Phil+Schichman+Your+Inner+Fish

Your Inner Fish

Post #1

“The fossils inside these rock layers also follow a progression, with lower layers containing species entirely different from those in the layers above. If we could quarry a single column of rock that contained the entire history of life, we would find an extraordinary range of fossils. The lower layers would contain little visible evidence of life. Layers above them would contain impressions of a diverse set of jellyfish-like things. Layers still higher would have creatures with skeletons, appendages, and various organs, such as eyes. Above those would be layers with the first animals to have backbones. And so on. The layers with the first people would be found higher still.” (Shubin 6) This excerpt is directly related to evolution. Over time species on earth have changed and have adapted to become more successful in their varying environments. As organisms traveled from water to land, they developed different features that allowed them to survive this extreme change. Fish like vertebrates living in water, developed limbs and lungs before even migrating onto land. (PBS) The transition from the earliest fish like vertebrates to tetrapods is the overall theme of __Your Inner Fish__. This concept/fact is an example of one of the major themes of biology, and science in general: Science as a process. The development and creation of successful species has been a process which has been continuously progressing from approximately 4 billion years ago when life first appeared on earth. These 4 billion years can be seen from a different perspective when broken up into increments of time. As described by Shubin, different rock layers are home to different adaptations of life on earth. Starting from the most simplistic living organisms to the species of ‘man kind’, life on earth has developed and changed drastically. Earth’s existence has been broken up into a geological time scale in which living organisms can be classified. The different layers of rock in a rock column are “layers of time” or periods. If a rock containing the entire history of life was found, it would be divided into distinct layers from the different time periods of the earth. As the periods progressed the organisms and species would become more and more advanced. The geologic time scale has been broken up through eons, eras (3), periods (12), and epochs (bigger time frame to smaller time frame). Earth’s existence has been divided into three eras: The Paleozoic Era from 540 to 248 million years ago, The Mesozoic Era from 248 to 65 million years ago, Cenozoic Era 65 million years ago to present day. One celled organisms were formed in the Archeozoic Eon from 3.9 billion to 2.5 billion years ago, while the first “visible” life existed in the Paleozoic Era. The Paleozoic Era would create different divisions in the rock based on specific periods. (Enchanted Learning) For example, in one of the layers of rock, the Silurian Period, fossils of the first jawed fish would be found. This hypothetical rock proposed by Neil Shubin would be the entire geologic time scale in a different form. The different layers would represent the different periods of time, holding onto valuable fossils of species living in those times. The proposed thought of a sedimentary column of rock is very intriguing. Although the discovery of this column seems to be impossible, if it did exist, any hypothesis refuting the ideas of the development and adaptations of species would be refuted. The rock would be a concrete piece of evidence, as a true timeline of the existence of life. It would be one of the greatest geologic findings ever. PS

Geologic Time Scale (Enchanted Learning)

h a n e r o z o i c
 * EON || ERA |||| PERIOD || EPOCH || PIVOTAL EVENTS ||
 * ** P

E o n

"Visible Life"

Organisms with skeletons or hard shells.

540 mya through today.

P h a n e r o z o i c

E o n

"Visible Life"

Organisms with skeletons or hard shells.

540 mya through today.

P h a n e r o z o i c

E o n

"Visible Life"

Organisms with skeletons or hard shells.

540 mya through today.

P h a n e r o z o i c

E o n

"Visible Life"

Organisms with skeletons or hard shells.

540 mya through today. ** || **[|Cenozoic Era]

"The Age of Mammals"

65 mya through today** |||| **Quaternary Period "The Age of Man" 1.8 mya to today** || **[|Holocene] 11,000 ya to today** || Human civilization || The Last Ice Age 1.8-.011 mya** || The first humans (Homo sapiens) evolve. [|Mammoths], mastodons, [|saber-toothed cats], giant ground sloths, and other Pleistocene megafauna. A mass extinction of large mammals and many birds happened about 10,000 years ago, probably caused by the end of the last [|ice age]. || 65 to 1.8 mya** || **Neogene 24-1.8 mya** || **[|Pliocene] 5-1.8 mya** || First hominids (australopithecines). Modern forms of whales. [|Megalodon] swam the seas || 24-5 mya** || More mammals, including the horses, dogs and bears. Modern birds. South American monkeys, apes in southern Europe, Ramapithecus. || 65-24 mya** || **[|Oligocene] 38-24 mya** || Starts with a minor extinction (36 mya). Many new mammals (pigs, [|deer], [|cats], rhinos, tapirs appear). [|Grasses] common. || 54-38 mya** || Mammals abound. Rodents appear. [|Primitive whales appear]. || 65-54 mya** || First large mammals and primitive primates, plesiadapiforms. ||
 * ^  ||^   ||||^   || **[|Pleistocene]
 * ^  ||^   || **Tertiary Period
 * ^  ||^   ||^   ||^   || **Miocene
 * ^  ||^   ||^   || **Paleogene
 * ^  ||^   ||^   ||^   || **Eocene
 * ^  ||^   ||^   ||^   || **[|Paleocene]
 * ^  || **[|Mesozoic Era]

