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1/29/2020

BioChemistry

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today we will learn the basics of chemistry in life science


Picture

​https://www.etsy.com/no-en/listing/249009051/cell-to-helix-science-science-art?ref=shop_home_active_45

Picture

http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/chemistry10.htm
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Picture

http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/chemistry10.htm
​


Atoms, Elements, and the periodic table


Picture

​https://www.wuwm.com/post/periodic-table-elements-turns-150#stream/0
​

Element groups



​Metals, semimetals (metalloids), and nonmetals.

​Further grouping:
 transition metals, rare earths, alkali metals, alkaline earth, halogens, and noble gasses.

​http://insidechem.blogspot.com/2017/03/different-categories-of-elements-in.html
​


​An element is a pure substance that is made up entirely of one type of atom.
Picture

https://www.livescience.com/37206-atom-definition.html


Picture

​https://www.google.com/search?tbm=isch&q=carbon+atom+model&imgrc=OonInJRfAI1nxM:&cad=h

​

reading atomic symbols


Picture
https://www.classzone.com/books/earth_science/terc/content/investigations/es0501/es0501page06.cfm


​The atom is the basic unit of matter.

Atoms are made up of protons, neutrons, and electrons.

Protons and Neutrons are particles that are bound together by strong atomic forces and for the center of the atom, we call it the nucleus. 


Protons have a positive charge 

Neutrons carry no charge

Protons and electrons have around the same mass.

Electrons are negatively charged, they are 1/1840 of the mass of a proton.

Electrons in constant motion around the nucleus of the atom.

Electron are arranged in a series of orbits called shells:


Picture

​https://www.quora.com/What-is-the-outermost-shell-of-an-atom-called

Picture

​https://socratic.org/questions/how-many-electrons-go-on-each-ring-according-to-the-bohr-model


​The shells can only hold a certain number of electrons.

The first shell can hold two electrons.

​The second shell can hold up to eight electrons.

Atoms have an equal number of protons and electrons, so all atoms are electrically neutral because the positive charge f the protons and the negative charge of the electrons cancel out.


Picture

​http://www.chem4kids.com/files/elements/020_shells.html

Isotopes

Are atoms of the same element that contain different number of neutrons. They have a different mass.
​
Picture

​https://skepticalscience.com/print.php?n=3962

Ions

Sometimes atoms gain or lose electrons.  The atom then loses or gains a "negative" charge. These atoms are then called ions.

Positive Ion - Occurs when an atom loses an electron (negative charge) it has more protons than electrons.

​Negative Ion - Occurs when an atom gains an electron (negative charge) it will have more electrons than protons.
The following image shows Na losing an electron and Cl gaining an electron

Thus the Na becomes Na+

​The Cl becomes Cl-


Picture

https://personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/chemistry1.htm
​


​Ionic bonds 

Form when atoms transfer electrons between each other, forming 
ions that are electrically attracted to each other forming a bond between them. Sodium chloride (NaCl) is a typical ionic compound. 


Picture

http://itc.gsw.edu/faculty/speavy/spclass/chemistry/bonds.htm


​A 
polar bond is a covalent bond between two atoms where the electrons forming the bond are unequally distributed. This causes the molecule to have a slight electrical dipole moment where one end is slightly positive and the other is slightly negative.
​
​
Picture
https://www.thoughtco.com/definition-of-polar-bond-and-examples-605530
​

Picture

​A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding.

​Atoms can share between two and six electrons.
​
https://en.wikipedia.org/wiki/Covalent_bond
​


Van der Waals FOrces



Dipole: a pair of equal and oppositely charged or magnetized poles separated by a distance.

Picture

​https://socratic.org/questions/what-is-a-net-dipole

Picture

https://socratic.org/questions/how-are-van-der-waals-forces-and-ionic-bonds-similar
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Picture

http://www.wag.caltech.edu/home/jsu/Thesis/node48.html
​

Picture

​https://www.slideshare.net/jingjie97/chem-matters-ch7covalentbonding

Picture

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1/27/2020

Ecosystem

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What is an ecosystem?


