Nick+Weiler+Your+Inner+Fish

**Your Inner Fish By: Neil Shubin**


 * Post #1:** “Every species in the zoo and the aquarium has a head and two eyes. Call these species ‘Everythings.’ A subset of the creatures with a head and two eyes has limbs. Call the limbed species ‘Everythings with limbs.’ A subset of these headed and limbed creatures has a huge brain, walks on two feet, and speaks. That subset is us, humans. We could, of course, use this way of categorizing things to make many more subsets, but even this threefold division has predictive power” (Shubin 7).

Shubin uses a simple method of organization to classify zoo and aquarium animals. All animals are “Everythings”, and the ensuing subsets he creates contain animals with slight differences in their body plan. For example, some are “Everythings with limbs”, animals that have a head, two eyes, and jointed appendages. As the number of subsets increases, it is clear that the complexity of the animals situated in these subsets also increases. Therefore, this simple method of classification portrays the progression of evolution from the simplest of animals to the most complex of animals, and the differences in morphology of animals as evolution has occurred over time.

Neil Shubin’s creation of this simplistic method for classification of animals ties into our study of phylogeny, which encompasses “the connections between all groups of organisms as understood by ancestor/descendant relationships” ( "Introduction to Phylogeny."). Although we classified a wider variety of organisms in Biology this year, our system of classification is similar to that of Shubin’s in that both categorize organisms based on specific phenotypic characteristics. For example, in the Animal Diversity lab we dissected and classified thirteen different organisms, ranging from the simplest of organisms, a sponge, to a complex mammal, a rat. As the complexity of the organisms increased, the organisms had all three tissue layers (ectoderm, mesoderm, endoderm), cephalization, a coelom, segmentation, jointed appendages, vertebrae, and often times bilateral symmetry. Organisms can thus be classified by the different characteristics that they possess. An evolutionary trend is apparent when examining the animal kingdom, that “as animal complexity increases, acquired characteristics also increase” (//Animal Diversity//).

In my opinion, Shubin does an excellent job of making phylogeny and the classification of animals simplistic. With this short quote, he makes the general concept of classification, which is rather complex, understandable and accessible to almost any reader. Shubin's "oversimplification" of the scientific process of classifying organisms is extremely clever in that it allows any reader to grasp the theme that organisms with more characteristics are often more complex than those with fewer acquired characteristics.

-N.W.  Work Cited //Animal Diversity //. Burlington, NC: Carolina Biological Supply Company, 2007. Print "Introduction to Phylogeny." //UCMP - University of California Museum of Paleontology//. Web. 28 May 2010. . Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print. ​ ​ **Post #2:** "There is a fundamental design in the skeleton of all animals. Frogs, bats, humans, and lizards are all just variations on a theme. That theme, to Owen, was the plan of the Creator. Shortly after Owen announced this observation in his classic monograph //On the Nature of Limbs,// Charles Darwin supplied an elegant explanation for it. The reason the wing of a bat and the arm of a human share a common skeletal pattern is because they shared a common ancestor" (Shubin 32).

Neil Shubin contrasts anatomist Sir Richard Owen’s theory that the fundamental design in the skeleton of all animals is simply the plan of the Creator with Charles Darwin’s theory of evolution and natural selection. Shubin’s juxtaposition of the theories of Owen and Darwin is applicable due to the ongoing, and heated, debate between the two theories of creationism and evolution. Owen seemed to believe that “the Creator” (Shubin 32) played a significant role in the design of the skeleton of all animals, and that minor differences between the animals’ skeletal structure are simply “variations on a theme” (Shubin 32). On the contrary, it is probable that Darwin believed that animals simply evolved from a common ancestor, and that a supernatural force did not play a role in the development of life on Earth.

Creationists believe “in a god who is absolute creator of heaven and earth, out of nothing, by an act of free will. Such a deity is generally thought to be constantly involved (‘immanent’) in the creation, ready to intervene as necessary, and without whose constant concern the creation would cease or disappear” ( "Creationism (Stanford Encyclopedia of Philosophy).”). Creationism essentially entails the taking of the early chapters of Genesis, and the Bible as a whole, “ as literally true guides to the history of the universe and to the history of life” ( "Creationism (Stanford Encyclopedia of Philosophy).”). In addition, Creationism involves a number of different beliefs. The first is that there has only been a relatively short amount of time since the beginning of life on Earth (many accept Archbishop Ussher’s approximation of 6,000 years) ( "Creationism (Stanford Encyclopedia of Philosophy).”). They believe that there were six days of creation (some take this literally and others more flexibly) and that “ there was a miraculous creation of all life including //Homo sapiens” //( <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"Creationism (Stanford Encyclopedia of Philosophy).”). Creationists ultimately believe that all life forms on Earth were placed here in their “final form”, and many reject the theory of evolution as a plausible theory.

