Nick+Tan+Your+Inner+Fish

=**//__Your Inner Fish__ //**=
 * by Neil Shubin **

Book Report
//*I've previously read "Your Inner Fish" for an Independent Reading Project for English class, and had to write a book report on it. Here it is://toc

**Phylogenetic Phase from Fishy Fins, Forming Feet, Fingers Following **

The missing link from ape to man is outshined by the endearing, curious-eyed amphibian displayed on the cover of Neil Shubin’s __Your Inner Fish__ as it gives insight on the connection of modern-day man to our fishy friends in the ocean. Shubin offers a walk in his shoes as he takes readers on his journey to prove that //Tiktaalik//, his revolutionary archeological finding of a fish sporting a pair of arms, was an intermediate organism in the transition from marine to terrestrial life.

Through his refreshing, colorful perspective of his work, Shubin shares with us his experience and excitement of discovering the fossil, comparing archeology to a “giant jigsaw puzzle,” while also instilling an appreciation of his field in readers (Shubin 7). He exemplifies the importance to delve deep into our evolutionary history in order to fill in the gaps. By doing so, our understanding of the world is inadvertently heightened. Upon closing the back cover, my eyes have been widened in respect to the world around me. All animals look strikingly similar as they share the same essential anatomical machinery described in the book. However, I am now also able to appreciate the unique characteristics of each species because the subliminal implication of the astounding power of evolution is embedded within the text.

As a paleontologist, Neil Shubin categorizes fossils in a very organized manner. His organization spills into his writing as the book has a clear structure. Each detail of the fossil is glorified with its own chapter, all supporting his argument that //Tiktaalik// is part of our evolutionary lineage with scientific analysis of the fossil itself and comparisons to the anatomy and behavior of extant species. He compares the hox genes, nasal passages, among other anatomical structures of a zoo-like variety of organisms. Because of the many aspects of the fossil, the book effectively encompasses many topics including archeology, anatomy, embryology, phylogeny and genetics.

Shubin walks us through each concept and its corresponding terms to avoid excluding the average person, widening the variety of readers. He simplifies the development of limbs by describing it as having a “one bone-two bones-lotsa blobs-digits pattern” (Shubin 32). While educating the readers, he uses the concepts explained to further support his argument. By dissecting the arm complex, he simultaneously proves the homology of limbs between us and the legged fish fossil. “Exceptional similarities” are found within “all creatures with limbs, whether those limbs are wings, flippers, or hands” as they all share “a common design” (Shubin 30). His scientific approach to validating his thesis by utilizing compelling evidence is almost infallible.



Like a textbook, the book is informative, but the plentiful diagrams dispersed throughout suggest more of a children’s book’s intriguing quality, having readers eagerly flipping those pages. It does not bore thanks to Shubin’s professional, yet satirical, energetic tone and distinct voice in his work. Describing lungfish humorously, he writes: “Scientists found lungfish to be essentially a cross between an amphibian and a fish. Locals found them delicious” (Shubin 33). Each chapter and subchapter is also titled with a pun to make it all the more comical. For example, Shubin labels a chapter describing the development of wrists and hands “Getting a Grip” (28) and a section dedicated to nasal passages is title “Making Scents” (139).

However, because the span of scientific fields the book covers is vast, Shubin lacks the focus of his arguments in multiple areas of the book. He diverges into slightly irrelevant topics such as visual and scent apparatuses. Although it does contribute to the overarching theme of evolution, it fails to shed light on //Tiktaalik//’s fossil and its relation to terrestrial organisms. Not to be nitpicky, but the title might give rise to a common misconception in the science of phylogeny as it implies that we are a direct descendant of the organism, when it is highly unlikely. Rather, we share a common ancestor, but Shubin does not address this important clarification in text.

Regardless of the minor flaws of his work, Neil Shubin’s book is an overall entertaining, educative and enlightening read. As to the audience, the book is not suitable for the whole public. Although __Your Inner Fish__ does explain scientific concepts effectively, a more advanced scientific vocabulary as well as an interest and/or aptitude in learning would enhance the grasping of these topics. Darwinians would feel right at home and even creationists should give this book a chance despite its topic as it would allow them to better formulate their opinions on evolution. A scientific paper converted into novel-form, the book combines a collection of his findings and a thorough biology lesson along with a story to be told about our evolutionary transition from surf to turf. Ultimately, the book has augmented my devout faith and appreciation for evolution and has the potential to inspire high school students to be aspiring biologists. I’m sure Darwin would be proud.

**Works Cited**

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print.

Posted Monday, May 24 Last Edited Thursday, May 27
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**-Post #1- **
"...//exceptional similarities// among creatures as different as frogs and people. All creatures with limbs, whether those limbs are wings, flippers, or hands, have a __common design__ . One bone, the humerus in the arm or the femur in the leg, articulates with two bones, which attach to a series of small blobs, which connect with the fingers or toes. __This pattern underlies the architecture of all limbs__. Want to make a bat wing? Make the fingers really long. Make a horse? Elongate the middle fingers and toes and reduce and lose the outer ones. How about a frog leg? Elongate the bones of the leg and fuse several of them together. The differences between creatures lie in differences in the shapes and sizes of the bones and the numbers of blobs, fingers, and toes. Despite the radical changes in what limbs do and what they look like, this underlying blueprint is __always present__ ." (Shubin 30).

