2D blog

NEILD JOSEPH

Essential knowledge 2.D.1: All biological systems from cells and organisms to

populations, communities and ecosystems are affected by complex biotic and abiotic interactions involving exchange of matter and free energy.

1.Provide examples of how biotic and abiotic factors affect organism behavior,

community interactions, and ecosystem structure. Utilize the following examples

in your responses:

Biotic factors affect food chains and food webs because if one species becomes instinct it can lead to another institution of another because that was their food and source of energy this will disrupt the community interaction. Water availability is an abiotic factor that affects the ecosystem structure because the desert has very little water availability so the consequence is that is become dry and almost lifeless other than a place with tons of water, which has many different species.

○ Water availability

○ Sunlight

○ Symbiosis (mutualism, commensalism, parasitism)

○ Predator–prey relationships

○ Water and nutrient availability, temperature, salinity, pH

○ Availability of nesting materials and sites

○ Food chains and food webs

○ Species diversity

○ Population density

○ Algal blooms

Essential knowledge 2.D.2: Homeostatic mechanisms reflect both common

ancestry and divergence due to adaptation in different environments.

1.     How do homeostatic mechanisms relate to evolution? Homeostatic mechanisms relate to evolution by the adaptation of a specific environment for example when you are hot u begins to shiver your body is finding a way to adapt to the temperature. As in evolution the more the world changes the more we began to adapt to the changes

2. How is the concept of common ancestry supposed by continuity in homeostatic

mechanisms.  Changes may occur in response to different environmental changes.

3. How do changes in environmental conditions affect this continuity. They impact the continuity because if the environment changes, a specific homeostatic mechanism may no longer be needed and may become inactive after a prolonged amount of time.

4. Explain how the following mechanisms are used for obtaining nutrients and eliminating wastes.  The following mechanisms are used for obtaining nutrients and eliminating wastes because they all take something in and takes everything it need and what is doesn’t it eliminates it by exchanging it over again or just pooping it out.

○ Gas exchange in aquatic and terrestrial plants

○ Digestive mechanisms in animals such as food vacuoles, gastrovascular cavities, one-way digestive systems

○ Respiratory systems of aquatic and terrestrial animals

○ Nitrogenous waste production and elimination in aquatic and terrestrial animals

5. Explain how homeostatic control systems in species of microbes, plants an animals support common ancestry. Use the following to help illustrate your explanation: Excretory systems in flatworms, earthworms and vertebrates support common ancestry by many other organisms previous to the current modern organism have evolved into this specific form to maintain fitness and survive.

○ Excretory systems in flatworms, earthworms and vertebrates

○ Osmoregulation in bacteria, fish and protists

○ Osmoregulation in aquatic and terrestrial plants

○ Circulatory systems in fish, amphibians and mammals

○ Thermoregulation in aquatic and terrestrial animals (countercurrent exchange)

Essential knowledge 2.D.3: Biological systems are affected by disruptions to their dynamic homeostasis.

1. How do disruptions at the molecular and cellular levels affect the health of the organism? Use the following to explain your answer: Dehydration affects the health of the organism by primarily showing minor symptoms of sickness, such as headaches, dry mouth, and lack of tears then progressing to more major consequences such as loss of coordination, blurred vision, and loss of consciousness, and the most severe consequence is death.

○ Physiological responses to toxic substances

○ Dehydration

○ Immunological responses to pathogens, toxins and allergens

2. Provide examples of how disruptions to ecosystems can affect the dynamics of the  ecosystem. Utilize the following examples in your responses: Human impact can affect the dynamic of the ecosystem by destroys home to build ours which result in the free roaming of wild animals with out shelter.

● Invasive and/or eruptive species

● Human impact

● Hurricanes, floods, earthquakes, volcanoes, fires

● Water limitation

● Salination

Essential knowledge 2.D.4: Plants and animals have a variety of chemical

defenses against infections that affect dynamic homeostasis.

1. Explain how plants, invertebrates and vertebrates have multiple, nonspecific (innate) immune responses. Include how they work and structures/chemicals involved. Plants, invertebrates, and vertebrates’ nonspecific responses include macrophages that are used to flag pathogens/antibodies.