On the other hand, many people side with Darwin and believe in his theories of evolution and natural selection. Evolution is defined as “a change over time in the genetic composition of a population” (Campbell Reece 438). Darwin proposed a mechanism for the process of evolution, natural selection, which is the idea that “a population can change over generations if individuals that possess certain heritable traits leave more offspring than other individuals” (Campbell Reece 438). Evolution was a primary theme of our AP Biology curriculum, and helped to explain the differences and similarities between organisms in the Animal Diversity lab, as well as the reasoning for the multiple return events of land mammals to the ocean in the Whales Activity. Evolution may occur as a result of mutations, specifically point mutations, which are alterations in the genetic material of the cell. Base-pair substitution describes the replacement of one nucleotide and its complementary base pair in DNA with another pair of nucleotides. Missense mutations are substitutions enabling the codon to code for an amino acid; however it may not be the correct one. Whereas, nonsense mutations occur when substitutions change a regular amino acid into a stop codon. In addition, insertions and deletions describe the additions and losses of nucleotide pairs in a gene. Mutations may harm an organism, however they also may bring about beneficial evolutionary change. Also, evolution may occur as a result of genetic variation in offspring, as a result of crossing over and independent assortment. In crossing over, an exchange of genetic material on homologous chromosomes between nonsister chromatids occurs. Independent assortment describes the pairing up of homologous chromosomes along the metaphase plate at random, again increasing genetic variation in offspring. Genetic variation in offspring can result in evolutionary advantages in offspring, and can increase their chance of survival. <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;"> In my opinion, I believe that the theory of evolution is correct because there are many apparent similarities genetically and physically between certain species that indicate their evolution from a common ancestor. However, at this point in time, there is much that science cannot explain about the origin of life on Earth, and thus I believe there must be a supernatural force (god) at work as well.

-N.W. <span style="display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%; text-align: center;">Work Cited <span style="color: black; display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; text-align: center;">Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print. "Creationism (Stanford Encyclopedia of Philosophy)." //Stanford Encyclopedia of Philosophy//. Web. 01 June 2010. []


 * <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">Post #3: **<span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;"> "The answer lies in understanding which pieces of DNA (the genes) are actually turned on in every cell. A skin cell is different from a neuron because different genes are active in each cell. When a gene is turned on, it makes a protein that can affect what the cell looks like and how it behaves. Therefore, to understand what makes a cell in the eye different from a cell in the bones of the hand, we need to know about the genetic switches that control the activity of genes in each cell and tissue" (Shubin 46).

Shubin’s description of gene expression ties in closely to what we discussed in class this year about the gene expression of bacteria. In bacteria, genes are grouped into units called **operons**, which consists of three parts (Campbell Reece 353). The first is an operator which controls the access of RNA polymerase to the genes; the operator is found within the promoter site of the operons. The second is the promoter, which is where RNA polymerase attaches to the operons. The third and find part are the genes of the operons, which is the entire stretch of DNA required for all of the enzymes produced by the operons.


 * Regulatory genes** are located some distance from the operons. Regulatory genes produce repressor proteins that might bind to the operator site, thus, RNA polymerase is blocked from the genes of the operons and the operons is turned off (Campbell Reece 353). The presence of regulatory genes in bacteria results in two unique types of operons. **Repressible operons** are normally on, but can be inhibited (Campbell Reece 354). They are often anabolic, and are involved with building a vital organic molecule (Campbell Reece 354). The repressor protein produced by the regulatory gene is inactive (Campbell Reece 354). However, if the organic molecule being produced by the operons can act as a corepressor and bind to the repressor protein produced by the regulatory gene, thus activating it (Campbell Reece 354). The newly activated repressor protein then binds to the operator site, shutting down the operon. **Inducible operons** are normally off but can be turned on (Campbell Reece 355). They are generally catabolic, and thus break down macromolecules for energy (Campbell Reece 355). In inducible operons, the repressor protein produced by the regulatory gene is active, and thus binds to the operator site (Campbell Reece 355). But, a specific small molecule called an inducer can bind and inactive the repressor protein, therefore allowing RNA polymerase to access the genes of the operon (Campbell Reece 355).