An ecosystem involves all living and no-living components in an area.  Energy flows and matter cycles through an environment.

Atmosphere: this includes the wind speed and direction, humidity, light intensity and quality, precipitation and temperature.
​

Biotic Factors: These are all the living organisms in the environment, including their interactions.

  • Plants
  • Animals
  • Microorganisms (bacteria)
  • Fungi
  • Protists (algae and protozoans)
​
Abiotic factors: elements that are not alive: soil, rocks, mountains, rain, clouds

Soil:
​
  • Nutrient availability
  • Soil moisture & pH
  • Composition
  • Temperature 
​
Water:

  • Dissolved nutrients
  • pH and salinity
  • Dissolved oxygen
  • Temperature

Living organisms interact with each other in their habitat, they influence matter by walking around and moving things around.

Habitat: the natural environment in which a creature lives including the biotic and abiotic factors.

Each organism occupies a niche, an ecological niche of an organism is their function in the ecosystem: where they live, what organisms they interact with, how they respond t changes in the health of the environment. 


Tolerance rage: each species has a tolerance range, this is their comfort zone, at what point they move to another environment.
​
​

Picture

​https://www.sciencelearn.org.nz/images/3795-how-the-distribution-of-a-species-is-affected-by-limiting-factors
​

CONTAMINANTS CONTRIBUTE to acid rain



Acid rain:
rainfall made sufficiently acidic by atmospheric pollution that it causes environmental harm, typically to forests and lakes. The main cause is the industrial burning of coal and other fossil fuels, the waste gases from which contain sulfur and nitrogen oxides, which combine with atmospheric water to form acids. -Oxford
​

Picture
https://www.epa.gov/acidrain/what-acid-rain
​

Normal, clean rain has a pH value of between 5.0 and 5.5, which is slightly acidic. However, when rain combines with sulfur dioxide or nitrogen oxides—produced from power plants and automobiles—the rain becomes much more acidic. Typical acid rain has a pH value of 4.0.

Picture

​https://www3.epa.gov/acidrain/education/site_students/phscale.html


Acid Rain has been known to damage natural ecosystems


Picture

https://www.britannica.com/explore/savingearth/acid-rain/https://www.epa.gov/acidrain/what-acid-rain
​

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1/26/2020

Watersheds

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The Earth has Slope, gradient, and Topography


In mathematics, the slope or gradient of a line is a number that describes both the direction and the steepness of the line.
​

Picture

​https://learnzillion.com/lesson_plans/5946-find-the-slope-and-y-intercept-of-a-line/


Topography is the study of the shape and features of land surfaces. 
​

Picture

http://reynolds.asu.edu/topo_gallery/intro_title.htm
​

Picture

​http://geology.wlu.edu/intro3d/topo_contours/topographic_contours.html

Picture
https://gisgeography.com/what-is-topography/

Water Basin Vocabulary 


​​
  • Watershed-area of land that drains water from higher land to lower land
 
  • Basin-a natural depression in the Earth’s surface, typically filled with water
 
  • Divide-ridge that separates two watersheds
 
  • Surface Water-water that is on the earth’s surface
 
  • Ground Water- water that collects in cracks and spaces beneath the earth’s surface
 
  • Non- Point Source Pollution- source of pollution that is not readily identifiable, as water runoff
 
  • Tributary- a river or stream flowing into a larger river or lake.
 
  • Percolation- Rainfall seeps underground through a process called percolation, where water travels downwards through the tiny spaces between rocks and soil particles.
 
  • Agricultural Land- land devoted to the systematic and controlled use of other forms of life—particularly livestock and production of crops—to produce food for humans.
 
  • Residential Area- a land use in which housing predominates, as opposed to industrial and commercial areas.
 
  • Urban run-off- a major source of flooding and water pollution in urban communities worldwide.   Water moving through cities instead of fields and natural waterways and carrying oil spills and debris.
 
  • Factory- a building or group of buildings where goods are manufactured or assembled chiefly by machine.
 
