Wk 5, Looking Ahead to Wk 6

Archaea, Bacteria, and Aliens

No, I don't mean little green men.  Current ideas around life in our solar system (outside of earth) are centered on microscopic life - the kind of life that evolved on earth early in it's 4.5 billion year history.  Astrobiology is the study of the origin, evolution, distribution, and future of life in the universe: extraterrestrial life and life on Earth. Astrobiologists currently study the extremophiles of earth, much of which are found in domains Archaea and Bacteria, to theorize what kind of life there might be and where it might be found.

In class this week we discussed some examples of extremophiles, the conditions in which they live, and similar conditions predicted on extraterrestrial - this just means outside of earth - bodies (moons, planets, comets, etc).  Astrobiology is currently a rather young and small field of science.  However, with ever increasing interest in space and in human travel in space, astrobiology will likely grow in importance.  And in the mean time it makes studying Archaea and Bacteria a little more interesting!

For week 6 we will begin our next mini project - Earth as a Model for Alien Worlds.

Looking Ahead to Wk 6

This week we will cover two of the kingdoms in domain Eukarya.  Recall that all life can be classified into one of three domains, Archaea, Bacteria, or Eukarya.  Archaea and Bacteria contain prokaryotic life, while Eukarya is full of eukaryotes.  Domain Eukarya is made up of four kingdoms - Protista, Fungi, Plantae, and Anamalia.  

Protista

Protists are a group of mainly unicellular eukaryotes, though some are colonial and some, like algae, are multicellular.  As eukaryotes they have a nucleus and membrane bound organelles.  Protists can be motile (move around) using a variety of means like flagella and cilia, or they can be immobile.  They have a variety of reproductive strategies - asexul, sexual, or sometimes combinations of the two.  They can be heterotrophs or autotrophs.  

Really, the group is best defined as all eukaryotes except animals, plants, and fungi.  In this sense kingdom Protista is not monophyletic.  As scientists study more about the great variety of protists the phylogeny (evolutionary relationships) will become more clear.  By the time you are teaching biology to your own children it is very likely the classification for this group will have changed.

Protists are generally categorized as animal-like (the protozoans), plant-like (the algaes, diatoms, dinoflagellates, and euglenoids) or fungus-like (the slime molds).

Fungi

Fungi have a great diversity of morphology and habitat. They are heterotrophic, typically secreting enzymes out of their bodies to digest other organisms and then reabsorbing the digested nutrients.  They have cell walls made of chitin, while the cell wall in plants is made of cellulose. They are often symbiotic or parasitic to plants or animals.  They have a variety of reproductive strategies - sexual and asexual, and even periods of their life cycle in which they do not reproduce at all.  Structurally, fungi are made up of fine, feathery filaments called hyphae.  These hyphae can combine into mycelium.  You may notice mushrooms have a spongey feel to them - this is because it is not exactly solid but made up of a mass of tightly packed hyphae.

Kingdom Fungi has five main phyla - the sac or cup fungui and yeasts (the ascomycota), the club fungus (the basidiomycota), the mostly single-celled, aquatic plant parasites called chytrids  (the chytridiomycota), the plant symbiotic mycorrhiza or AM fungi (the glomeromycota), and the zygospores (the zygomychota). 

And sometimes when you have protists and fungi living together you get lichen...

Lichen absorbing water from its surroundings (time-lapsed). Notice all the other critters living in the lichen.

Readings and Other Resources

6

RSO Ch. 32 Kingdoms Fungi & Protista

LOE ch 27 and ch 28

CK12 BC 8.1-8.6 and 8.8-8.14

CK12 LSC 6.1-6.11

Protists - transition, quick but thorough overview of the kingdom protista What is a fungus - transition, Scrapbook animation covering some highlights of kingdom fungi Paramecium - both, how a paramecium eats Amoeba lunch - both, video of an amoeba engulfing and digesting two paramcia Fungus: The Plastic of the Future - both, if you'd like to, watch this video about a very innovative idea: using fungi as structural material for things like packaging and furniture.  Protists - scholar, Bozeman Science gives an overview of kingdom protista Fungi - scholar, Bozeman Science gives an overview of kingdom fungi

This week:

• do the readings and watch the videos
• work on vocabulary
• locate your book of choice for the colloquium 

Wk 4, Looking Ahead to Wk 5

Frog Dissection Recap

You did it - you made it through frog dissection!! I was very pleased with lab this week.  There was some great dissecting skill, lots of discoveries and learning, and no one vomited or fainted.  It would have been nice if one of our specimen were a male, but we managed to get 8 our to 8 female frogs.  