Ah, the unifying theme of biology: Evolution! This excerpt from Neil Shubin's //Your Inner Fish// perfectly exemplifies the "thread" of evolution (if you will) that ties together and unites all organisms on Earth's surface. Because all animals innately share a primitive ancestor, we all carry a universal architecture, mutually present in even the most diverse organisms. That is evolution in its purest form, in all its beauty, creating a plethora of different organisms while still employing a fundamental blueprint! Shubin demonstrates this astounding evolutionary spectacle through the dissection of limbs in a great variety of animals. The image below, taken from the book, shows the unity between seals, lizards, birds, pterosaur, bat, whale, you name it! What Shubin is getting at is the analogous structures found within all animalian limbs, containing a "one bone-two bones-lotsa blobs-digits pattern" (Shubin 32). In humans, these refer to the humerus, the ulna and the radius, followed by the wrist with the digits. With that in mind, the long fingers of a bat wing closely resembles my typing fingers this very moment! (except I can't fly all that well...) In the book, he teaches his readers the process of evolution while proving how fossils like //Tiktaalik// can give us valuable insight into our evolutionary past.

What I have yet to cover is how and why evolution creates such unity. Well if I do recall correctly, my high school bio teacher taught me about this little thing that was invented many years ago called D.N.A, or if you want to confuse friends- deoxyribonucleic acid. This molecule, found in all cells, acts like a historical record of our evolutionary past. By analyzing similarities and differences of DNA sequences from different organisms, a phylogenetic tree could be constructed from this molecular evidence by comparing genomes! DNA sequences that are more similar imply a closer relative, whether human or not. For example, molecular records show that chimpanzees have a more recent common ancestor with humans compared to a gorilla, just as it would also show that your uncle is even //more// closely related...hopefully. The reason DNA can serve as a representation of our //past// is because it is also a representation of our //future//. In less corny and cryptic terms, I mean that the DNA molecule exists to pass on nucleotide sequences and thus genes to offspring. DNA replication is possible, thanks to DNA polymerase, which aligns nucleotides to create an identical copy of DNA. In tandem with replication, meiosis creates haploid gametes through Meiosis I and II. During meiosis, crossing over takes place which "randomizes" genes, allowing for more genetic variation, speeding evolution. Gametes are created to give a portion of both the mother's and the father's genome to the offspring, serving as another way to enhance genetic variation even further. This inheritance of genes fuels evolution because it allows natural selection of more favorable traits to an organism's survival, thus weeding out the bad. And to tie it back, creating a full circle, this, in turn, creates diverse organisms because of divergent evolution, where species split off, utilizing a different genetic makeup for survival. Factors such as allopatric (geographic) isolation can cause deviation and genetic drift. An example can be seen in the Galapagos islands, where a vast variety of species can be seen from island to island. However, the key genes are still kept in the pool, unifying all organisms regardless of speciation.

The above image shows such unity in animals, specific to embryonic development. The different organisms' embryos look strikingly similar as they all employ hox genes, which code for segment identity during early embryonic development. "In the middle of each gene was a short DNA sequence that was virtually identical in each species...when the scientists fished around for this gene sequence in other species, they found something so uniform that it came as a true surprise: //versions of the// Hox //genes appear in every animal with a body//" (Shubin 108).

I really am in awe when I step back and take a look at the big picture. Your Inner Fish passes insight onto its reader by exemplifying the astounding power of evolution. A closer look at the animals around us will reveal what unites all organisms on this planet: Evolution.

** Concepts Covered: **Phylogeny, Human Anatomy, Process of Evolution, DNA, Meiosis, DNA Replication, Divergent Evolution, Embryology, Hox Genes.

Photograph. //ScienceBlogs//. 15 Feb. 2007. Web. 28 May 2010. .
 * Works Cited **

Photograph. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. 31. Print.

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print.

Posted Friday, May 28 Last Edited Friday, May 28
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Tiktaalik's Song
Watch this video! media type="youtube" key="B9h1tR42QYA" height="385" width="480" **Below are Garrett's comments, not mine:**

Dude!!!! Great Song!!! does this count as a response? Judges??

Yes! No! Yes!

Looks like we have a 2 to 1 vote. It counts. (Thank you chuck norris) ...Dodgeball....anyone...? okay

The clip referenced above:

Counter-Counter Argument
** :::::::::::::::::[|Counter-Counter Argument] to [|Garrett Roell's Comment] on Post #1 on My Page:::::::::::::::: ** I do acknowledge how such an implication might have been derived, but I would like to argue that I only stated that all animals (not all living things) have the same evolutionary roots. And animals all DO share a common ancestor, and it would be extremely implausible to say otherwise as that contradicts pretty much all fossil, molecular, and physiological evidence. But I do realize your argument that life in maybe the single-celled stage might have been established more than once. However, not to mention the extreme odds against that happening twice on the SAME planet, it is the most plausible statement to say that all cellular organisms all derived from an ancestor that utilized the passing of genetic codes from generation to generation. It is highly (and I mean HIGHLY) unlikely for life to have started twice and then end up functioning EXACTLY the same way. The structure of DNA is complex and a completely separate instance of such a design is again, almost impossible. If all organisms adhered to “what works” as you have mentioned, then why do we even have diversity?! Even though I am reluctant to declare that you share a close common ancestor with myself, things just are how they are.