2. Describe mammalian specific immune responses.

• Describe the two types of specific responses in the Mammalian

immune system In the cell mediated response, cytotoxic t cells, a lymphocytic white blood cell, targets intracellular  pathogens when antigens are displayed on the outside of the cell humoral response is b cells a type of white blood cell produce antibodies against specific antigens.

• In the cell-mediated response, what is the role of cytotoxic T cells? a lymphocytic blood cell that target intracellular pathogens when antigens are displayed on the outside of the cell.

• In the humoral response, what is the role of B cells? to produce antibodies against specific antigens

3. Explain how antigens and antibodies work together.

• What is an antibody? a product of the b cell that’s created to replicate the similar antigen which your body becomes immune to it so it can harm you as much anymore

• How does a second exposure to an antigen differ from the primary exposure? the second exposure is different because the b cells have already created antibodies to stop it the se

2c Blog

Neild Joseph

2.C.1 – Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes.

·      Discuss how negative feedback works. Discuss the following two examples – Thermoregulation in animals and plant responses to water limitations. Negative feedback is a mechanism to maintain dynamic homeostasis it is used to set your body back to its normal conditions. Thermoregulation is when your body either gets too cold or too hot your body will send out signals to create a negative feedback to return back to its stability of 98.7 Fahrenheit. Plant response to water limitation is when the plant has a lack of water it begins to shrivel up.

·      Discuss how positive feedback works. Discuss the following three examples – lactation in mammals, onset of labor in childbirth, and ripening of fruit. Positive feed is a mechanism to amplify responses and processes. Lactation in mammals is an example of positive feedback because the suckling stimulates nerve endings in nipple and goes on carrying the process to provide milk for the offspring. Onset of labor in childbirth is when the head of fetus pushes against cervix then nerve impulses from cervix transmitted to brain and brain stimulate pituitary gland to secrete oxytocin and oxytocin carried in bloodstream to uterus and finally oxytocin stimulates uterine contractions and pushes fetus towards cervix. The ripening of fruit is also an example of positive feedback because the tree will go on sending stimulates to amplify the fruits ripeness so it can look better.

·      Discuss how an alteration in the mechanism of feedback can result in dire consequences by using the following three examples: diabetes mellitus in response to decreased insulin, dehydration in response to decreased antidiuretic hormone and Grave’s disease. Diabetes mellitus in response to decrease insulin is dire because your body needs it to level the blood glucose. Dehydration in response to decreased antidiuretic hormone and grave’s disease and graves disease is a dire consequence because its drain your body of the glucose it needs and soon can result in death.

2.C.2 – Organisms respond to changes in their external environments.

·      Discuss how organism respond to changes in their environment by using the following examples:

o   Photoperiodism and phototropism Photoperiodism and phototropism are a physiological response to photoperiod, such as flowering.

o   Hibernation and migration in animals Hibernation and migration in animals is almost automatic response in animals to move or sleep through rough weather conditions. Estivation lets animals survive periods of high temperature and scarce water.

o   Taxis and kinesis in animals Kinesis is a simple no directional, change in activity or turning rate in response to a stimulus. Taxis is a less automatic oriented move toward or away from stimulus such as removing a rock with pill bugs under they scatter to search for a similar habitat.

o   Chemotaxis in bacteria, sexual reproduction in fungi

Free Energy

     On earth, in order for living organisms to maintain life, all living systems require energy. Energy is a very interesting topic because without energy we would not have any order, growth, or reproduction. Although not all organisms use the same methods to maintain order, energy will always be required for that matter. In fact, organisms use various energy-related strategies to survive; For example, some include different metabolic rates, physiological changes, and variations in reproductive and offspring-raising strategies. With the lack of energy this would cause devastating deficiencies to individual organisms, also the changes in free energy can impact heavily the population size and cause huge disturbances at the ecosystem level.

        There have been many methods to capture, use and store free energy that have evolved within organisms. Cells are able to capture free energy through two methods either photosynthesis or chemosynthesis. Autotrophs, who are your plant organisms feed themselves by capturing free energy from the environment, including the energy that comes from the sun and chemical sources. On the contrary heterotrophs harvest free energy from carbon compounds produced by other organisms. So the difference between autotrophs and heterotrophs is simply that autotrophs provide themselves with food (energy) and heterotrophs rely on other organism for their income as food (energy). Photosynthetic organisms capture energy present in  sunlight while chemo-synthetic organisms capture free energy from small inorganic molecules present in their environment  and this can happen in the absence of oxygen these are two methods used by autotrophic organisms. Heterotrophs metabolize carbohydrates,lipids, and proteins by hydrolysis as a source of  free energy.