2nd Hour at work

T shows off her mad scalpel skills (beautiful heart specimen!)

I hope that in examining the frogs you have a better understanding of your own anatomy.  Of course you aren't a frog, but on the grand scale of life you are so very close in structure to a frog (much more so than to a bacteria).

And speaking of bacteria, we are spending week five covering the two prokaryotic domains, Archaea and Bacteria.

Archaea and Bacteria

We read last week about classification, or putting organisms into different groups (taxa) with similar organisms.  The most inclusive taxon (single of taxa) is the Domain.  All life is classified into one of three domains - Archaea, Bacteria, or Eukarya.  Eukarya includes the four Kingdoms Protista, Fungi, Plantae, and Anamalia.  We will cover these kingdoms in the next several weeks...

...but for this week we will focus on domains Archaea and Bacteria.  Bacteria and Archaea both are prokaryotes: single-celled organisms lacking true nuclei and other membrane-enclosed organelles. Bacteria and archaea, however, differ in cell wall characteristics and membrane lipid composition. They also differ in RNA polymerase structure and, therefore, protein synthesis.

Archaea are the oldest, evolutionarily, and came into existence at a time the earth was still young - about 3.5 billion years ago.  The conditions on earth at that time were much more extreme - excessive UV radiation, extremes of temperature, very high concentrations of salt, extremes of pH, no atmospheric oxygen, and loads of atmospheric carbon monoxide, carbon dioxide, methane, and ammonia.  Today, archaea are still found in these extreme environments where they persist on earth, places like hydrothermal vents on the sea floor, high altitude ice sheets, permafrost, hot springs, and the Dead Sea.  We call organisms which live in these extreme environments extremophiles. Note, not all members of Archaea are extremophiles, and there are also extremophiles in domains Eukarya and Bacteria.

Bacteria arose about 3 billion years ago, and they are everywhere.  There are more bacteria in one person's mouth than there are people on the earth!  In fact, there are so many bacteria in the average human body that if we could isolate them all they would weight about 4 pounds.  If you think that is amazing, here's a link with more amazing bacteria facts. Many types of bacteria cause disease in humans, but many other types of bacteria live symbiotically or commensally in or on use. Bacteria are found not just in and on humans, but in and on places all over the earth.

Readings and Other Resources

5

RSO Ch. 29 Domains Bacteria & Archaea

LOE this week Read either CK12 BC or CK12 LSC

CK12 BC 7.1-7.7

CK12 LSC 5.1-5.7

Domains and Kingdoms of life - transition, Ricochet Science covers Bacteria and Archaea (and Eukarya, but we will cover Eukarya in the next several weeks) Bacteria: The Good, the Bad, and the Kind of Gross - transition, Amoeba Sisters talk about bacteria and anti biotics Microbe Evolution and Classification both - excellent animation on the topic, with the bonus of reviewing some things we've already covered this year.  *You have to click on the link in the right hand column found under Microbiology=> Scientific Animations, and then choose Microbe Evolution and Classification (lower right of the 4 animations that come up).  It moves fast, but if you click on the box in the upper left corner of the animation it will stop - you can use this as a kind of pause button in order to finish reading before the animation moves on. Antibiotic-Resistant Superbugs - both, It's Okay to Be Smart, gives some relevancy to studying Bacteria The Three Domains of Life - scholar, Bozeman Science covers al three domains and what characteristics distinguish each Old & Odd: Archaea, Bacteria &Protists - scholar, Crash Course covers Bacteria and Archaea (and Protista, even though we will cover it next week)

Don't forget to:

• do the readings and watch the videos
• keep building your vocabulary list
• hand in Respiratory-Cardiovascual lab (if you haven't already)
• email me pictures of your petri dishes (if you haven't already)

See you Thursday!

Wk 3, Looking ahead to Wk 4

Please excuse my absence

 I hope that you had fun reviewing some past topics from our course this week.  I am sad that we will not be able to do the activity on Taxonomy, but be sure to read the blog post, the readings, and watch the videos.

Also, I forgot in the last update to remind everyone about the Respiratory-Circulatory Connection lab write-up! Please don't forget to bring your lab write-up to class this week.

Taxonomy

Taxonomy is the systematic classification of life on earth.  With all those millions of species on earth, we need a universal way of talking about them.  The answer is taxonomy.