"The Age of Reptiles"

248 to 65 mya** |||| **[|Cretaceous Period] 146 to 65 mya** || Upper 98-65 mya || High tectonic and volcanic activity. Primitive marsupials develop. Continents have a modern-day look. Minor extinction 82 mya. Ended with large extinction (the [|K-T extinction]) of dinosaurs, [|pterosaurs], [|ammonites], about 50 percent of marine invertebrate species, etc., probably caused by asteroid impact or volcanism. || 146-98 mya || The heyday of the dinosaurs. The first crocodilians, and [|feathered dinosaurs] appear. The earliest-known butterflies appear (about 130 million years ago) as well as the earliest-known snakes, ants, and bees. Minor extinctions at 144 and 120 mya. || 208 to 146 mya** || Many dinosaurs, including the giant [|Sauropods]. The first birds appear ([|Archaeopteryx]). The first [|flowering plants] evolve. Many ferns, cycads, gingkos, rushes, conifers, [|ammonites], and [|pterosaurs]. Minor extinctions at 190 and 160 mya. || 248 to 208 mya** || The first [|dinosaurs], mammals, and crocodyloformes appear. Mollusks are the dominant invertebrate. Many reptiles, for example, turtles, [|ichthyosaurs]. True flies appear. Triassic period ends with a minor extinction 213 mya (35% of all animal families die out, including labyrinthodont amphibians, conodonts, and all marine reptiles except ichthyosaurs). This allowed the dinosaurs to expand into many niches. || 540 to 248 mya
 * ^  ||^   ||||^   || Lower
 * ^  ||^   |||||| **[|Jurassic Period]
 * ^  ||^   |||||| **[|Triassic Period]
 * ^  || **[|Paleozoic Era]