<span style="font-family: Verdana,Geneva,sans-serif;">(Tryptophan absent, repressor inactive, operon on. This figure is an example of a repressible operon, as described in the paragraph above.)

In bacteria, the regulatory genes play a crucial role in regulating gene expression. When activated, the repressor proteins that they produce bind to the operator site, halting transcription and thus protein production. But, when inactivated, transcription ensues and leads to the production of certain proteins. In my opinion, the fact that the body of a human can regulate gene expression is incredible. The feedback mechanisms and loops required in order to do so are intricate, and only increase my admiration for the complexity of the human body.

-N.W. <span style="display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%; text-align: center;">Work Cited <span style="color: #000000; display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; text-align: left;">"Chapter 18 Regulation of Gene Expression." //Bio1151 @ COD College of DuPage//. Web. 06 June 2010. [].


 * <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">Post #4: **<span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;"> “The key proposal was that it was the concentration of this unnamed molecule that was the important factor. In areas close to the ZPA, where there is a high concentration of this molecule, cells would respond by making a pinky. In the opposite of the developing hand, farther from the ZPA so that the molecule was more diffused, the cells would respond by making a thumb. Cells in the middle would each respond according to the concentration of this molecule to make the second, third, and fourth fingers" (Shubin 51).

The “unnamed molecule” is the Sonic Hedgehog protein, which, as the quote above implies, “ <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">plays an important role in limb development, specifically affecting the zone of polarizing activity (ZPA)” ( <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"Untitled Document."). The Sonic Hedgehog protein is concentration-dependent, and thus forms different digits depending on the concentration of the molecule present. A similar molecule to the Sonic Hedgehog protein is auxin. In this year’s Biology curriculum, we discussed the hormone auxin while learning about plants, which is one of the most vital plant hormones.

These molecules are similar because both are concentration dependent. Auxin is “any chemical substance that promotes the elongation of coleoptiles” (Campbell, Reece 794). However, in this case, auxin is used to refer to indoleacetic acid which is a naturally occurring auxin found in plants (Campbell, Reece 794). Indoleacetic acid (IAA) in plants “stimulates stem elongation, root growth, cell differentiation, and branching; regulates development of fruit; enhances apical dominance; functions in phototropism and gravitropism; promotes xylem differentiation” (Campbell, Reece 794). Indoleacetic acid has many functions, however its primary function is to stimulate elongation of the cells contained in young developing shoots. Indoleacetic acid is produced in the apical meristem, and then moves down into the region of cell elongation (Campbell, Reece 794). The hormone stimulates the growth of cells, likely by binding to a receptor in the plasma membrane (Campbell, Reece 794). IAA stimulates growth “over a certain concentration range, from about 10 to the -8th power to 10 to the -4th power M” (Campbell, Reece 794). On the contrary, at higher concentrations, IAA inhibits growth likely by producing ethylene, a hormone that inhibits elongation (Campbell, Reece 794). The Sonic Hedgehog protein and Indoleacetic acid function similarly in that they are both concentration dependent.

The concentration dependent concept in reference to the Sonic Hedgehog protein and indoleacetic acid relates to the AP Biology theme of regulation. The regulation of the amount of Sonic Hedgehog protein emanating from the Zone of Polarizing Activity results in different concentrations of the molecule, and thus the formation of different and unique digits. Similarly, the regulation of the quantity of indoleacetic acid produced by the apical meristem results in either growth, or the slowing of growth in the plant, depending upon the concentration of IAA synthesized. In my opinion, I find it incredible that the simple difference in concentration of the Sonic Hedgehog protein results in the growth and development of an entirely distinct new digit. Also, on a bit of a side note, I think it is remarkable that, when treated with retinoic acid, which is a form of vitamin A, a limb will form a second ZPA on the opposite side. As a result, two full sets of digits will be formed.

<span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">-N.W. <span style="color: #000000; display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%; text-align: center;">Work Cited <span style="color: #000000; display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; text-align: center;">"Untitled Document." //Biology @ Davidson//. Web. 09 June 2010. <http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Watson/Sonichedgehog.htm>.