Willard Gibbs

If you take a took to the left, you will see one of the most profound men in science. This genius by the name Willard Gibbs is responsible for the Gibbs free energy equation used in thermodynamics. the Gibbs free energy is a thermodynamic potential that measures the "usefulness" from a thermodynamic system at a constant temperature and pressure.To get a better understanding of Gibbs equation you must know the laws of thermodynamic. The laws of thermodynamics define the laws which temperature,energy, and entropy go under.The first law of thermodynamics which is also known as the law of conservation of energy states that energy cannot be created nor destroyed. The second law of thermodynamics says that the entropy in any isolated system not in thermal equilibrium almost always increases. The third law says that the entropy of a system approaches a constant value as the temperature approaches an absolute zero. Entropy is the lack of order within a thermodynamic system and enthalpy is a thermodynamic quantity that shows the total heat content of a system.

that energy cannot be created or destroyed in a chemical reaction.

Source: Boundless. “The Three Laws of Thermodynamics.” Boundless Chemistry. Boundless, 16 Nov. 2014. Retrieved 30 Nov. 2014 from https://www.boundless.com/chemistry/textbooks/boundless-chemistry-textbook/thermodynamics-17/the-laws-of-thermodynamics-123/the-three-laws-of-thermodynamics-496-3601/

that energy cannot be created or destroyed in a chemical reaction.

Source: Boundless. “The Three Laws of Thermodynamics.” Boundless Chemistry. Boundless, 16 Nov. 2014. Retrieved 30 Nov. 2014 from https://www.boundless.com/chemistry/textbooks/boundless-chemistry-textbook/thermodynamics-17/the-laws-of-thermodynamics-123/the-three-laws-of-thermodynamics-496-3601/

Gibbs free energy equation.

The AP Biology curriculum framework 2012-2013 is a great guide for such a hefty topic. I would suggest for you to click the link below. The curriculum gives a satisfying in depth understanding to the growth, reproduction, and maintenance of organization of living systems requiring free energy and matter. Once you click the link below follow through pages 15-22 for extra details such as the the whole process of different energy-related pathways in biological systems. 






 AP Biology Curriculum Framework 2012-2013



Sources

 AP BIOLOGY (n.d.): n. pag. Web.

 

"No. 119: J. Willard Gibbs." No. 119: J. Willard Gibbs. N.p., n.d. Web. 30 Nov. 2014.

 

 

"Chemical Thermodynamics." Gibbs Free Energy. N.p., n.d. Web. 30 Nov. 2014.

 

"Gibbs Free Energy." Gibbs Free Energy. N.p., n.d. Web. 29 Nov. 2014.

2.B.1

·      Discuss how cell membranes separate the internal environment of the cell from the external environment of the cell. Cell membranes separate the internal environment of the cell from the external environment of the cell by selective permeability being a direct consequence of membrane structure.

·      Cells are selectively permeable. Discuss each point below and how it allows the cell to be selectively permeable.

o   Discuss the following structures and the role the play in the cell membrane: phospholipids, embedded proteins, cholesterol, glycoproteins and glycolipids phospholipids give the membrane both hydrophilic and hydrophobic properties. Embedded proteins can be hydrophilic, with charged and polar side groups, or hydrophobic, with nonpolar side groups. Cholesterol help maintain the cells membranes fluidity. Glycoproteins are membrane protein with bound. Glycolipids serve as markers from cell to cell membrane.

o   Discuss the properties of a phospholipid (hydrophobic/phallic, polar/non, and fatty acids/phosphates. The hydrophilic phosphate portions of the phospholipids are oriented toward the aqueous external or internal environments, while the hydrophobic fatty acid portions face each other with the interior of the membrane itself.

o   Embedded proteins – how do they allow transport? Embedded proteins transport through active transport. Active transport is when proteins embedded in the cell's lipid bilayer. Those proteins do much of the work in active transport. They are positioned to cross the membrane so one part is on the inside of the cell and one part is on the outside. Only when they cross the bilayer are they able to move molecules and ions in and out of the cell.

o   Discuss which molecules can easily pass through the membrane and which can’t. Why? Water and oxygens and smaller molecules can go through.