[|Paleozoic Era] 540 to 248 mya** |||||| **Permian Period "The Age of Amphibians" 280 to 248 mya** || "The Age of Amphibians" - Amphibians and reptiles dominant. Gymnosperms dominant plant life.The continents merge into a single super-continent, Pangaea. Phytoplankton and plants oxygenate the Earth's atmosphere to close to modern levels. The first stoneflies, true bugs, beetles, and caddisflies, The Permian ended with largest mass extinction. Trilobites go extinct, as do 50% of all animal families, 95% of all marine species, and many trees, perhaps caused by glaciation or volcanism. || Wide-spread [|coal swamps], foraminiferans, corals, bryozoans, brachiopods, blastoids, seed ferns, lycopsids, and other plants. Amphibians become more common. 360 to 280 mya |||| **Pennsylvanian Period 325 to 280 mya** || First reptiles. Many ferns. The first mayflies and cockroaches appear. || 360 to 325 mya** || First winged insects. || "The Age of Fishes" 408 to 360 mya** || Fish and land plants become abundant and diverse. First tetrapods appear toward the end of the period. First amphibians appear. First sharks, bony fish, and ammonoids. Many [|coral reefs], brachiopods, crinoids. New insects, like springtails, appeared. Mass extinction (345 mya) wiped out 30% of all animal families) probably due to glaciation or meteorite impact. || 438 to 408 mya** || The first jawed fishes and [|uniramians] (like insects, centipedes and millipedes) appeared during the Silurian (over 400 million years ago). First vascular plants (plants with water-conducting tissue as compared with non-vascular plants like mosses) appear on land (Cooksonia is the first known). High seas worldwide. Brachiopods, [|crinoids], corals. || 505 to 438 mya** || Primitive plants appear on land. First corals. Primitive fishes, seaweed and fungi. Graptolites, bryozoans, gastropods, bivalves, and echinoids. High sea levels at first, global cooling and glaciation, and much volcanism. North America under shallow seas. Ends in huge extinction, due to glaciation. || "The Age of Trilobites" 540 to 500 mya** || "Age of Trilobites" -The [|Cambrian Explosion] of life occurs; all existent phyla develop. Many marine invertebrates (marine animals with mineralized shells: shell-fish, [|echinoderms], trilobites, brachiopods, mollusks, primitive graptolites). First vertebrates. Earliest primitive fish. Mild climate. The supercontinent Rodinia began to break into smaller continents (no correspondence to modern-day land masses). Mass extinction of trilobites and nautiloids at end of Cambrian (50% of all animal families went extinct), probably due to glaciation. || 2.5 billion years ago to 540 mya ** || - |||||| [|**Vendian/Ediacaran Period**] 600 to 540 Million Years Ago || [|Vendian biota] (Ediacaran fauna) multi-celled animals appear, including [|sponges]. A mass extinction occurred. The continents had merged into a single supercontinent called Rodinia. || 3.9 to 2.5 billion years ago ** || - |||||| - || "Ancient Life" - The first life forms evolve - one celled organisms. Blue-green algae, [|archaeans], and [|bacteria] appear in the sea. This begins to free oxygen into the atmosphere. || 4.6 to 3.9 billion years ago ** || - |||||| - || "Rockless Eon" - The solidifying of the Earth's continental and oceanic crusts. ||
 * ^  ||^   || **Carboniferous**
 * ^  ||^   ||^   |||| **Mississippian Period
 * ^  ||^   |||||| **[|Devonian Period]
 * ^  ||^   |||||| **[|Silurian Period]
 * ^  ||^   |||||| **[|Ordovician Period]
 * ^  ||^   |||||| **[|Cambrian Period]
 * ** [|Proterozoic Eon]
 * ^  ||^   |||||| - || First multicellular life: colonial algae and soft-bodied invertebrates appear. [|Oxygen build-up] in the Mid-Proterozoic. ||
 * ** [|Archeozoic Eon(Archean)]
 * ** [|Hadean Eon]

Sources:

Post #2

"Mike Levine and Bill McGinnis, in Walter Gehring's lab in Switxerland, and Matt Scott, in Tom Kauffman's lab in Indiana, noticed that in the middle of each gene was a short DNA sequence that was virtually identical in each species they looked at. This little sequence is called a homeobox. The eight genes that contain the homeobox are called Hox genes....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 108-1100)

This excerpt is connected to two of Biology's man themes: Continuity and Change and Structure to Function. Continuity and Change is explained by the AP Biology Developement Committee; "All species tend to maintain themselves from generation to generation using the same genetic code. However there are genetic mechanisms that lead to change over time, or evolution". The homobox and hox genes in the middle of each gene directly relates to this idea of Continuity and Change. The hox genes in every animal with a body are continuously uniform, while evolution leads to different growth and developement of specific species led by this 'master switch'. The connection to structure and function can be understoodthrough the deeper understanding of the role of hox genes.

Homeobox genes are discussed in the AP Biology curriculum when discussing animal body plans, but were directly touched upon this year through a hand-out titled: Animal Body Plans: Homeobox Genes. The article begins with the idea that all vertebrates look very similar in the early stages of developement, and then makes a connection between diverse animal species. "Certain genes called homeotic genes (homeo=alike) are amazingly similar in structure and function in all animals; they serve as molecular architects and direct the building of bodies according to detailed plans". The excerpt directly states and explaines the connection between shubin's words and the theme of Sructure to Function. The article then discusses the sequencing of homeotic genes controlling the developement of a fruit fly's body by two German Biologists. Once finding the identical DNA sequence, or homeobox, the scientist discovered its ability to controll the transcription in cells. The homeobox translates into a protein sequence which then binds to DNA. This activates and deactivates the expression of genes into proteins (transcription). The Hox genes therefore indirectly determine a cells developement.

An "outside of box" connection to this excerpt is Transcription (the DNA-directed synthesis of RNA). Transcription is broken into three stages: initiation, elongation, and termination. In initiation, the polymerase initiates RNA synthesis from the start of the template strand. (This occurs after the binding of RNA polymerase to the promoter and the unwinding of DNA). In elongation, the polymerase moves down unwinding the DNA while elongating the RNA transcript form 5'-3' (The DNA recoils, reforming the double helix after the polymerase passes). In termination, the RNA transcript is released while the polymerase detaches from the DNA.

