Wk 8 and 9, Looking Ahead to Wk 10

Animalia

We spent two weeks on kingdom Animalia.  During week 8 we covered invertebrate animals and their phylogenetic relationships.  In class we practiced using a dichotomous key to classify sample invertebrate organisms.

 Remember, a dichotomous key is for identifying things you come across and is NOT indicative a any sort of relationship between organisms on the key.  It relies heavily on morphology.  

If you missed out on the dichotomous key activity (or you just loved it and can't get enough) here is an activity on using dichotomous keys.

The second week was spent with chordates, including the vertebrates.  We practiced making a cladogram - a chart showing the evolutionary relationship between groups of organisms based on shared derived characteristics. 

If you missed out on the cladogram activity (or you just loved it and can't get enough) here is an activity on cladograms - what they are, what they show, how to build them, and a chance to make a simple one of your own.

Though our example cladogram was imperfect and relied on morphology as well, typically cladograms utilize embryological, developmental, or genetic shared derived characteristics because these more accurately reflect an evolutionary relationship.

And speaking of evolution...

Wk 10 Evolution 1 - History of Life on Earth

This week begins our unit on evolution.  Evolution is a fundamental concept in biology. The Theory of Evolution is often seen as the main overarching theme that ties all topics of Biology together. It includes Genetics, Population Biology, Anatomy and Physiology, Ecology, Animal Behavior, and Embryology, among others.  The topic is controversial for some, and I encourage you to talk with your parents about it (and all the things we cover in class!), but our class will study the theory of evolution as it is currently understood and accepted by the scientific community at large.  We will not cover the origins of life, as evolution does not address this directly, but rather the (inheritable) change in life.

• Evolution is the heritable (genetic) change in a population or species over generations.
• Species is a group of organisms which can successfully interbreed and whose offspring could also successfully interbreed.
• Population is a group of interacting individuals belonging to one species and living in the same geographic area.

Before we get into the process of evolution (wk 11) we need to discuss the history and diversity of life on earth.  We just spent six weeks covering taxonomy and diversity.  The variety of  living (extant) organisms on earth is quite amazing!  And collectively, all current living organisms represent only a portion of the many, many organisms that have lived (and become extinct).  The earth has existed for over 4.5 billion years, and evidence of life goes back over 3 billion years.

In that 3+ billion years of life on earth many species have evolved, and then become extinct, or evolved into new species. There is a complex interaction between organisms and their environment (by the way we call the study of this ecology), and as the earth changed, the life on it also changed.  There have been major periods of heating and cooling, changes in the composition of the atmosphere, changes in the amount of available water, asteroids hitting the earth, periods of extensive volcanic activity, and the shifting of tectonic plates (and therefore land mass) on the surface of the earth.  All of these environmental factors interacted in a dynamic (back and forth) way with the organisms on earth, creating periods of growth and diversification of life as well as extinction events.

Readings and Other Resources

Evolution 1 -History of Life on Earth

Ch. 20 A Story of Luck

LOE 4.3

CK12 BC 5.1-5.9

CK12 LSC 4.12-4.14

Life Has a History - both, choose Level 2, this is an interactive overview of the topics covered in the three weeks of our evolution unit History of the Earth in 5 1/2 Minutes - both, this animated comic gives you an idea of the length of geologic time, the age of the earth, the amazing events that have happened, and where modern life fits in to that scale. The History of Life on Earth - scholar, CrashCourse, I know this is from their Ecology course, but it covers this first week of evolution very well

So for this week make sure to:

• do the readings and other resources on the chart
• email me if you need anything for your astrobiology project
• keep working on your vocabulary lists
• read in Frankenstein/Jekyll & Hyde

Wk 7, looking ahead to wk 8

Plantae!

We covered the four major plant groups in lab.  These are the bryophytes, seedless vascular plants (tracheophytes, pteridophytes, lycophytes, etc), gymnosperms, and angiosperms.  There are other plant groups, but these four comprise the majority of plant life.  Remember all plants:

• are eukaryotes
• are multicellular
• are autotrophs
• have cell walls composed of cellulose
• undergo alternation of generations

Some major differences between the four groups are summarized in the table below.

	Bryophyta	Pteridophyta, etc.	Gymnosperms	Angiosperms
Dominant phase	Gametophyte	Sporophyte	Sporophyte	Sporophyte
Ploidy of plant body	Haploid	Diploid	Diploid	Diploid
Vascular Tissues	absent	present	advanced	advanced
True Leaves	absent	present	advanced	advanced
Roots	absent	absent	advanced	advanced
Seed and covering	Seed absent	Seed absent	Seed present, naked	Seed present, coverings
water required for fertilization	yes	yes	no	no
Flower presence	absent	absent	absent	present

There was insufficient time to get around to all the plant specimen and examine them, so there will be no write-up for this lab!  Don't worry, there are still 3 more write-ups before the end of the year ;-)

Introducing Animalia

What is an animal? Lions, tigers, and bears (oh my!)? Sure.  

Sponges, corals, and urchins? Yes, those too. 

Rotifers and nematodes? Yup.

Weird? Well, there is incredible variety in kingdom Animalia!  But organisms in this kingdom all share a few key characteristics:

• eukaryotic
• multicellular
• heterotrophic
• motile

We start to break the animals into different groups by first looking at whether or not the organism has tissues, and whether the developing embryo has germ layers. How animals develop from a fertilized zygote into a morula, then into a blastula, and then possibly a gastrula, and the associated germ layers, is used extensively in classifying animals.  

