Honors Biology schedule and homework for March 20-24, updated March 19 @ 10:30 AM PDT.
NOTE: It is not realistic to expect that your first exposure to a concept will result in understanding....just like learning a new language. Do not allow yourself to become frustrated. With effort and repetition, you will gain the clarity your brain so desires.
TEST ON BACTERIA AND ECOLOGY ON TUESDAY, MARCH 28.
Soil community lab, the microbes: On Thursday we got to see some of the members of soil communities, but we were not able to see the most abundant of them all....the microbes. We will check our petri dishes to see some of the bacteria and fungi that were hiding in plain sight. Even on our nutrient rich plates, most of the microbes present in soil will not grow. They need something that we can't replicate in a petri dish, and we usually don't know what that is.
* Monday - Niche; nutient cycles; Review 24.3, read 24.4, and see notes below; Draw and label the nitrogen cycle (see instructions below)
* Tuesday - Population dynamics and factors that limit population growth: Read 24.5
* Wednesday - Virtual field study; Read notes below. Read 24.6, and print and bring this to class coral_study.doc
* Thursday - Biomes and ecosystem types: Read 25.1, and 25.2 (notes below)
* Friday - Biological succession; Read 25.3 and 25.4. Nitrogen cycle drawing DUE.
Population density: Simple concept; The number of individuals of a population per unit area. For example, the number of deer per square mile in Thurston County, or the number of earthworms per square meter in your backyard, or the number of humans per hectare in Seattle (or Beijing). Obviously, critical resources limit population density. So can diseases or predators. We will discuss this on Tuesday.
The Nitrogen Cycle: With the nitrogen cycle you get to review your chemistry (inorganic and organic), learn something about plants, and gain an even better appreciation for the role of bacteria in ecosystems. There are plenty of nitrogen cycles available on the web (make sure to cite your source). The nitrogen cycle is also pictured and discussed in your text on page 642, but I prefer other approaches. You drawing must include 1. nitrogen fixation, 2. nitrification, 3. assimilation, ammonification, and denitrification. Plus, each of these processes must be defined on the back of your drawing. 10 points.
Virtual Field Study: Coral reefs are sensitive ecosystems. Recent studies have sadly determined that much of the Great Barrier Reef north of Australia is dying. Warmer water and pollutants can have significant consequences on these organisms. For this reason, it is important to conduct ongoing field studies in coral reefs around the world to monitor their health as an indicator of the health of larger, interdependent ecosystems. One such study involves a mesophotic coral off the coast of Honduras in the Caribbean Sea. Corals are animals in the same group with jellyfish. They do not progress to the common adult body shape of jellyfish, and remain in what looks like a jellyfish larva called a polyp. Like jellies, corals can extend their tentacles to capture prey....making them predators. Corals live in reef communities constructed of calcium carbonate in what amounts to huge apartment complexes. Mesophotic corals have co-evolved with single-celled algae. The algae live in the "jelly" layer of the coral's body (mesoglea), and the two species live in an obligate (no other option) mutualistic relationship. The corals provide a safe home for the algae, and the algae provide the corals with food from photosynthesis. Because light penetration is limited in the oceans (limited to the photic zone), so are the mesophotic corals. We will take a virual tour of a MCE (mesophotic coral ecosystem), and collect data to determine the relationship between coral population density and depth.
Niche, and the competitive exclusion principle. Every organism has its niche (rhymes with witch or quiche, depending on your preference). Niche is the sum of all interactions with the biotic and abiotic components of the ecosystem. The Fundamental Niche is the potential for any organism, but there is competition for resources in every ecosystem, so no organism actually achieves its fundamental niche. The niche an organism is left with is its Realized Niche....you could even say it's real niche. Since competition prevents organisms from realizing their fundamental niche, we refer to the "compromise" as the competitive exclusion principle.
Biomes and ecosystem types: Because these concepts are human constructs (not discoveries), different sources will present different versions of what we might call any given ecosystem. Biomes typically refer to terrestrial ecosystem types (tropical rain forests, deserts, tundra, temperate grasslands, savannas, etc)..... Section 25.1 (7 pages including pictures). Aquatic ecosystems might be lakes and rivers (freshwater), or marine. (Section 25.2, 4 pages) Estuaries are ecosystems where rivers meet the ocean (or Puget Sound).