To your statement about amphibian’s bones being fused- think about arthropods. Segmentation often included the fusing, modifying, and specializing of certain segments, yet they all still share the common design. The frog has an overall similar design to the rest, but only that modification of those bones by fusing was present. Oh, and the argument with the frogs and the fusing of bones actually derived directly from Neil Shubin. I am but a messenger. To the retrovirus argument- that starts a whole discussion of life altogether, bringing the concept of what constitutes something as living. And personally, I think nothing is living and that we are really no different than that of a rock, just much more complex. We are only a system of nonliving materials that has started the ball of heredity rolling, causing all this evolution stuff. But even retroviruses have the same evolutionary roots as they utilize DNA. Either that or they “stole” the design, by somehow accepting it into their system and actually using it to reproduce. But I digress.
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**-Post #2- **
 "...As they looked at embryos, they found something __fundamental__: //all organs in the chicken can be traced to one of three layers of tissue in the developing embryo//. These three layers became known as the germ layers...Von Baer compared the three layers of Pander's chicken embryos with everything else he could get his hands on: fish, reptiles, and mammals. Yes, __every animal organ originated in one of these three layers__. Significantly, the three layers formed the __same structures__ in every species . Every heart of every species formed from the same layer. Another layer gave rise to every brain of every animal. And so on. No matter how different the species look as adults, as tiny embryos they all go through the __same stages of development__. " (Shubin 99).



Connecting to the ideas of my previous post, of how a universal design can be traced back to the development of embryos of different species due to hox genes, this excerpt outlines yet another example of unity between animals present in embryonic development. Shubin describes the germ layers of an embryo, which forms through gastrulation. During gastrulation, the multicellular blastula, which resembles a hollow ball of cells, undergoes a rearrangement of the embryo in which one end of the embryo folds inward, expands, and eventually fills the blastocoel, producing the layers of embryonic tissues. As development progresses, these concentric layers form the various tissues and organs of the body. The ectoderm is the first tissue layer that forms as it covers the surface of the blastocoel. The ectoderm develops into the central nervous system, the epidermis, hair, mammary glands, the cranial and sensory systems, among many others. The endoderm is the innermost tissue layer, lining the digestive tube, or archenteron, and gives rise to the lining of the digestive tract, and organs derived from it, such as the liver and the lungs. The archenteron is the pouch formed by gastrulation and opens to the outside via the blastopore. The mesoderm forms in the embryos of tripoblastic organisms, which have all three germ layers. It gives rise to most other organs between the digestive tract and the outer covering of the animal, forming the skeletal system, skeletal muscle, the heart, and connective tissue. Tripoblasts include all bilaterally symmetrical animals, including the phyla echinodermata, mollusca, chordata, arthropoda, annelida, platyhelminthes, among many others. Diploblasts, which include cnidarians, only have 2 germ layers, lacking the mesoderm. Even less fortunate are sponges, which lack true tissues all together, having no symmetry. These spineless bottomfeeders just don't have the guts. Pun quite obviously intended. :P .

To classify triploblastic organisms even further, we can differentiate organisms based on the presence of a coelom, or body cavity. Coelomates such as annelids have a true coelom, with a body cavity completely lined by tissue derived from the mesoderm. However, acoelomates such as flatworms lack a body cavity, having the region between the ectoderm and endoderm completely filled with tissue form the mesoderm. Pseudocoelomates such as nematodes have a body cavity only partially lined by tissues of the mesoderm.

And yet ANOTHER way of differentiating tripoblasts is the distinction between protostomeal and deuterostomeal development. Protostomes include molluscs, annelids and arthropods, and cleavage during the eight-cell stage is spiral and determinate. During coelom formation in the gastrula stage, the coelom forms from a split mesoderm, being schizocoelous. The blastopore develops into the mouth in protostomes as well. However, deuterostomes seem to have their own way of doing things. Their cleavage of the zygote is radial and indeterminate, coelom formation being enterocoelous, meaning that the folds of the archenteron form the coelom, and the blastopore develops into the anus. The only point for this differentiation, I think, is so we don't end up with our anus where it shouldn't be. That would be problematic. Just kidding.

Anyway, Shubin's explanation and walk-through of the germ layers were a tad irrelevant to his paleontological study, but also allowed him to educate his readers on the subject for the purpose of using it to prove a common evolutionary development present in almost all multicellular organisms. His use of words such as "frisbee" to describe the embryo as a blastocyst and "ball" to describe the embryo as a blastocoel simplifies these explanations to his readers, widening the audience. However, the vocabulary he utilizes of objects often associated with throwing to describe a little human embryo slightly worries me.


 * Covered Concepts**

Germ Layers, Gastrulation, Embryogenesis, Various Phyla, Diplo/Triploblasty, Coelomates, Deuterostome v. Protostome Development

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

Photograph. Web. 2 June 2010. .

Photograph. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. 103. Print.

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print. Posted Wednesday, June 2 Last Edited Wednesday, June 2
 * -NT **

Comment #1
**:::::::::::::::::::::::::::::::::[|Comment #1] on Nick Weiler's Post #2, Regarding Evolution v. Creationism::::::::::::::::::::::::::::::::: ** "Of course, without a doubt, the theory of evolution is the most accurate explanation for the diversity of organisms as well as the striking similarities between organisms. As compared to Creationism, Evolution has much more factual, concrete evidence to support its verity. For example, as you already have mentioned, there are irrefutable similarities between organisms molecularly, with DNA, as well as anatomically, with the structures of their body representing a “common theme,” due to the sharing of a common ancestor. For example, as I have elaborated in Post #1 on my page, DNA comparisons and comparisons of genomes lend molecular evidence toward the theory of evolution. By comparing DNA sequences, we can determine how closely we related we are from another species due to the mutations you have explained. Because evolution is fueled by such alterations of the nucleic code, by mapping the number and extent of differences and alterations, one can establish how much an effect evolution has acted upon two species. Also, as you have mentioned, physical similarities are present in various organisms. For example, as I have also explained in Post # 1 on my page, the morphological and anatomical parallels present within the limbs of many animals show analogous structures, hinting towards being derived from a common ancestor. The differences between the varying versions of limbs such as bat wings, flippers, or our own hands lie within the deviations and alterations from an original blueprint, to increase our chances of survival. To combine BOTH molecular and anatomical evidence, hox genes more blatantly show this correlation. The embryos of many different organisms look strikingly similar as they all employ hox genes, which code for segment identity during early embryonic development.