All in all the discovery and recongnition of Hox genes helped to further understand the ideas of evolution. "Changes in Hox genes and in the genes that regulate them in turn can have a profound impact on morphology....the evolution of tetrapods from an ancestral aquatic vertebrate. During this process, four of the ancestral vertebrate's fins evolved into limbs." (Campbell 485) The evolution of Hox genes has led to the evolution of different species. The way Shubin connects his ideas is very interesting. Although the ideas may seem very far fetched and unrelated at first, thay all connect in the end. After all biology is based on evolution and connections.

Sources: Work Sheet: Animal Body Plans: Homeobox Genes AP Biology Text Book (my sources from the last update got deleted when I first entered text)

Post #3

"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." (Shubin 188)

This except directly relates to the theme of structure to function when discussing blood vessels. Blood vessels, either arteries veins or capillaries, have similar yet different structures as a result of their required functions. All blood vessels have structural similarities. The wall layers of arteries and veins, for example, are very similar. The outside tissue layer consists of connective tissue with elastic fibers. The middle tissue layer is composed of smooth muscle and elastic fibers. Finally the tissue layer lining the lumen consists of endothelium, a layer of flattened cells. All three tissue layers are associated with different functions. The outermost and middle layers allow the vessel to stretch and return to its original shape, while the endothelium in the inner layer provides a smooth surface for minimized blood flow resistance. The different structures of capillaries, veins, and arteries relate to their different functions.

The lack of the two outer layers in capillaries, along with their very thin walls of endothelium and its basement membrane allows for easy transfer of substances between the blood and the interstitial fluid. The arteries need to provide strength and to accommodate the rapid and high pressure flow of blood, while maintaining blood pressure even during the heart's contractions is made possible by their infrastructure. Their infrastructure includes thick middle and out layers, which provide strength while having elastic qualities. The thin walls of the veins allow blood to travel back to the heart at a low speed and pressure. Tissue flaps in large veins serve as 'one-way' valves, only allowing blood to move towards the heart. Muscle action leads to the blood flow through veins. Movement leads to the contraction of veins by the skeletal muscles, which forces the blood back to the heart.

An "out of the box' connection to this excerpt is the relationship between a sedentary lifestyle and the structure and function of the circulatory system. Although cardiovascular diseases can be inherited, lifestyle habits can directly lead to them as well. "Healthy arteries have smooth inner linings that promote unimpeded blood flow. The deposition of cholesterol thickens and roughens this smooth lining. A plaque forms at the site and becomes infiltrated with fibrous connective tissue and still more cholesterol. Such plaques narrow the bore of the artery, leading to a chronic cardiovascular disease known as atherosclerosis. The rough lining of an atherosclerotic artery seems to encourage the adhesion of platelets, triggering the clotting process and interfering with circulation." (Campbell 883).

Overall the structures of varying blood vessels lead to their differing roles or functions in the circulatory system. Atherosclerosis is an example of a circulator disease which was also discussed in a connection. PS



Post #4

" The problem is that the brain stem originally controlled breathing in fish; it has been jury-rigged to work in mammals...In fish, the nerves that control breathing do not have to travel vary far from the brain stem. The gills and throat generally surround this area of the brain. We mammals have a different problem. Our breathing is controlled by muscles in the wall of our chest and by the diaphragm, the sheet of muscle that separates our chest from our abdomen. Contraction of the diaphragm controls inspiration" (Shubin 191).

This except is derived from the major theme of evolution. Shubin, when explaining the breathing in fish, makes a connection to the breathing of human and other mammals. As written in the excerpt, mammals' respiration has been 'jury-rigged to work in mammals'. This is the evolution of respiration, and in particular the nerves that control it. Evolution has, in this case, led to a poor layout that can lead to the blocking of the function of nerves from the brain stem. The point is that this 'layout' of the brainstem, relating to respiration, has evolved to 'fit into' the human body. Because respiration is a key concept in this excerpt and in the AP Biology Curriculum, the mammalian respiratory system can be discussed.