​ <span style="font-family: Verdana,Geneva,sans-serif;">​ **Post #5**: "What holds a clump of cells together, whether they form a jellyfish or an eyeball? In creatures like us, that biological glue is astoundingly complicated; it not only holds our cells together, but also allows cells to communicate and forms much of our structure. The glue is not one thing; it is a variety of different molecules that connect and lie between our cells" (Shubin 123).

<span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">The intercellular junctions between cells of the human body are an essential portion of the “biological glue” that allows our cells to both communicate and maintain their unique structure. There are three separate types of intercellular junctions in the human body, each of which is equally important in communication and in maintaining the configuration of cells in the body. Tight junctions are the portions of animal cell membranes where two adjacent cells are fused, thus making the cell membranes water tight (Chapter Six Study Packet). Desmosomes “fasten neighboring animal cells together, functioning like rivets to fasten cells into strong sheets” (Chapter Six Study Packet). Gap junctions “provide channels between adjacent animal cells through which ions, sugars, and other small molecules can pass” (Chapter Six Study Packet). Plasmodesmata, which are found in plants only, are channels that perforate neighboring plant cell walls and allow for the passage of molecules from cell to cell and are very similar to gap junctions in animal cells. Intercellular junctions allow mainly for the maintenance of the structure of cells in the bodies of animals.



Yet another important element of the “biological glue” is the extracellular matrix. The extracellular matrix of animal cells is positioned external to the plasma membrane, and is composed of glycoproteins secreted by cells (the most prominent glycoprotein is collagen) (Chapter Six Study Packet). In essence, the extracellular matrix “greatly strengthens tissues and serves as a conduit for transmitting external stimuli into the cell, which can turn genes on and modify biochemical activity (Chapter Six Study Packet). Our cells cannot “survive unless they are anchored to the extracellular matrix” (<span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"The Extracellular Matrix.") <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">and thus they are anchorage dependent. Cells attach to the extracellular matrix through transmembrane glycoproteins called integrins ( <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"The Extracellular Matrix."). The extracellular section of integrin proteins binds to the various types of extracellular matrix proteins such as collagens, laminins, and fibronectin <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">( <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"The Extracellular Matrix."). The intracellular portion binds to the actin filaments of the cytoskeleton, therefore anchoring the cell <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">( <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">"The Extracellular Matrix."). Together, the intercellular junctions and the extracellular matrix form key components of the “biological glue” that allows for cell structure and communication between cells.

In my opinion, Shubin does a good job of simplifying the factors that allow for cell structure and communication by defining these factors in their entirety as “biological glue”. Although he doesn’t expand on the ideas of cell structure and communication much, he does an excellent job of simplifying the concepts to allow the average reader to grasp them.

-N.W <span style="display: block; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%; text-align: center;">Work Cited <span style="font-family: Verdana,Geneva,sans-serif;">"Learning Histology of the Human Body." //Academic Web Server - Kellogg Community College//. Web. 12 June 2010. []. <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt;">"The Extracellular Matrix." //RCN D.C. Metro | Digital Cable TV, High-Speed Internet Service & Phone in the D.C. Metro Area, including Washington, D.C., Bethesda and Silver Spring in Maryland and Falls Church in Virginia//. Web. 12 June 2010. <http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/ECM.html#Composition_of_the_ECM>.

<span style="font-family: Verdana,Geneva,sans-serif;">
 * Commentary #1 on Garrett's Post #1:**

I agree with much of what you stated in your first post, and I think that you did an excellent job of “thinking outside of the box” by connecting such a simple quote to several important topics in the biology curriculum. You insinuate that mutations often occur through base pair substitutions that happen to be uncorrected by “proof reading” enzymes. I completely agree that this occurrence is a cause of mutation and thus introduces new traits into the gene pool; however there are several other ways that new traits or genetic variability can be introduced into a population. Genetic variation may come as a result of meiosis, and thus new or different genes may be passed on to offspring. During prophase one of meiosis the “exchange of genetic material on homologous chromosome between nonsister chromatids occurs” (Chapter 13 Study Packet), resulting in crossing over. As a result, all four chromatids that make up a tetrad are unique and different (Chapter 13 Study Packet). Therefore, in metaphase two when the sister chromatids separate, each unique chromosome results in a higher chance of genetic variation in offspring (Chapter 13 Study Packet). Independent assortment of chromosomes also contributes to genetic variation in offspring. During metaphase one when the homologous chromosomes are situated along the metaphase plate, “they can pair up in any combination, with any of the homologous pairs facing either pole” (Chapter 13 Study Packet). As a result, there is a 50-50 chance that a particular daughter cell will get a maternal chromosome or a paternal chromosome from the homologous pair” (Chapter 13 Study Packet). Crossing over and independent assortment of chromosomes are two processes that contribute greatly to genetic variation in a population.