·      Cell walls are a structural boundary that provides extra barrier for some organisms.

o   Discuss the cell wall of plant cells, prokaryotes and fungi, and what they are composed of. Plant cell walls, prokaryotes and fungi are made up of cellulose.

2.B.2

·      Passive transport does not require the input of energy; the net movement of molecules is from high to low. Discuss the following factors relating to passive transport.

o   Discuss how primary transport allows for export of waste. Primary transport allows for the export of waste by the movement of molecule down the concentration gradient. From an area of high concentration to low concentration.

o   Discuss how membrane proteins play a role in facilitated diffusion of charged/polar molecules in the membrane. Use the examples of glucose and Na/K transport. Membrane proteins play a role in facilitated diffusion of charged and polar molecules through a membrane example of this are glucose transport and na+/K+ transport.

o   Discuss the following solutions and their effect on a cell. Hypotonic, hypertonic, and isotonic. Hypotonic solutions have a higher water concentration and lower solute concentration. Hypertonic solutions have a lower water concentration and a higher solute concentration isotonic solution is equal for both.

o   Discuss water potential and the formula for solving for it. Water potential is just potential energy of water relative to pure water. The formula for solving is just solute potential plus the pressure potential.

·      Active transport requires free energy to move molecules against their concentration gradient from areas of low to high. Discuss the following factors relating to active transport:

o   Discuss where the free energy used in active transport comes from.

o   Discuss the membrane proteins needed for active transport.

o   Explain how molecules are moved against their concentration gradient. Use the example of the Sodium Potassium Pump. 

o   Discuss the difference between endocytosis and exocytosis.

§  What happens in each? Endocytosis in inside and exocytosis is outside of the cells what occurs is in endocytosis is the cellular uptake of biological molecules and particulate matter via formation of new vesicles from the plasma membrane. Exocytosis is the cellular secretion of biological molecules by the fusion of vesicles containing them with the plasma membrane.  

§   

o   Discuss the difference between pinocytosis and phagocytosis. Pinocytosis is the drinking and phagocytosis is the eating inside the cell membrane.

2.B.3

·      Discuss how internal membranes facilitated cell process by minimizing competing interactions by describing the activities of the lysosome.

·      Membranes and membrane bound organelles in eukaryotic cells processes. Discuss each of the following and how they compartmentalize: ER, mitochondria, chloroplast, Golgi, and nuclear envelope.

·      Discuss how prokaryotic cells function since they have no membrane bound organelles.

Origin of life

Miller-Urey Experiment

         The origin of life, probably the most spoken subject ever since the beginning of human wisdom. Since the beginning of human existence we have always wondered about the origin of life. Some have tried to explain the origin of life through illogical reasoning such as biblical theories. However, if you are simply a logical person you will not be able to accept this because it has no factual evidence. A number of experimental investigations have provided evidence of how life began on planet Earth. For example the Miller-Urey experiment, this experiment showed that organic compounds could be synthesized from inorganic precursors. This also follows the hypothesis of the "organic soup" model which hypothesized that the primitive atmosphere contained inorganic precursor from which organic molecules could have been synthesized through natural chemical reaction catalyzed by the input of energy.
        

The Murchison meteorite may be a fragment of a comet. It contains ancient grains that formed in stars long before the solar system was formed. Also present are organic molecules such as amino acids — the building blocks of life — that may provide clues to the origins of life.  

          There are also many other hypotheses about the natural origin of life on earth, which mostly have scientific factual evidence. For instance, a meteor seeding earth with organic molecules from space.This hypothesis came about because a meteorite hit Australia in 1969 and is very rich in organic compounds, including 70 amino acids and nucleotide bases. Which are extremely vital for life, especially when our physiological proteins consist of 20 different amino acids. So this lead to scientist hypothesize that a meteor hit earth 4.6 billion years ago and from these simple molecules came about more complex molecules.The monomers produced polymers with the ability to replicate, store and transfer information. 
    