  • Livestock- farm animals that are intentionally raised as an asset. 
 
  • Erosion- The process of moving away or being moved away by wind, water, or other natural agents.  The action of processes that remove soil, rock, or dissolved material from one location on the Earth's crust, and then transports it to another location.
​
Picture

​https://www.cityofberkeley.info/Public_Works/Sewers_-_Storm/Watershed_Resources.aspx
​

Picture
https://outdoordiscovery.org/odc-network/macatawa-river-greenway/macatawa-greenway/macatawa-watershed/

Watersheds are involved in many cycles


Picture
https://cfpub.epa.gov/watertrain/moduleFrame.cfm?parent_object_id=593

​https://cfpub.epa.gov/watertrain/pdf/modules/WatershedEcology.pdf

​https://extension.usu.edu/waterquality/files-ou/Watershed-information/NR_WQ_2005-pH.pdf

​http://www.hawaii.edu/gk-12/evo/erinb.streams.factors.htm

​http://butane.chem.uiuc.edu/pshapley/environmental/l24/2.html

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1/17/2020

PH Experiment And Environmental Significance

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What is PH and why does it matter?


The term pH refers to the acidity or alkalinity of a solution.

Substance that release hydrogen ions when dissolved in water are acids.

The more hydrogen ions they release the more acidic they are.

Substances that release hydroxide ions when dissolved in water are bases.

Alkalinity increases with the concentration of hydroxyl ions.

Each pH unit represents a 10-fold change in concentration.


Picture
https://mitte.co/2018/01/30/alkaline-water-is-it-really-good/
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Our Experiment


We will compare the pH of the following:

Vinegar

​Ammonia Solution

Lemon Juice

Baking Soda Solution

Alka-Seltzer Solution


Record your results in your worksheet
​


Why does pH matter?


Picture
https://water-research.net/index.php/ph-in-the-environment
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Picture
https://www.fondriest.com/environmental-measurements/parameters/water-quality/ph/

​
In general, fish reproduction is affected at pH levels below 5.0

Fish begin to die when pH falls below 4.0 

A pH change of 1 means a ten fold change in the ions.

pH 9 is ten times more basic than pH 8

pH stands for potential of hydrogen, a measurement of the acidity r alkalinity of a solution

7 is neutral

1 to 6 are acids

​8 to 14 are bases
​

Acids


Acids are substance that break apart in water to form a hydrogen ion.

  • Have a pH that is less than 7, smaller number means more acidic
  • React with metals and carbonates
  • Release Hydrogen ions (these are created when Hydrogen loses an electron so it has a positive charge)
  • Have a sour taste
  • React with bases to form water and salt

Everyday Acids
​
  • Tea
  • Vinegar
  • Citrus foods 
​
Acids react with carbonates to give off carbon dioxide
​

Bases


Bases are substance that break down in water and form hydroxide ions (OH-).

The greater the concentration of OH- ions the stronger the base is.

Have a pH from 8 to 14

pH 9 is ten times more basic than pH 8

Bases


  • Release hydroxide ions (negatively charged ions made of one hydrogen bonded to one oxygen). 
  • feel slippery
  • bitter taste
  • react with acids to form water and salt

Everyday examples:

  • Baking soda
  • Bleach 
  • Soap

More on Acids and Bases



​Some plants tell us the pH of their soil by expressing different colors of flowers. 
​
  • For true blue flowers, the hydrangeas need to be grown in acidic soil (pH 5.5 and lower).
 