<span style="font-family: Verdana,Geneva,sans-serif;"> There is also one statement that I disagree with in your post. You state that “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.” However, haven’t the most complex of animals also developed due to natural selection? As you say in your post, the theory of evolution “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.” So, the most complex of organisms may have also evolved due to natural selection, because the organisms with the most favorable traits would have passed these traits on to offspring.

-N.W.


 * Commentary #2 on Emma's Post #1:**

As Mrs. Galuska explained to the entire class, your post deserves a three out of three and I am taking a bit of a chance by commenting on it. I think that it is an excellent post because you explain both Darwin’s theory of evolution as well as the process through which genetic variation in gene pools comes about. However, there is one specific portion of your post that I would like to add on to. In your post, you state that the excerpt you chose “concentrates on different methods of constructing phylogenies. For example, fossil evidence supports the fact that bats forelimbs and bird wings arose independently from walking forelimbs of different ancestors. Therefore, the bat’s forelimb is ‘homologous to those of other animals, but analogous in function to a bird’s wing’ (1)”. The fact that bat forelimbs and bird wings developed independently from the walking forelimbs of different ancestors is an example of convergent evolution. Convergent evolution takes place when two organisms develop similarities as they adapt to similar environmental challenges, not because they evolve from a common ancestor (Chapter 26 Study Guide). Another example of convergent evolution is the streamlined bodies of a tuna and a dolphin, which allow these animals to swim more quickly through water. Like you state in your post, the bat’s forelimb is analogous in function to a bird’s wing, meaning that they “do not indicate relatedness, but rather similar solutions to similar problems” (Chapter 13 Study Guide). On the contrary, homologous structures are similarities due to shared ancestry (Chapter 13 Study Guide). Yet another example of convergent evolution is the evolution of marine mammals as a result of the multiple return events to water by separate ancestors. We explored this theory in the Whales Activity, and most students in the class determined that this was the most likely theory explaining the evolution of marine mammals. Marine mammals share many similar characteristics, however the phylogenetic trees that we created display the idea that marine mammals likely evolved from multiple return events to the water by separate mammals. Overall I think your post is excellent, but I just wanted to add this bit of information!

-N.W.


 * <span style="font-family: 'Verdana','sans-serif'; font-size: 10pt;">Commentary #3 on Phil’s Post #4: **

<span style="font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">In my opinion you did an excellent job of relating the mammalian respiratory system to the AP Biology theme of evolution, because the mammalian respiratory system has been “jury rigged to work in mammals” (Shubin 191). In addition, I think that in your post, you do an excellent job of explaining the mammalian respiratory system in a detailed and precise manner. While reading your post, I thought of another possible connection that could be made to the AP Biology curriculum. As you state in your post, the job of the alveoli in the lungs is to function in gas exchange and that “ <span style="color: black; font-family: 'Verdana','sans-serif'; font-size: 10pt; line-height: 150%;">oxygen in the air entering the alveoli dissolves in the moist film and rapidly diffuses across the epithelium into a web of capillaries that surrounds each alveolus. Carbon dioxide diffuses in the opposite direction..." (Campbell, Reece 887). The alveoli in our lungs are a prominent example of the theme structure to function. Gas exchange occurs across the “thin epithelia of the lung’s millions of alveoli, which have a total surface area of about 100 square meters in humans, sufficient to carry out gas exchange for the entire body” (Campbell, Reece 887). The massive surface area of our alveoli (structure) is crucial in maximizing gas exchange in order for cellular respiration to occur (function). Without the unique and surface-area maximizing structure of alveoli, humans would be unable to perform enough gas exchange with the environment in order to survive. Along with displaying the theme of evolution, the mammalian respiratory system, particularly the alveoli, also demonstrates the theme of structure to function as well.

-N.W.

Work Cited Campbell, Neil A., and Jane B. Reece. //<span style="font-family: 'Verdana','sans-serif';">Biology //. San Francisco: Pearson, Benjamin Cummings, 2005. Print.