However, I think you could have also touched on fossil evidence as a mean to support the Theory of Evolution. Analyzing and juxtaposing fossils of extinct and extant would also lend itself in the favor of Evolution. For example, by finding fossil evidence of alterations of morphological features from an individual of a certain group and comparing it to an existing, present-day organism, one can point out how evolution has modified the organism. Fossil evidence directly gives the correlation between the temporal (time), chronological factor as opposed to physical, anatomical changes present.

Oh, and just to satiate Mrs. Galuska’s requirement of needing an actual opposing argument, I will argue about your opinion on how theological (God-like) and scientific forces work in concert in the creation of life. While I do undoubtedly support and agree with your position on how evolution contributes to present day organisms, I do have trouble agreeing with you standpoint of how the origin of life stems from supernatural powers. First of all, such religious beliefs are the creation of the seemingly imaginative human minds, and therefore cannot be used as a suitable explanation of “real-world” things such as the origin of life. And while theological beliefs might be a makeshift explanation, I believe that we should at least elect more plausible causes such as the theory of abiotic synthesis of organic compounds. Stanley Miller’s experiment supported that, under the right conditions (with electrical discharge and “primordial soup”), organic molecules can be synthesized abiotically. An explanation of his procedure can be found here: [] Really, self-awareness, the theory of vitalism (life force), and most of all religion, only came about due to the evolutionary development of cerebral organs, and to go into Freudian theory, the development of the ego.

We should not place our trust in and rely on a human-made work (the Bible) that believes a higher entity is in the form of a Homo Sapiens above all other species, which I might add is extremely egocentric toward the human need of superiority over others. Also, it could have been very well written by some schizophrenic, drugged, or extremely manipulative guy. Thus it cannot be used as concrete, factual evidence. If it can be, then any children’s fiction literature must as well be taken as irrefutable fact! Six days of creation also obliquely contradicts the First Law of Thermodynamics: the law of Conservation of energy, which states that matter cannot be created nor destroyed And also, DAYS are a measure of time created by again, HUMANS, and therefore, since we were not present, the origin of life cannot be based on a human measure of time. I swear, I find it absurd how many religious people actually believe in this stuff."

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


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<span style="display: block; font-family: 'Palatino Linotype','Book Antiqua',Palatino,serif; font-size: 110%; text-align: center;">"To go from a generalized egg cell to a complete human, with trillions of specialized cells organized in just the right way, whole batter ies of genes need to be turned on and off at just the right stages of development. Like a concerto comp osed of individual notes played by many instruments, our bodies are a composition of individual genes turning on and off inside each cell during our development." (Shubin 46). <span style="font-family: Arial,Helvetica,sans-serif; font-size: 90%;">Having all the information compiled in every cell, DNA contains the instructions to form a complete organism. From the single cell at conception, multiple cellular divisions take place and each daughter cell is consequently differentiated to perform a specific action. Our developed bodies are an ordered arrangement of these differentiated cells ranging from neurons to epithelial cells. Embryonic stem cells are pluripotent, meaning that they can differentiate into each of more than 200 cell types of the adult body, of any of the three germ layers. Chemical signal molecules induce such differentiation, and at each stage of development, it is key that the correct messenger is released at the right time, so that the embryo's cells differentiate accordingly and the embryo develops correctly. Differentiation occurs with the aid of many proteins, which is coded for in the DNA. However, depending on the differentiation, different proteins are required, and thus, different DNA segments need to be transcribed. This is possible through regulation of gene expression, using the switches of genes.

<span style="font-family: Arial,Helvetica,sans-serif; font-size: 90%;"> The switches of genes are known as operators, positioned within the promoter region of a gene. They control the access of RNA polymerase to transcribe the genes to later be coded into proteins. An operon describes the group as a whole: the operator, promoter, and gene (or the entire stretch of DNA required for enzyme production). Repressor proteins bind to the operator to deny access of RNA polymerase to the gene strand. The repressor allows the gene to be regulated by acting as an “off switch”. Repressors themselves can be activated and inactivated with the help of corepressors, which can bind to repressors to activate them. Corepressors cooperate with the repressor protein to turn a gene off. Corepressors can be an example of a negative feedback system, where the production of a molecule such as tryptophan can act as corepressors to inhibit production as the product accumulates. In reverse, it can also allow production when levels are low. An operon that can be switched off is known as a repressible operon.

In contrast, an operon with the ability to be induced is known as an inducible operon. An inducer is involved in inactivating the repressor instead of activating it like corepressors. An example of this is the lactose operon, where the inducer is allolactose (which is an isomer of lactose and is usually found in the presence of lactose). When lactose is present (and thus allolactose), allolactose binds to the lac repressor, altering its conformation, and nullifying the repressor’s ability to attach to the operator. This allows the coding of lactase enzymes to catalyze the lactose.



To further allow regulation of genes, enhancers and transcription factors also come into play. These work with the control elements of the gene, which are non-coding segments of DNA designed to help regulate transcription by binding certain proteins. To initiate transcription, RNA polymerase requires the assistance of transcription factors, a collection of proteins that mediate the binding of RNA polymerase with each other. The polymerase can move along the DNA template strand, producing a complementary RNA strand only when the initiation complex is completely assembled. Enhancers, which are control elements further away from the actual gene, interact with activators, proteins that bind to enhancers and stimulate the transcription of a gene. Additionally, protein mediated bending of the DNA brings the activators on the enhancers closer to a group of mediated proteins, which interact with the transcription factors, ultimately, binding the RNA polymerase to the promoter region. Repressors are also present for gene regulation, which can block the activators from their control elements or from the proteins they need to bind to. Presence or absences of any of these elements further allow the regulative capabilities of gene transcription. The transcription initiation complex is suitably named as it is definitely complex!