People have been classifying their surroundings for time immemorial.  Aristotle developed a simple system of classifying living organisms over 2000 years ago.  About 300 years ago Carl Linnaeus also developed a system of classification, attempting to make the names we give organisms universal and concise.  He used morphology, or the shape (appearance) of things, to put them into groups, and ultimately give each type of organism a two-part name - it's binomial nomenclature.   This two part name is made up of two Latin words, one representing an organisms genus and the other the organisms species.  For example, the scientific name for a koala is Phascolarctos cinereus.     

Sometimes scientists get a little silly and create non-traditional names, but they are still Latin-ized and written in Genus species form.  Take for example this beetle in the genus Agra - it's scientific names is Agra cadabra  (no kidding!)

Silliness aside, we have a hierarchy of classification groups.  The first grouping, Domain, is the most inclusive, will the final grouping, species, is restricted to a single species.

We don't use the exact system that Linnaeus described any longer.  Modern taxonomy relies on more than just morphology to classify organisms.  We also use physiology, geography, behavior, and (probably most definitively) genetics.  Using modern biological technologies we can sequence organisms' DNA and compare them and attempt to put them into a Tree of Life.  This is known as phylogenetics.  The artistically rendered phylogenetic tree below gives you a visual idea of how we attempt to show the connection of all life to a single evolutionary ancestor.

Another tree-like chart we use to show the relationship between both living organisms and extinct ancestors, is called the cladogram.  A cladogram depicts the evolutionary relationships among these organisms, each branching point representing a common ancestor, and the spaces between branches representing shared derived characteristic of all the organisms beyond that point on the cladogram. Below is an example of a simple cladogram, with some shared derived characteristics listed.

Looking ahead to Week 4

• Frog Dissection is happening this week!! Come to class prepared, having done the prelab, on time, and ready to work.
• Respiratory-Circulatory Connection lab write up is due this week.
• Don't forget to be thinking about which book you would like to read for the colloquium, and get your hands on a copy.
• Keep working on those vocabulary lists (all sorts of great words in this week's readings!).

Here are the readings and videos for this week

4 Classification and Taxonomy

RSO Ch. 28 Taxonomy

LOE this week please use CK12 BC 5.11

CK12 BC 5.11

CK12 LSC extra reading

Classification of Life - transition, this is a very basic overview of classification Taxonomy - scholar, Crash Course covers basic ideas in taxonomy and overviews the domains and the kingdoms of eukarya Phylogenetics - scholar, Bozeman Science covers phylogenetics, and the basics of reading a cladogram

Wk 2, Looking Ahead to Wk 3

Systems, Systems, Systems...

We spent some time reviewing organ systems.  There's so much more we could cover with each system - the depth of knowledge in human anatomy and physiology is ever increasing.  This week we will ready about two more systems, the muscular and the skeletal.  These systems are interconnected, the skeletal system providing the framework and leverage for movement and the muscular system providing the work.  Most muscles in the human body work in pairs.  Below is an example for the upper arm.  The biceps and the triceps form a pair of complementary muscles to flex the arm (biceps) and extend the arm (triceps).  The humorous bone, which they surround, gives structure and acts as a lever.

Bones are living tissues.  There are three bone tissue types: compact tissue (hard, outer portion), cancellous tissue (the spongey inner portion), and subchondral tissue (smooth ends of the bone covered in cartilage).  These tissues are made up of different specialized cells, including osteoblasts (inside the bone, forms new tissues), osteoclasts (large cells in the bone marrow, remove unwanted tissue), osteocyte (long-lived, stay shaped cells which are networked together), and hematopoietic cells (found in the bone marrow, give rise to red blood cells, white blood cells, and platelets).  The skeletal system is made up of other tissues as well, including cartilage and ligaments.

The skeletal system is divided into two systems - the axial system and the appendicular system.  When bones come together they create a joint.  It is the system of joints which allow our rigid from work to also be flexible.  There are several different types of joints, each allowing for different types of movement.  Some examples are in the diagram below.  Besides movement, and blood cell creation, bones also protect your vital organs.

The muscular system is also composed of different types of tissues, namely smooth muscle (involuntary, in organs and blood vessels), cardiac muscle (involuntary, occurs in the heart walls), and skeletal muscle (voluntary, attached to the skeletal system).  Each type of muscle is composed of different specialized cells.