  • For pink flowers, the plants need neutral to alkaline soils (pH 6.5 and higher).
​
  • For purple blooms (or a mix of blue and pink flowers on the same plant), the pH of the soil must be 5.5 and pH 6.5.
​
Picture
https://www.espoma.com/learn-grow/gardening-projects/hydrangeas-true-blue-or-tickled-pink/
​


Venom is Acidic


A sting from a bee may be painful for many reasons, pH of bee venom is 5.0-5.5

Formic acid in ants has a pH of 2 to 3


Ph can be different in various parts on an environment



  • When it rains or we use water for irrigation, water goes downhill, down the gradient of the earth
 
  • There is a connection between the water that move across land and the pH of bodies of water such as lakes, rives, ponds, and the sea
​
  • Let's learn about watersheds

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1/15/2020

Word Web

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Find the connections between these concepts



​Mangroves


Coral reef

Protein synthesis

Energy transfer

Metabolism

Osmosis

Saltwater

Brackish water

Aquatic animals

Land animal

Erosion
Climate change

Carbon sink

Water filtering 
organisms

Roots

Biomass

Carbon Dioxide

Oxygen

Deforestation

Tourism

Ecotourism

Sodium Chloride

Molecular structure

Cell membrane

Cell wall

Nutrient transport

Coral bleaching

Zooxanthellae

Calcite

Algae


Stem Cells

Regeneration




​Pluripotent


Cell Differentiation

Photosynthesis
Sun

Shoreline

Food Web

Sea to Land Transition

Food Chain

Food Web

Axolotl

Biome

Tissue Regeneration Therapy

Environmentalism
​
Scuba Diving

Sustainability

Reforestation

Coral restoration 

Symbiote

Salamanders

Tissue 
Regeneration

Stem Cell Research

Ecosystem

Food chain

Food web

Continent

Coastline

El Nino Weather 
Pattern

Hurricanes

Shrimp farming

Green Fluorescent Protein (GFP)

Starfish




Concept Maps



A concept map helps us see the connections between words and concepts, you can present a concept map as a web, a tree, in circles, any way you would like.  A concept map is a form of creative self expression.
​

The shoreline of most continents is naturally lined with a network of plants and animals.

We see coral reef and mangroves, coral reef systems are where about 75% of tropical fish begin their lives.  Here we find starfish, sea sponges, turtles, a huge variety of sea creatures. Coral are a symbiotic relationship between an type of algae named zooxanthellae and a type of animal, calcite is secreted by the animal to make the coral reef structures that we see, the algae gives coral the color that we see and when there is coral bleaching it means that the symbiote algae has left the coral.  Beautiful sites such as coral reefs are valuable for ecotourism and scuba diving.  Many coral species glow thanks to green fluorescent protein (GFP), this protein is used as a biomarker in biomedical research.

As the ocean transitions into the land we see mangroves, these trees have large roots that essentially hold the coastline in place, they dig deep into the earth and absorb more carbon dioxide than most trees making them a carbon sink.  Mangroves are threatened by deforestation and shrimp farming.

Natural habitats are homes to thousands of creatures and slow down erosion, especially during complex weather patterns that cause storms  like El Niño.   These trees live in salt water and create a brackish environment where organisms that like semi-salty water can live.  Many animals that live in these environments have amazing regenerating abilities, many salamanders live in brackish water.  A type of salamander that lives in brackish water but not on the coast is the Axolotl, they are only found in lake Texcoco in Mexico where a saltwater spring makes the water salty.  Axolotls have helped us learn more about stem cells because they are able to regenerate any body part, this research has contributed to stem cell therapy for humans. 


Shorelines and COasts of the Continents


Picture
https://www.nationsonline.org/oneworld/small_continents_map.htm
​


Coral Reefs live along the edges of continents


Picture
https://www.denix.osd.mil/nr/focus-areas/habitat/crid/Coral_Reef_Info.cfm
​


So do Mangroves


Picture
http://theconversation.com/mapping-the-worlds-blue-carbon-hot-spots-in-coastal-mangrove-forests-105793

What is coral?



Coral is a symbiotic relationship between a polyp which is a type of animal and an algae called zooxanthellae.  The polyp secretes calcite and builds the coral reef.

Picture
https://algaeresearchsupply.com/pages/how-do-coral-get-their-zooxanthellae

Coral Reef Health


Picture

​https://www.scientificamerican.com/podcast/episode/fishy-trick-lures-life-back-to-coral-reefs/


In warmer water the zooxanthellae leave the polyp and this causes coral bleaching.  Bleached corals are at risk of dying because the algae photosynthesizes and gives the polyp sugars that help it survive. 