        Many scientist believe that earth formed 4.6 billion years ago but the environment was way to harsh for life because of the lack of oxygen, numerous amounts of volcanoes, and etc. Only until 3.9 bya do scientist believe that life actually formed on earth. The earliest fossil record evidence can be dated back to 3.5 bya. With this evidence  is gives a reasonable range of when the origin of life could have occurred. Molecular and genetic evidence from extant and extinct organisms also tell scientist that all organisms share a common ancestral origin of life. A lot of evidences that scientist have found include a common genetic code.
  
        Sources: "Meteorite Sites in Victoria." : Melbourne Museum. N.p., n.d. Web. 14 Oct. 2014.

"The Miller/Urey Experiment." The Miller/Urey Experiment. N.p., n.d. Web. 12 Oct. 2014.

Speciation

Example of Speciation

Example of an extinct animal

    In my last blog I spoke about phylogenetic trees and how organisms are placed upon the diagram. This blog I will be speaking a bit more in depth as to why the organism earned their spot on the cladogram or phylogenetic tree. The reason to why they earned a spot on both diagrams is due to speciation. Speciation is the evolutionary process by which new biological species arise. Hence, being able to place them on a phylogenetic tree according to when they arose. When speaking about speciation is vital to not forget extinction because it also plays an important role in the evolutionary process. Extinction occurs when a species is dying out or is completely terminated. So a good way to distinguish the two is to remember that speciation is when 1 species goes to 2 species and extinction is when 1 species goes to 0 species. Speciation and extinction have been happening throughout the entire history of Earth. Although, the rates of speciation and extinction can be very random at times. Speciation has tendencies to be slow or as described in punctuated equilibrium, can happen at any given moment followed by certain periods of nothing. Moments of ecological stress, extinction rates are extremely rapid and can be seen before your eyes, and mass extinctions are followed by adaptive radiation. Adaptive radiation is simply the rapid evolution of species when they're exposed to new environments.

       Species are groups of individuals capable of interbreeding or exchanging genetic information to produce fertile offspring. Speciation occurs when two populations diverge from a common ancestors and become reproductively isolated. Reproductive isolation is when two populations that live in the same environment are unable to reproduce because their genes are no longer able to interbreed. Although speciation can happen by different processes, reproductive isolation must be maintained so species can remain distinct. Speciation creates a diversity in life formations. Species are spread throughout the earth which causes a geographical barrier, for example species on land and species who live in the ocean. Also pre- and post-zygotic mechanisms can maintain this reproductive isolation and also prevents gene flow. So the main thing to grasp is that new species arise from reproductive isolation over time.

Darwin's Finches

       Something interesting to know is that even today population are continuing to evolve. Everyday is a new day of possibility for species to speciate or become extinct. There is scientific evidence to back this up. Scientific evidence has also proved that evolution has occurred in all species. Take Grants' observation of darwin's finches for example in the Galapagos for example. The "Grants'" are a married couple who have recently studied and observed the continuation of evolution happening on the Galapagos Island. They saw how the finches of the birds are still evolving from when darwin studied them. This is a directional phenotypic change in population.     




SOURCES

"Darwin's Finches." Wikipedia. Wikimedia Foundation, 10 Nov. 2014. Web. 11 Oct. 2014.

"Speciation." Evolution 101:. N.p., n.d. Web. 09 Oct. 2014.

"007 - Speciation and Extinction." Bozemanscience. N.p., n.d. Web. 11 Oct. 2014.

Phylogenetic Trees

   

Figure 1 - Tree of life

     Its time, to speak on the unspeakable, the truth about phylogenetic trees. You may have been told things which are totally false of phylogenetic trees and unlike christmas trees, this is the tree of life. Phylogenetic trees represent traits that are either derived or lost due to evolution. For a better understanding, think of the absence of legs in some sea mammals.  Originally whales were four footed land animals but due to evolutionary changes these legs began to disappear and become a vestigial structure. The Phylogenetic tree can explain this process by illustrating the speciation that has occurred, in that relatedness of any two populations on the tree is illustrated by how recently two groups came from a common descendant.

     

 Figure 2 - Cladogram.