**Covered Concepts:** <span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 90%; text-align: center;">Differentiation in Development, Stem Cells, Transcription, Chaperonin, Operons, Gene Regulation, Negative feedback system, Transcription Initiation Complex **Works Cited** Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.

Photograph. //Biolegend.com//. Web. 6 June 2010. <http://www.biolegend.com/media_assets/pathways/Hematopoiesis%20from%20Pluripotent%20Stem%20Cell.jpg>.

Photograph. Web. 6 June 2010. <http://www.life.illinois.edu/bio100/lectures/s97lects/16GeneControl/lac_operon_ind.GIF>.

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print. Last Edited Sunday, June 6
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Comment #2
**<span style="display: block; font-family: 'Palatino Linotype','Book Antiqua',Palatino,serif; font-size: 80%; text-align: center;">:::::::::::::::::::::::::::::::::[|Comment #2] on Garrett Roell's Post #2, Regarding Protein and Gene Regulation::::::::::::::::::::::::::::::::: ** Hey Garrett, I think you suitably covered protein structure in relation to differentiation of cells. However, I do feel that a more pronounced direct connection between the two subjects as well as consistent correct spelling of *protein* (not protien) would have enhanced the cohesiveness of your explanation. You did mention that inhibitor proteins can suppress transcription and thus production of a protein as a method of regulation. But for the sake of this comment as well as to be picky, I want to elaborate on gene to protein regulation a little further.

As I have explained in Post #3 on my page, the switches of genes are known as operators, positioned within the promoter region of a gene. They control the access of RNA polymerase (as you have mentioned) to transcribe the genes. You mention inhibitor proteins binding to the promoter to deny access of RNA polymerase to the gene strand, but what I think you are referring to are the repressor proteins that can bind to the operator (not promoter) to perform this task. The repressor allows the gene to be regulated by acting as an “off switch”. And I could also go into corepressors and inducers, which allow more functionality of regulatory proteins, but it would be a little extensive. I have explained them on Post #3 on my page if you would like to review the concept. Basically, they just bind to the repressor, either activating or inactivating it.

To further allow regulation of genes, enhancers and transcription factors also come into play. The enhancer region, mediator proteins, transcription factors, and RNA polymerase all bind to initiate transcription. Presence or absences of any of these elements regulate the gene transcription. Repressors (not to be confused with the other repressors) further allow regulating capabilities by blocking the assembly of the transcription initiation complex.

**Works Cited** Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print
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<span style="background-color: #b208e2; color: #f2f63c; display: block; font-family: 'Comic Sans MS',cursive; font-size: 160%; text-align: center;">-Post #4-
<span style="color: #000000; display: block; font-family: 'Palatino Linotype','Book Antiqua',Palatino,serif; font-size: 110%; text-align: center;">"Mitochondria exist inside every cell of our bodies, doing a remarkable number of things. Their most obvious job is to turn oxygen and sugars into a kind of energy we can use inside our cells. ...Many of the processes we use to live reflect our mitochondria's history. The chain reaction of chemical events that turns sugars and oxygen into usable energy and carbon dioxide arose billions of years ago, and versions of it are still seen in diverse microbes.Mitochondria carry this bacterial past inside of them: with an entire genetic structure and cellular microstructure similar to bacteria, it is generally accepted that they originally arose from free-living microbes over a billion years ago. In fact, the entire energy-generating machinery of our mitochondria arose in one of these kinds of ancient bacteria." (Shubin 197).

Vaguely, Shubin brushes the surface of multiple key concepts of cellular biology that we have studied in our course with much more depth and detail. He discusses and describes a fundamental organelle found in nearly all eukaryotic cells that supplies the cell with ATP. Mitochondria are the sites of cellular respiration, thus where most ATP is generated. The unique traits this organelle has apart from all others except chloroplasts is that they have at least two membranes separating the innermost space from the cytosol, and their membrane proteins are not made by the endoplasmic reticulum (which secretes proteins produced by the ribosomes attached to the rough ER). Instead they obtain their proteins from the free ribosomes in the cytosol and the ribosomes located within these unique organelles as well. Not only do mitochondria have their own separate supply of ribosomes, but they also have their own DNA, which programs the synthesis of the proteins made with their ribosomes. Holding their own DNA, they are also semi-autonomous and can grow and reproduce within the cell! Mitochondria are so independent, it's like they have a "mind' of their own, moving around the cell, changing their shape, and even dividing in two! But just what makes up this little bean-shaped organelle?

The mitochondrion is enclosed within two phospholipid bilayers with a unique collection of embedded proteins. The outer membrane is smooth, but the inner membrane is convoluted, containing many infoldings called cristae. These foldings are much like the villi in our intestines, which greatly increase the surface area upon which phosphorylative oxidation occurs, thus maximizing efficiency and productivity of cellular respiration. This is a prime example of structure fitting function (A MAIN THEME OF BIOLOGY!!!). The inner membrane separates the mitochondria into two internal compartments: the intermembrane space (the region between the two membranes) and the mitochondrial matrix, which is enclosed within the inner membrane. Despite its name, it has nothing to with alternate realities or Keanu Reeves dodging bullets in slow-mo, to my disappointment. However, if it's any consolation, many different enzymes are built into the inner membrane, which include the many intermediate electron carries that make up the electron transport chain and ATP synthase, which has the job of chemiosmosis.