Literature Selection

Part of our Biology course is two colloquia - one on a scientific article, and one on a literary selection.  We will hold our colloquia at the end of April.  I am hoping to have the literary colloquium on 29th or 30th, in connection with a monster movie! I will poll the class to see who intends to participate and which day works best.  The literary selection is actually a choice of Frankenstein, or the Modern Prometheus by Mary Shelly OR The Strange Case of Dr. Jekyll and Mr. Hyde by Robert Louis Stevenson.  You may read either book, or an easier adaptation of the book which is true to the original (both the Great Illustrated Classics and the Classic Starts Series are good adaptations).  Another option is to listen to the book read aloud (audiobooks rule!).

I will provide reading guides for the non-adapted versions in a couple of weeks.  This will have basic synopses of chapters, some vocabulary, and some things to think about while you read.


I am telling you almost 12 weeks in advanced so that you can select a book now and work it into your busy schedules :-)

Here at Librivox you can access free recordings of Frankenstein, or the Modern Prometheus read aloud.  Librivox also has free online type versions of the book.  Pierce County, Tacoma city, and Timberland Regional libraries all have copies of the book.

Here at Librivox you can access free recordings of The Strange Case of Dr. Jekyll and Mr. Hyde read aloud.  Librivox also has free online type versions of the book. Pierce County, Tacoma city, and Timberland Regional libraries all have copies of the book.


Readings and Other Resources

3

Ch. 18 Skeletal & Muscular Systems

LOE ch 16

CK12  BC 13.6-13.13

CK12 LSC 11.6-11.11

Skeletal System - transition, an overview of the skeletal system Muscular System - transition, overview of the muscular system with a little extra info about ways muscles move Skeletal System - scholar, Bozeman Science overviews the skeletal system Muscular System - scholar, Bozeman Science overviews the muscular system, with special attention to the contraction action of skeletal muscle

There are several things to keep track of so let me recap:

- do the Frog Virtual Dissection preLab
- do the weekly readings/videos
- choose a book/version for the literary colloquium
- keep up your vocabulary lists

It's Not Easy Being Green - Frog Dissection Pre-Lab

I know some of you are not looking forward to the frog dissection, and here's Kermit to  sympathize with you.

However, you should all be excited!  Through dissections we have learned and continue to learn a great deal about the structures and functions of animal life.  Our current understanding of human physiology, and a great deal of our modern medical practice, would be missing without the ground work laid by dissection.

To prepare for Thursday's lab complete the Virtual Frog Dissection, both the External Anatomy and the Internal Anatomy portions.  This worksheet, while not required (I am not collecting it), will aid in your understanding of the process and the structures of the dissection.  It is meant to be completed as you do the Virtual Frog Dissection.

• You will need to be prompt to class, prepared with serious demeanor.
• Our times is limited and we will be using sharp instruments - horse play or other silliness will not be tolerated.  
• Plan to stay 10-15 minutes over class time.  
• If you have long hair, please bring a means to pull it out of your way (elastic).  
• Aprons and gloves will be worn during dissection.  
• All structures of the frog will be properly disposed of at the end of the lab.  
• Although the specimens are dead, we will treat them respectfully.
• No eating, drinking, chewing (gum, candy, etc) in the lab.

Can't wait to see you Thursday!

Wk 1, Looking Ahead to Wk 2

Respiratory and Circulatory Systems

Did you know just how important your circulatory system is? The circulatory system is the transport system for the majority of body functions.  The lymphatic system and the nervous system also play a large role in sending things around your body, but the circulatory system is the standout delivery system.

In lab this week we worked on making the circulatory connection with the respiratory system.  We got everyone's heart's pumping, measuring responses in their blood pressure and pulse rate.  We also measured the VO2, or oxygen volume consumption, and used that to estimate the VO2 max, or maximal oxygen consumption.  This is a good measurement of aerobic fitness.

Here are some take-home points for the respiratory and circulatory systems.

• circulatory system's primary organ is the heart, which pumps the blood throughout the body
• the human heart, and those of all mammals and birds, have 4 chambers, and the system is closed
• there are a variety of circulatory systems in the animal kingdom
• the respiratory system's primary organ is the lungs, made of 3 lobes
• blood circulates in a figure 8 pattern, heart to lungs, lungs to hear, heart to body, body to heart
• the oxygen needed for cellular respiration is breathed into the lungs, diffused into the blood at the alveoli of the lungs, and delivered to the cells of the body by the circulatory system
• the carbon dioxide waste of cellular respiration is picked up by the blood and delivered to the alveoli of the lungs, where it passes into the lungs and is exhaled
• the circulatory system is responsible for delivering many other things (besides oxygen and carbon dioxide) to and from the cells

This week's lab, The Respiratory-Circulatory Connection, needs to be completed and turned in in 2 weeks (Feb 11th).  The hypotheses and tables should be filled out, and the Analysis Questions answered on a separate piece of paper.  Don't be afraid to ask for help in doing calculations from a parent or sibling!  If you need another copy of the lab you can find it here.  However, you will want to collaborate with your classmates to get the data you need.