     Cladograms also play a major part when dealing with phylogenetic trees. A cladogram is a diagram used in cladistics which also shows relations among organisms. Basically these two diagrams are identical when explaining how organisms lost or gained certain traits. Click the link to have a more broad understanding of cladogram.  Video on Cladograms 

    Now that I have explained the significance and the use of Phylogenetic trees and cladograms. Stay tuned so I can explain how phylogenetic trees and cladograms can be constructed from morphological similarities of living fossil species, and from DNA and protein sequence similarities. Usually phylogenetic trees are constructed from morphological similarities. Such as if you begin to look at the vertebrae of one animal this can lead to the conclusion of how other animals may have, "so to speak", came from this this organism. If you take a glance at the image in figure 2  you can see that sharks were the first ones to have a vertebrae and from this came the Ray-finned fish and so on. Now when looking at DNA sequences you get the exact similarities in an organisms so this will be much easier to place organism along a phylogenetic tree or cladogram.

Newly founded skull.

     It is also important to remember that phylogenetic trees and cladograms are dynamic, meaning that they are constantly being revised. These changes happen because of the progression of technology and are based on the biological date used, new mathematical and computational ideas, and current and emerging knowledge. For example theres been a new skull that has been found recently and reports are saying that is will spark evolution controversy. If this skull is accepted by scientist it will have the possibility to change the current phylogenetic tree. 


Sources

"Reading Trees: A Quick Review." Reading Trees: A Quick Review. N.p., n.d. Web. 05 Oct. 2014.

"How to Read a Phylogenetic Tree." Emergence, Evolution and Epidemiology. N.p., n.d. Web. 06 Oct. 2014.

"UNM Biology Undergraduate Labs." Untitled 1. N.p., n.d. Web. 06 Oct. 2014.

Natural Selection

  

Charles Darwin: Age 7

"Natural Selection", why is this even a topic to speak about? Well if you read through this blog I will be able to explain to you how much this topic has to do with you and every living thing around you. In other words, I am saying that natural selection is basically what made you what you are today so,and who would not want to know more about themselves? With this in mind please allow me to explain Natural Selection, Natural Selection is a simple concept that really has different fundamentals attached to it due to it being a major mechanism of evolution. 

   Although many people associate Charles Darwin with being the inventor of Natural Selection this is false because most educated people in the 19th century in Europe already had exposure to the concept of evolution. However, Charles  Darwin did carry out the necessary research to document that evolution has occurred and then made the idea acceptable for scientists and the general public. Charles Darwin's theory of natural selection states that inheritable variations occur in individuals in a population.

Diversity in Gene Pool 

Its also important to remember that genetic variations along with mutations are vital parts in natural selection because you need more than one specific type of gene to have a stable surviving species. For example you and I have different genetic variations such as our physical attributes, I may be able to run faster than you and this will help me survive better because I'm less likely to be captured by a predator. Although this certain trait may not be past down to my offspring because chance and random events can influence the evolutionary process. 

Hardy-Weinburg Equilibrium equation

  Although the mathematical point of view to look at natural selection can be overlooked and may seem non-interesting, it gives lots of necessary information to learn more about natural selection. Math is used in natural selection to calculate the changes in allele frequencies, and gives evidence for the happening of evolution in a population. Such  as graphical analysis of allele frequencies in a population and the application of the Hardy-Weinburg equilibrium equation. Which may seem a bit foreign to you but actually a really simple equation, p^2+ 2pq + q^2=1, p just simply stands for the dominate trait in an allele and q stands for the recessive trait. The most important key to dissecting a Hardy-Weinburg problem is just to be able to identify specifically what they're asking. Take a look at the picture to the right to have a better grasp of this.
 Another fundamental of natural selection is its act on phenotypic variation in populations. This simply means that environments change and act as selective mechanism on population. To emphasize on this think of flowering time in relation to global climate change. Also keep in mind that phenotypic variations are not caused by the environment but happen through random switch ups in the DNA and through new gene combinations.
Now with these things considered you can come to conclusion that natural selection is basically what made you and without it you would not even be able to read this or be alive.








Sources: 
Bio.com. A&E Networks Television, n.d. Web. 23 Sept. 2014. 
"Evolution." Sources of Variation: Meiosis and Sexual Reproduction. N.p., n.d. Web. 25 Sept. 2014.
"The Hardy Weinberg Equation." Ecology: Web Extension 6.1. N.p., n.d. Web. 25 Sept. 2014.