxygen in the blood is needed by all then the body besides cells in the body. This is because oxygen is critical in the process of cellular respiration, turning glucose's energy into the more usable ATP. These cells are dependent on the circulatory system for their survival.

The arteries are dependent on the veins because the veins complete the circuit. The veins transport the blood from the end of the arteries, the arterioles, back to the heart, then to the aorta, the major artery. Without the veins, and their special structure that Phil described, the blood would never return to the heart. This would cause the arteries to have no blood inside them.

Both Arteries and Veins are dependent on capillaries. Capillaries touch every almost every cell. The capillary walls are only one cell thick. This trait helps with diffusion of oxygen and glucose into the cells. The walls of the veins and arteries are made up of living cells. in order to get the substances they need the walls of the arteries and veins have capillaries running through them. Without the capillaries the cells of veins and arteries would die. Without the veins and arteries, the capillaries themselves wouldn't have a supply of nutrient rich blood, and those cells would die. This is the epitome of interdependence. Beautiful, Raw, Savage, interdependence.

The capillaries also play a key role completing the circuit by bridging the gap between the arteries and the veins.

Works Cited.

Campbell, Neil A., and Jane B. Reece. Biology. San Francisco: Pearson, Benjamin Cummings, 2005. Print.