Just what is this chemiosmosis and oxidative phosphorylation stuff I keep referring to? While I do agree that the names are unnecessarily complex, I have to admit they're fun to say to confuse people. They are actually part of a greater process named cellular respiration, which is an exergonic breakdown of glucose and oxygen into carbon dioxide, water, and energy in the form of ATP and heat. The energy "extracted" out of the chemical bonds of glucose is stored in a chemical "battery" called Adenosine Triphosphate. There I go using confusing words again. More commonly referred to as ATP, the ATP synthase in the mitochondria don't actually produce these compounds, but rather recycle their supply of ADP and an inorganic phosphate by recombining them. ATP acts like a spring with the last of the "tri" phosphates containing a lot of potential energy. The cell hydrolyzes ATP to transfer its energy into doing work. Just add water!



The production of ATP begins in the cytosol, where glycolysis occurs. This degradation of glucose splits the molecule into two pyruvate molecules which is consequently fed into the citric acid cycle. This occurs within the mitochondrial matrix and it completes the breakdown of glucose, releasing carbon dioxide.Upon entering the mitochondria, pyruvate is first converted into a compound called acetyl coenzyme A. In both glycolysis and the citric acid cycle, substrate phosphorylation is utilized to produce a small amount of ATP. In glycolysis, a net of 2 ATP molecules are formed. And in the Krebs (citric acid) cycle, 2 more ATP molecules are produced in the total 2 turns. In both glycolysis and the citric acid cycle, NAD+ is reduced to NADH by electrons released during the breakdown of the sugar. Additionally, in the citric acid cycle, FADH2 is also produced by reducing FAD and is employed to store the chemical energy. These compounds, NADH and FADH2, serve as electron carriers, which carry the high-energy electrons to the electron transport chain. In the electron transport chain, the electrons from the carriers are accepted and are passed from one cytochrome (enzymes embedded in the inner mitochondrial membrane's cristae) to the next, cascading down the energy gradient (to a more electronegative acceptor) to the final electron acceptor, oxygen, which is the most electronegative out of all. This final transfer of electrons to the oxygen molecule forms water. With each consecutive redox reaction of each cytochrome, hydrogen ions are actually being pumped into the intermembrane space for the oxidative phosphorylation of chemiosmosis to occur. This step produces 90% of all ATP generated during respiration. The active pumping of hydrogen ions in the electron transport chain actually create a chemical gradient of a high concentration of hydrogen ions in the intermembrane space, allowing work to be passively done when the hydrogen ions diffuse back across the membrane, down the chemical gradient. This gradient is referred to as the proton-motive force, which emphasizes the capacity of the gradient to perform work. An enzyme called ATP synthase is the only entrance back into the mitochondrial matrix, forcing the hydrogen ions to pass through it, thus "spinning" it to phosphorylate the inorganic phosphate and ADP to create ATP. With each ion, the protein spins, producing one ATP molecule.



Carrying out such complex processes within itself, maybe mitochondria do have a "mind" of their own! In class, we discussed the Endosymbiotic Theory, which hypothesizes that mitochondria might have originated from a free-living prokaryotic organism that was in a symbiotic relationship with a eukaryotic cell. The prokaryotic cell would carry out the processes of cellular respiration, thus supplying the eukaryotic cell's necessity for energy to be converted into work, while the eukaryotic organism offered an abundant supply of nutrients in the rich cytosol as well as protection from predators. Perhaps some of the mitochondrial DNA was transferred to the nuclear DNA, thus establishing the endosymbiotic relationship due to dependence on the host cell. Evidence that support this theory include the fact that mitochondria possess their own set of DNA, of which they can replicate, as well as their own ribosomes. They can also reproduce asexually, resembling the prokaryotic process of binary fission. Additionally, they have membranes with a composition very similar to that of a prokaryotic cellular membrane. Finally, mitochondria are of the same size as prokaryotic bacteria, which are significantly smaller in size the eukaryotic cells, explaining their ability to live in another cell. Although this excerpt discusses topic completely irrelevant, I don't mind. I do appreciate the inclusion of this topic as it makes my job to connect quotes from the book to our curriculum all the more easier.

**Covered Concepts**

Cellular Biology, Mitochondria, ER, ATP, Cellular Respiration: (Glycolysis, Citric Acid Cycle, Electron Transport Chain, Chemiosmosis), Endosymbiotic Theory, Eukaryotes vs. Prokaryotes

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

Photograph. Web. 9 June 2010. <http://course1.winona.edu/sberg/ILLUST/fig916.gif>.

Photograph. Web. 9 June 2010. <http://dm.ncl.ac.uk/helencollard/blogger/wp-content/uploads/2009/04/atp.gif>.

Photograph. Web. 9 June 2010. <http://www.mitochondrial-disorder-information.com/images/mitochondria.gif>.

Photograph. Web. 9 June 2010. <http://vinayvasan.files.wordpress.com/2009/12/matrix_30.jpg>.