Picture

https://www.marineconservation.org.au/coral-bleaching/
​

Picture

​https://www.vox.com/science-and-health/2017/4/18/15272634/catastrophic-coral-bleaching-great-barrier-reef-map
​

Coral Restoration Efforts



corals glow using Green Fluorescent Protein



Starfish live in the same area and have been known to REGENERATE parts of their body



This diverse ocean ecosystem neighbors the Mangroves


Picture

​https://birdsheadseascape.com/conservation-science/mangrove-and-seagrass-beds-provide-different-biogeochemical-services-for-corals-threatened-by-climate-change-by-emma-camp-and-others/



Mangrove roots are large and prevent erosion 
​

Picture

​https://reefresilience.org/blue-carbon/blue-carbon-introduction/


Picture

​https://www.resilience.org/stories/2018-11-28/blue-carbon-an-effective-climate-mitigation-and-drawdown-tool/


Mangrove ecosystems are destroyed for shrimp farming


Picture

​https://medium.com/sustainable-seafood/4-best-countries-to-get-your-farmed-shrimp-f05f602a193c


Mangrove trees are a powerful carbon sink, they take in large amounts of co2 and hold it in their roots and branches, parts of living matter are called biomass


Picture

​http://www.jeremiahjamescreates.com/mangrove-ecosystem-illustration/
​

We call this biosequestration


Picture

​http://www.oceanhealthindex.org/methodology/components/mangroves-condition


Biosequestration
 is the process of capturing and storing carbon in living organisms such as plants and algae
​

Picture

​https://reefresilience.org/blue-carbon/blue-carbon-introduction/
 

​Blue carbon is the term for carbon captured by the world's ocean and coastal ecosystems
.


Natural Weather Patterns lead to Land Erosion



Mangroves produce oxygen, reduce carbon dioxide, and reduce erosion
​


Mangroves are able to live in salt water and secrete salt through their leaves


Picture

https://ocean.si.edu/ocean-life/plants-algae/mangroves
​

https://asknature.org/strategy/glands-remove-excess-salt/
​


Saltwater dehydrates most roots through osmosis but mangroves are able to live in it


Picture

​https://asknature.org/strategy/glands-remove-excess-salt/#jp-carousel-6145



Specialized glands remove excess salt and create brackish water, semi-salty water, where many creatures can thrive such as frogs and salamanders
​

https://www.miamiscapes.com/mangrove-animals.html
​


Saltwater can travel underground and go to lakes through springs


Picture

https://www.nps.gov/features/yell/tours/fountainpaint/geyser_works.htm
​
Picture
https://www.nationalgeographic.org/media/aquifer-illo/

Axolotls live in Brackish water that is not on the coast


Picture

​https://www.sutori.com/story/rise-and-fall-of-the-aztec-empire--bqPcmVyeWaudDGviMDtyaa41

Picture

​https://www.sciencedirect.com/science/article/abs/pii/S1040618217301477


Axolotls are salamanders that are known for tissue regeneration



They Help us develop biomedical advances through stem cell research 


Picture

https://ib.bioninja.com.au/standard-level/topic-1-cell-biology/11-introduction-to-cells/stem-cells-2.html

Picture

​http://www.stemcellhealthclinic.com/


​Destroying natural habitats hurts biomedical research

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1/13/2020

Create a PSA

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Public Service Announcement (PSA)


Create a poster that promotes something that you are passionate about and promotes environmental well being.

You choose: 

Your Audience

​Your Message 
​

  • Explain the topic to someone that does not know about it.​

  • Explain why it is important to think about the topic

  • List three reasons the topic has an impact on the environment

  • Have a visual aid, art

  • Write a complete paragraph about your presentation with five full sentences.​

  • Read your paragraph to the class, create a presentation.