Next we look at what kind of symmetry the organism has - radial or bilateral - and the number of germ layers - 2 (diploblastic) or 3 (triploblastic). (Sponges are the only phyla in kingdom Animalia which are asymmetrical, but they were already branched off our classification system because they have no tissue or germ layer).

Of those organisms which are triploblastic with bilateral symmetry, we can make a further distinction based on whether they have a body cavity (called a coelom).  Those without body cavities are called acoelomates, those with an incompletely lined, fluid-filled coelom are called pseudocoelomate, and those with a completely lined, fluid-filled coelom are called coelomates (sometimes the word eucoelomate is used).

We can further divide the coelomates into protostomes and deuterostomes, depending on whether the first opening formed in embryological development is the mouth or the anus.

So, a visual representation of all these classification can be put into a cladogram like the one below.

The phyla on this cladogram (Porifera, Cnidaria, Ctenophora, etc) are representative groups, but only a few of the 35+ phyla in the animal kingdom. 

This week we are focusing on invertebrate phyla, or every single phylum in the animal kingdom except phylum chordata.  Next week we will focus on phylum chordata.

Readings and Other Resources

14 Kingdom Animalia -  Invertebrates

Ch. 31 Kingdom Animalia  pgs 639-943

LOE ch 30, 31, 32

CK12 BC 10.1-10.8 11.1-11.3 11.4-11.6 11.8-11.10 11.12-11.13 (these sections are short)

CK12 LSC 10.1-10.7 9.1-9.4 9.6 9.7 9.13 9.10  (these sections are short)

Animals - transition, Bozeman science does an overview of the kingdom and the ways we classify animals within the kingdom Marine Invertebrates - transition, simple video with a variety of beautiful and interesting invertebrate animals Animal Development - scholar, CrashCourse covering animal development, which is used in classifying the organisms in the kingdom  - or - Introduction to Animal Diversity - advanced scholar, if you want deeper understanding then watch this instead of the CrashCourse Animal Development Video. It is an excellent overview of the classification of the animal kingdom! There's much in here that is lacking in the readings.  While you don't have the lecture note outlines he talks about, it would be very helpful to get a blank piece of paper, when prompted, and create the Animalia classification key along with him Simple Animals: sponges, jellies, and octopuses - scholar, CrashCourse covers a few of the simpler animal phyla Complex Animals: Annelids and Arthropods - scholar, CrashCourse covers more complex animal phyla

  

Wk 6, Looking Ahead to Wk 7

I hope you read all about Protista and Fungi in week 6.

 If you couldn't get enough of it, here are links you might be interested in.   This one is about a group of fossilized fungi thought to be the oldest fossil of a land dwelling organism. And here is an article about an amoeba with an immune response and how it might be helpful in developing treatments for human immune diseases. This one features the musical talents of some teenage biology students extolling the wonders of Protista. And apparently Protista, besides giving rise to Fungi, Plantae, and Animalia, are the ancient Muses of biology rap and have inspired yet another video.

Oh, and check out this article about sending cryptoendolithic fungus into space to see how it fared in mars-like conditions.

ET Found Home?

And speaking of life beyond earth... This week in class we discussed the conditions necessary for life on earth or anywhere for that matter.

Liquid Water
Source of Energy (for photosynthesis, chemosynthesis, etc)
Raw Materials (i.e. organic molecules for building cell structures)
Protection from Radiation
Temperatures at which life has been known to exist (roughly -15 to 120 degrees C)

We then took these parameters and evaluated extraterrestrial planets (and moons) to see which are the most likely to be able to support life. Here is a video that explains astrobiology in simple terms.
This week we will quickly finish up talking about astrobiology, hand out the Astrobiology Mini Project, and move on to the evolution and diversity of kingdom Plantae.

Kingdom Plantae

The plant kingdom has amazing variety, but all species in the kingdom share certain characteristics.  They are all

• eukaryotes
• autotrophs
• multicellular
• have cell walls made of cellulose
• undergo alternation of generations (spend a portion of their lives as haploid organisms, and a portion in diploid form)

The kingdom is made up of many monophyletic groups, but four of these represent the overall phylogenetic diversity of the kingdom.  These are the primitive non-vascular  mosses and liverworts (Bryophytes), the vascular but seedless ferns (Pteridophytes), the vascular naked-seeded plants like pines (Gymnosperms), and the vascular flowering plants (Angiosperms).

Kingdom Plantae includes species which have undergone amazing adaptations (we'll talk more about this in the evolution and ecology units), which account for both variety in beauty and function.  They've also made some pretty weird adaptations too.  Check out this week's videos for more.

13

RSO Ch. 30 Kingdom Plantae

LOE ch 29

CK12 BC 9.1-9.10 and 9.18-9.24

CK12 LSC 7.1 and 7.4-7.14

Plant Evolution - transition, this video has no sound, but gives you a visual walkthrough of plant evolution and the major groups (taxa) of plants Plants Intro - scholar, Bozeman Science video that gives a great intro to the variety of plant Life 10 Most DEADLY Plants on Earth - both, making plants more intriguing, and showing some variety Monocots vs Dicots - both, how to identify these two types of flowering plants, and a few exceptions Plants Behaving Badly: Murder and Mayhem - IF YOU WANT here is a 45 documentary about carnivorous plants, narrated by David Attenborough.  This also makes nice connections to evolution and ecology, our next two units

So for week 7

• do the readings and watch the videos
• keep accumulating vocabulary words
• get your copy of Frankenstein or Jekyll and Hyde lined up (begin reading if you wish, but  if you get stuck or feel overwhelmed I will be handing out a reading guide for Frankenstein in week 8)

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