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print. Last Edited Sunday, June 11
 * <span style="display: block; font-family: 'Courier New',Courier,monospace; font-size: 140%; text-align: right;">-NT ** Posted Sunday, June 9

Comment #3
**<span style="display: block; font-family: 'Palatino Linotype','Book Antiqua',Palatino,serif; font-size: 80%; text-align: center;">:::::::::::::::::::::::::::::::::[|Comment #3] on Lindsey Racz's Post #5, Regarding Technology, Death, and Evolution::::::::::::::::::::::::::::::::: ** To start, I want to genuinely applaud your brave endeavor if taking on a bold argument, especially with such entertaining commentary on the pathetic state of our species. I also find it interesting how you pointed that individuals want to avoid death and aging, even if it means compromising the survival of our species. Thinking about the dynamics of evolution, we can actually see how this desire to cheat death was not accounted for evolutionarily. What I mean is- since our genetics really are only perfected and optimized for our survival until reproduction and nothing further, evolution abandons in that it leaves us to age and deteriorate, not giving us predispositions to continue our lives. In turn this makes us go to great (and humorously pathetic) lengths to selfishly extend our time on this Earth. Don’t get me wrong- I’m not saying that this is a flaw in evolution. I entirely agree with your opinion that death actually improves our chances of survival, thus proving to actually be an evolutionary mechanism, with the carbon cycle and the recycling of nutrients and whatnot. Since niches cannot possibly have a carrying capacity to support life of immortal organisms AND the generations to come, of course the older versions must be eliminated somehow. The species practically doesn’t care about those prototypes as they have already served their purpose of reproducing and no longer prove beneficial to our survival, but instead take up space and resources. It sounds really cold, but hey, it’s the truth, unfortunately.

Stepping away from my worryingly cold, heartless, and purely scientific perspective of life, I do also agree with you in that I see a beauty in life’s brevity. Stories don’t mean anything without an ending. Plus, it allows us to make the best of our time as well as to not take things for granted. For example, my grandfather, who had just passed away last night, unfortunately, had lived a great life to a respectable age. His death allowed me to really step back and analyze the picture as a whole. We shouldn’t take the people around us for granted, and we also should definitely not take OUR lives for granted. We only have one life and we should live it to the fullest. Of course, mourning shouldn’t be a solemn sorrowful experience, but rather an enlightening, cathartic one. It allows us to reflect on the good traits of our loved ones, good times we’ve spent with them, and keep them sacred in our memory, while also reflecting on our own lives. If we are to die tomorrow, are we satisfied to leave our lives in the state it is at the moment? But, to avoid making this post too personal and irrelevant to our scientific discussion, I will move on to my next point.

Your post also kind of reminded me of some Freudian theory, dealing with the id and the death drive. The id was subtly implied as it represents the selfishness wired into our mental framework. It is the part of our mind where pure greed, sloth, envy, pride, gluttony, and lust influence our actions. (Interesting how all these attributes are the 7 deadly sins, huh? Kinda shows the contradiction of religion and science…) However, it isn’t necessarily a negative aspect as it hugely increases our individual chances of survival. Without it, we wouldn’t want to eat if we’re hungry or reproduce to prolong our species’ line. This relates to your post because of our selfish nature to believe that our lives are important enough to extend indefinitely, even if it completely “pauses our evolution”. It could also be applied to the capitalist companies preying on human weaknesses. However, our mind isn’t completely corrupt in that sense as we have the death drive, which is an instinct that isn’t essential to our survival in anyway, but rather serves as a counter-intuitive measure to denature our state of living. It’s hard to wrap your head around, but believe it or not, certain everyday indulgences are linked to this drive, such as delving into the life of a fictional character in a book or movie or taking drugs to numb our senses, preventing us from experiencing further suffering of our pitiful lives. Wow, that was depressing. Anyway, these actions allow us to escape the reality of our lives. Ah, darn it, I think I’ve gone on an irrelevant track once more. However, I do hope that you at least find some of this interesting as I do.

On yet another note, another example I would like to add on how technology is contradicting evolution as a process is genetic modification. Imagine if we were to hold the ability to alter our genes in any way we’d want to. In such an instance, evolution will lead to the human ideals (which unfortunately include mostly aesthetic, useless, vain attributes). Evolution would not sculpt our genetics based on what’s beneficial to our survival, but rather what we THINK would be beneficial. We’d all be perfect to the eye, but our species would probably be wiped out in no time.

Anyway, in conclusion, I think your post really gives food for thought, as you can see in my extensively long post (Sorry!) as it deals with a wide variety of controversial and intriguing concepts. I apologize if you actually read my rambling on about nonsense I find interesting… >.<” I’ll stop now.

PS. I think one Garrett is more than enough. :]


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<span style="background-color: #ff0003; color: #15f2f4; display: block; font-family: 'Comic Sans MS',cursive; font-size: 160%; text-align: center;">-Post #5-
<span style="color: #000000; display: block; font-family: 'Palatino Linotype','Book Antiqua',Palatino,serif; font-size: 110%; text-align: center;">"Our sedentary lifestyle affects us in other ways, because our circulatory system originally appeared in more active animals. Our heart pumps blood, which is carried to our organs via arteries and returned to the heart by way of veins. Because arteries are closer to the pump, the blood pressure in them is much higher than in veins. This can be a particular problem for the blood that needs to return to our heart from our feet. Blood from the feet needs to go uphill, so to speak, up the veins of our legs to our chest. If the blood is under low pressure, it may not climb all the way... When we walk we contract [our leg muscles], and this contraction serves to pump the blood up our leg veins. ...This system works superbly in an active animal, which uses its legs to walk, run, and jump. It does not work well in a more sedentary creature. If the legs are not used much, the muscles will not pump the blood up the veins." (Shubin 188). Although this excerpt was repeated by Phil by mistake, as I had previously claimed it at an earlier date, I will instead briefly discuss topics he had already covered, but adding more connections as well. Shubin once again coincidentally refers to a topic that has been covered in the AP Biology curriculum in this excerpt dealing with our circulatory system. The circulatory system is designed to allow distribution of materials obtained from the external environment throughout a multicellular body. Because diffusion across far distances is inefficient, circulatory systems have structures that allow substances to diffuse to cells in short distances. This is possible through the use of capillaries, which have thin walls to allow a shorter distance of diffusion. The materials required to be distributed to the cells of a body include those that are obtained through the digestive and respiratory systems. The food that we eat are broken down into tiny molecules via the digestive system and our high surface area intestines absorb these nutrients through a thin epithelium, enriching our bloodstream so that individual cells can obtain said nutrients through diffusion from the capillaries to the cytosol of a cell. The same concept is applied to the respiratory system where air exchange occurs in the alveoli of our lungs, which are sponge-like to increase the surface area and allow diffusion across a thin membrane.The blood vessels surrounding the alveoli allow the diffusion and gas exchange of the oxygen we require for cellular respiration for the carbon dioxide and water vapor we produce as products of the process. The oxygen is also transported via the arteries and capillaries.