The lungs of mammals, located in the chest cavity, have a spongy texture with an epithelium that functions as the respiratory surface. Branches ducts carry air to the lungs. The navel cavity is the first part of the system. "From the nasal cavity and the pharynx, inhaled air passes through the larynx, trachea, and bronchi to the bronchioles, which end in microscopic alveoli lined by a thin, epithelium.” (Campbell) The epithelial lining helps to cleanse the respiratory system. A mucus lining on the epithelium traps particulate contaminants and the cilia transfers the mucus to the pharynx to be swallowed into the esophagus. Gas exchange occurs across the epithelia of the alveoli. "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). The mammalian respiratory system is depicted in the image below.



The alternate inhalation and exhalation of air is known as breathing. Mammals breathe by way of negative pressure breathing, where air is pulled in to the lungs. The changing in volume of the rib cage and chest cavity are equaled by the lungs. It is the idea of surface tension that makes the movement of the lungs connected to the movement of the rim cage, through a small fluid layer. The diaphragm and intercostals muscles lead to human respiration. The increasing of the thoracic cavity and therefore the lungs is due to the contraction of the diaphragm and the relaxing of intercostal muscles. Negative pressure breathing is depicted in the image below.

Because this excerpt is from a section of the book containing information about the brain controlling the diaphragm, a connection to the nervous system can be made. The brain involuntarily sends nerve impulses through a chain of neurons. When the never impulse or action potential reaches the target cells or the muscle cells of the diaphragm, the diaphragm contracts. All in all, the brain stem originally controlling the respiration of fish has evolved to fit a human’s body. The negative pressure breathing is a direct result of the contraction of the diaphragm, which is controlled by the nervous system.

Post #5

"The several parts of the inner ear are filled with a gel that can move. Specialized cells send hairlike projections into this gel. When the gel moves, the hairs on the ends of these cells bend. When these hairs bend, the nerve cells send electrical impulses to the brain, where it can record as sound, position, or acceleration" (Shubin 164-165).

This excerpt is directly related to the human ear and its functions. The major biological theme relating to this excerpt can be seen as structure to function. The complex structure and organization of the ear leads to its advanced fuctioning involving sound, possition and acceleration as stated in the excerpt. " In mammals, as in most other terrestrial vertebrates, the sensory organs for hearing and equilibrium are closely associated in the ear" (Campbell 1050). The human ear can be divided into three parts: the outer, middle and inner ear.

The externa pinna and the auditory canal of the out ear collect sound waves and chanel the waves to the eardrum, or tympanic membrane. The eardrum separates the outer and middle ear. The middle ear consists of three bones: the malleus, incus, and stapes. These three bones transmit vibrations to the noval window, a membrane under the stapes. The Eustachian tube which connects with the pharynx is also a component of the inner ear. The Eustachian tube serves to equalize pressure between the inner ear and the outside atmosphere; allowing one to 'pop' their ears in changing altitudes. Fluid filled chabers in the temporal bone of the skull are part of the inner ear. The chambers function in equilibrium through the semicircular canal, and hearing through the cochlea.

The cochlea, as stated previously as part of the inner ear, is composed of multiple parts. It has two canals know as the upper vestibular canal and a lower tympanic canal which contain perilymph, a fluid. Between these two canals is a cochlear duct filled with another fluid, endolymph. In the cochlear duct is the Corti, an organ containing hair cells,or the mechanoreceptors. The movement of the basilar membrane in the Corti cause the hairs to bend and depolarize the hair cells as mentioned in the excerpt from Your Inner Fish.



"Several of the organs in the inner ear of humans and most other mammals detect body position and balance' (Campbell 1052) This concept as stated in the AP Biology textbook is directly related to the excerpt with the mentioning of position. Two chambers called the utricle and the saccule are contained in a vestibule behind the oval window of the middle ear. These two chambers are directly linked to the balance of humans.

The study of numerous types of specialized cells in the human body and plants can also be indirectly linked to this excerpt. Gaurd cells in ths leaves of plants are an example of a specialized cell. The gaurd cells have a specific function opening and closing to help prevent water loss and obtain water for the average plant. Lysosomes are another example of specialized cells. A lysosome is a membrane sac of hydrolytic enzymes that an animal cell uses to digest all kinds of macromolecukes. All in all the fuctionings of the ear are very interesting. The ear has a greater affect than just the precieved (hearing) on the human body. Specialized cells allow the ear to record sound position and acceleration. PS