Looking Ahead

Reproductive, Endocrine, Immune, and Lymphatic Systems
The readings and videos this week are one four of our body systems! In class we are going to be focusing on only the immune system, however.  Best sure to read and watch about all the systems.

2 Immune System, Lymphatic System, Endocrine System, Reproductive System

Ch. 16 Endocrine & Reproductive Systems Ch. 19 Immune & Lymphatic Systems

LOE Ch 19 & ch 20

CK12 BC 13.48-13.69

CK12 LSC 11.53-11.73

Cell vs Virus both, a cartoon metaphor that shows different organelles functioning in response to a virus Immune System Explained - both, shows a simplified explanation of the complicated response of the immune system to a pathogen Endocrine System - transition, a bit silly but does cover the basics of the endocrine system Immune System - scholar, Bozeman Science covers the various aspects of the immune system Endocrine System - scholar, Bozeman Science overview ten of the endocrine glands and an example hormone for each Reproductive System - scholar, Bozeman Science goes over anatomy, hormones, formation of gametes, and zygote growth development into a fetus

Don't forget to be working on your vocabulary lists, too!

Looking further Ahead

Week three (Feb 11th) we are going to cover skeletal and muscular systems in the readings and videos, and we will be doing our Frog Dissection!! The dissection will take some time - we have 11 systems to find in those frogs!!! Please plan to be to class promptly (early if possible) and to stay a little late into lunch or the end of co-op.  You don't have to wield a scalpel to participate in lab, so please come even if you don't want to do any cutting.

Wk 15, Looking Ahead to Wk 1

The Nervous System

In class this week we experimented with our nervous systems.  This system is so amazing, and controls so much of our body functioning, both intentionally and autonomically.  Ask you students about the activities we did.

We also shared our mini project #2 - Designer Dragons.  Wow - some very talented artists out there! Combined with their understanding of genetic inheritance, these artists rendered a dragon hatchling.  All hatchlings were from the same clutch (i.e. the parents had the same genetic make up), yet we had a variety of expressed phenotypes in our dragons.  This point is very important for later when we study ecology and evolution!

For those who did not submit all of your project materials and would like to please bring them this week.  Here are a few of the completed dragons.

Looking Ahead

This Thursday we will be looking at the circulatory and respiratory systems.  These two systems are incredibly interconnected.  Please make sure you read/watch so that you will be ready for the lab activities.  Also, we will be coming back to these systems and all the body systems in a couple of weeks when we dissect frogs ;-)

To be completely honest, I have been so swamped with other FILA responsibilities that I am canceling the write-up for the plant lab (don't cheer too loudly).  There's still plenty of great biology work to be done.  I will work hard to get your dragon mini projects back to you soon, with comments and completed rubrics.

Readings and Other Resources

1

RSO Ch. 17 Circulatory & Respiratory Systems

LOE ch 17

CK12 BC 13.27-13.36

CK12 LSC 11.21-11.35

Circulation - transition, fun School House Rock take on the circulatory system What do the lungs do? - transition, Ted Ed explains how the respiratory system works Circulatory System - scholar, Bozeman Science cover the circulatory system The Respiratory System - scholar, Bozeman science covers the respiratory system

Looking even further ahead

Here is the outline for the rest of the year

Week 1 Circulatory & Respiratory Systems

Week 2 Endocrine, Reproductive, Immune, and Lymphatic Systems

Week 3 Skeletal and Muscular Systems

Week 4 Taxonomy

Week 5 Domains Bacteria and Archaea

Week 6 Kingdom Plantae

Week 7 Kingdoms Fungi and Protista

Week 8 Kingdom Animalia

Week 9 Kingdom Animalia continued

Week 10 Evolution How

Week 11 Evolution Evidence

Week 12 Evolution When

Week 13 Ecology Systems

Week 14 Ecology Cycles

Week 15 Ecology Implications