The circulatory system consists of a circulatory fluid, a set of tubes, and a muscular pump. In the human body, these are our blood, arteries, veins, capillaries, and heart. Our venous structures include arteries, which carry blood away from the heart, veins which carry them back, and capillaries, which I have already covered. Our hearts not only illogically represent our capacity for empathy and the bonds of relationships, but it also powers circulation by using metabolic energy to elevate the hydrostatic pressure of our blood to cause it to flow in a circuit back to the heart. consist of two atria and two ventricles. Atria in the systemic circuit receive blood returning to the heart while the ventricles in the circuit pump blood out of the heart. The journey of blood throughout the circulatory system can be summarized: To start, the right ventricle pumps blood to the lungs via pulmonary arteries, bringing it to the capillary beds in the two lungs for gas exchange. The oxygen rich blood will then return to the heart via the pulmonary veins to the left atrium of the heart. The blood then flows into the left ventricle where the blood is pumped to the body tissues through the systemic circuit. The blood leaves teh left ventricle through the aorta, which conveys blood to the arteries leading throughout the body. This then leads to arterioles which split into the caplillary beds located in the head, forelimbs, abdominal organs, and legs. Gas exchange occurs, dumping CO2 into the bloodstream while oxygen diffuses into the cell. The capillaries then rejoin, forming venule, which convey the blood to the veins, taking it to the two vena cava (superior and inferior). The vena cava empty the blood into the right atrium, from which the oxygen-poor blood flows into the right ventricle, restarting the cycle.



The atria serve as collection chambers for blood returning to the heart, which flow into the ventricles as the atria relax and fills the ventricles when they contract. The ventricles contracts much more strongly than the atria because of their thicker walls. The left ventricle is especially powerful due to it needing to pump blood throughout the body through the systemic circuits. The cardiac cycle describes the complete sequence of filling and contracting of the chambers. The contraction phase is the systole and the relaxation phase is the diastole. During the relaxation phase, which accounts for half of the cardiac cycle, blood flows into the atria and ventricles. A brief period of the atria systole forces all remaining blood into both ventricles .1 seconds before the ventricle systole which pumps blood into their respecting large arteries. A region of the heart called the sinoatrial node controls the rate and timing at which the cardiac mucles contract. It generates electrical impulses like those from nerve cells which spread through the walls of the atria, causing them to contract in unison. The impulse reaches to a relay point known as the atrioventricular node, at which the impulses are delayed for that .1 second before spreading to the walls of the ventricles. This ensures that all the blood is emptied from the atria before the ventricles contract, enhancing efficiency.

Because blood needs to counter the force of gravity, going uphill back to the heart, evolution has accounted for this by developing venous structures that help this climb. Lining the lumen of all blood vessels is an endothelium, which is a single layer of flattened cells that provides a smooth surface to minimize the resistance of the blood flow. Structural differences are seen in arteries and vein due to their slightly different functions. Because arteries are closer to the "pump", or the heart, they have an increased blood pressure to push the blood along. However, veins lack such increased pressure. We tested this effect in our heart rate and pressure lab, where we stood up and lay down to examine the effects of gravity. Skeletal muscles mainly push the blood by squeezing the veins to counter this disadvantage. To fight gravity, large veins also have one-way valves to only allow blood to flow towards the heart.



Our evolutionary mechanisms of our venous system and heart were developed to suit the conditions of our hunting ancestors and our present-day lifestyles of sitting at a desk and eating unhealthily and in excess pose issues for such designs as we do not receive nearly as much exercise as our ancestors and because our diet clogs our arteries with cholesterol, raising our blood pressure (atherosclerosis). I think this excerpt just shows how our rapid transition in lifestyle habits and development in technology that facilitates daily tasks can negatively impact our health with our already existing evolutionary mechanisms which have yet to be updated.

**Covered Concepts** Circulatory System, Blood Pressure, Electrical Impulses and Muscles, Venous Structures, Heart Rate and Pressure Lab, Evolution vs. Modern Society Campbell, Neil A., and Jane B. Reece. //Biology//. San Francisco: Pearson, Benjamin Cummings, 2005. Print.
 * Works Cited**

Photograph. Web. 13 June 2010. <http://ftp.schoolnet.lk/CAL_12th_march_2009/Science/CirculatorySystem/circulatory_system.jpg>.

Photograph. Web. 13 June 2010. <http://www.rbch.nhs.uk/images/dorset_health_centre/heart_diagram.jpg>.

Photograph. Web. 13 June 2010. <http://www.upt.pitt.edu/ntress/images/42-09-BloodFlowInVeins-L.gif>.

Shubin, Neil. //Your Inner Fish: a Journey into the 3.5-billion-year History of the Human Body//. New York: Vintage, 2009. Print.

"Why Cholesterol Matters." //Www.heart.org//. Web. 13 June 2010. <http://www.heart.org/HEARTORG/Conditions/Cholesterol/WhyCholesterolMatters/Why-Cholesterol-Matters_UCM_001212_ Article.jsp>. Last Edited Sunday, June 13
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Randomness

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