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1/7/2020

Geography

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Coral Reefs and Mangroves


Picture
https://www.denix.osd.mil/nr/focus-areas/habitat/crid/Coral_Reef_Info.cfm

​https://www.nationalgeographic.com/news/2016/03/160321-coral-bleaching-great-barrier-reef-climate-change/


Where Mangrove FOrests are


Picture

Super Continents


Picture
Picture

http://maps.unomaha.edu/Maher/plate/week12/super.html
​


Geological Timescale


Picture

https://www.digitalatlasofancientlife.org/learn/geological-time/geological-time-scale/
​


Pangea


Picture
https://www.britannica.com/place/Pangea
​

Picture

https://www.the-scientist.com/features/life-thrives-within-the-earths-crust-64805
​

Picture

https://simple.wikipedia.org/wiki/Earth%27s_crust

Picture

​https://earthhow.com/7-major-tectonic-plates/

Picture

​http://www.backroadswest.com/blog/san-andreas-fault-wrightwood/



Do you think that the similar species along the coast lines of the continents are connected to the super continents?
​


Mud skipper Natural Habitat Distribution


Picture
https://repository.si.edu/bitstream/handle/10088/57124/Parenti_Lynne_R_-20161021-C2_Parenti_and_Jaafar.pdf?sequence=1&isAllowed=y
​


Some of these Environments are Brackish



​Brackish water is water having more salinity than freshwater, but not as much as seawater. It may result from mixing seawater with fresh water together, as in estuaries, or it may occur in brackish fossil aquifers.
​


Axolotl Live in Brackish water in Xochimilco and Lake Texcoco in Mexico CIty


Picture

​https://www.nationalgeographic.com/news/2016/10/endangered-axolotls-conservation-mexico-city-chinampa/

Picture

https://www.theguardian.com/cities/2018/dec/04/axolotls-in-crisis-the-fight-to-save-the-water-monster-of-mexico-city


The only Place where the Axolotl Naturally Lives


Picture

​https://www.sciencedirect.com/science/article/abs/pii/S1040618217301477
​

Picture

​https://www.sutori.com/story/rise-and-fall-of-the-aztec-empire--bqPcmVyeWaudDGviMDtyaa41

https://www.sutori.com/story/rise-and-fall-of-the-aztec-empire--bqPcmVyeWaudDGviMDtyaa41
​


Mexico City During Aztec Times, years 1324-1430


Picture

https://www.vision.org/mexico-city-lake-8602
​

Picture

https://www.mexicolore.co.uk/aztecs/home/water-in-valley-of-mexico
​


Lake Life


Lake Texcoco has brackish water, Axolotl are able to live there

Chinampas (raised crop beds, or “floating gardens”), which provided much of the population’s food.  (Nahuatl languages: chināmitl [tʃiˈnaːmitɬ]) is a type of Mesoamerican agriculture which used small, rectangular areas of fertile arable land to grow crops on the shallow lake beds in the Valley of Mexico.

Picture

http://www.ancientpages.com/2016/05/17/chinampas-artificial-islands-created-aztecs-improve-agriculture/
​


A Lake with Salty Water


The lake is fed from groundwater aquifers; fresh water poured in from Lake Chalco and Xochimilco's freshwater springs, and the thermal springs of Zumpango and Xalcotan, as well as some in Texcoco itself, provide saline water.

To overcome the problems of drinking water, the Aztecs built a system of dams to separate the salty waters of the lake from the rain water of the effluents.


https://en.wikipedia.org/wiki/Lake_Texcoco
​


Thermal SPrings


Picture

https://www.nps.gov/features/yell/tours/fountainpaint/geyser_works.htm
​

Picture
https://www.nationalgeographic.org/media/aquifer-illo/
​


Modern Day Efforts to Protect Axolotls 


Picture

​https://www.journeymexico.com/itinerary/axolotls-and-chinampas-in-xochimilco


How Protecting the Axolotl can help humans



Cell Differentiation


Picture

https://ib.bioninja.com.au/standard-level/topic-1-cell-biology/11-introduction-to-cells/stem-cells-2.html
​

Picture
Picture
http://www.stemcellhealthclinic.com/

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    Author: Jazmin Gannon

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