Trophic cascades: Apex predators have a profound effect on all other trophic levels. There is a really cool video embedded in this article/link. https://www.theguardian.com/environment/georgemonbiot/2014/dec/12/how-whale-poo-is-connected-to-climate-and-our-lives
Soil Community Lab: We can't go out into some pristine ecosystem and survey the community of organisms that live and interact within that system. However, we can examine a small quantity of soil to examine as a model of a larger ecosystem. Soil (not dirt) is a complex system of its own. If the soil we examine is undisturbed forest soil with the surface debris (fallen leaves and twigs), then we can sort through it and recover numerous examples of plants, animals, fungi, bacteria, and a whole lot of tiny little things that will certainly escape our detection. If there were any vertebrate animals interacting with our soil sample, they will certainly exit the scene quickly when a human approaches with a shovel. But if we play Sherlock Holmes in our examination, we just might find evidence of organisms that are a part of that piece of an ecosystem. Does not a leaf, twig, or root provide evidence of a plant, possible a very large plant? I will prepare some agar based media for the recovery of bacteria (TSA) and fungi (MEA w/kanamycin). Is there anyway you might determine if there are tiny little seeds disguising themselves as bits of mineral debris?
We've had some really wet weather lately, and this lab can be really messy. I think we'll reverse the lab for this one and work on the tables...away from lab equipment. So the clutter removal from the work area will be a reverse of usual. I cannot stress enough the importance of quality soil. Garden soil has been disturbed. Ideally, about a gallon by volume of undisturbed forest soil would be nice. Work it out among your lab groups to see who has access. We only need one sample per group.
Lab Report: Title; Introduction ; Results and Observation; Analysis and conclusion. Your introduction should provide the reader with a succinct background on gram positive and gram negative bacteria, as well as a succinct background on the two modes of action of the various antibiotics we used. There should also be a question or objective addressing what we expect to learn from the lab. The Results and observations should include the bar graph we discussed with the zone of inhibition (which relates directly to antibiotic efficiency) as the dependent variable (y axis) and the 4 combinations of G+/CWSI; G+/PSI; G-/CWSI; G-/PSI as the 4 bars on your histogram. Include also observations that appear to contradict the trends that will be evident in the bar graph (so that this too can be referenced in the analysis). The Analysis/Conclusion should address the obvious trends in the data, and offer deductive reasoning to offer possibilities regarding how these trends might be explained. Be careful not to draw conclusions that are too broad based on such a limited data set. In fact, it is important that you make the reader aware of these limitations. Try to think about all that you have learned about biology this year and see if you can come up with some overarching themes. I've given you more than enough information here. I will not write your reports for you. I will look for thought on your part, and as always, if you find information from outside sources, you must cite it. I prefer parenthetical citations even if you have full citations at the end. sample_data_analyses.doc
The 2 videos and .doc below will help you with background information for analyzing our data from the G+/-: Antibiotic mode of action lab report. See also notes below.
Notes for the week:
This lab involves two experimental variables (G+/G- bacteria; CWSI/PSI antibiotics). To understand the concepts behind the lab, you must do the reading and watch the videos for Monday and Tuesday. Otherwise you may not have a clue what we're doing. Because there is no printed protocols for this lab, it is imperative that you keep detailed notes about everything you do and observe. I will provide you with more background information in class, and it is incumbent on you to make sure you get it. Be responsible.
The video for Monday may seem like a spoiler for the lab results, but this can be very misleading. The video states that gram negative bacteria are more resistant to antibiotics. Try telling that to a person infected with MRSA (methicillin resistant Staphylococcus aureus), or to someone suffering from infection with "multi drug resistant" Clostridium difficile. Both of these organisms are gram positive and neither of them is the least bit easy to take out with antibiotics...sometimes almost or entirely impossible. The lab results will be the basis for our analysis, not some video on youtube.
ECOLOGY...THE STUDY OF ECOSYSTEMS: It may seem like a sudden course change to move into ecology right now, but since we'll be discussing the role of various groups of organisms in their ecosystems, it makes sense to me that we familiarize ourselves on the different roles organisms can play within their ecosystems. If you think about it, we were introduced to bacteria because they were the first cells to emerge from the primordial soup. In ecology, you will see the very significant role of bacteria.
History of life on earth assignment: The document is writable history_of_life_on_earth.doc , but I see a lot of people out there with copies that lost formatting in translation to google docs or whatever. So here's a .pdf version: history_of_life_on_earth-14.pdf What you need to do is fill in the significant biological events for each of the designated periods. First appearance of significant groups, like land plants, seed plants, flowering plants, fish, amphibians, reptiles, mammals, birds, insects, etc. Tiny little drawings would help. Don't forget to indicate the 5 major extinctions with a red horizontal line. The back of the sheet should include the linear timeline. You can use your text or some online source....make sure you indicate any source that is not from class or your text.
Timeline: From radiometric dating, scientists have determined that the earth formed 4.56 billion years ago. There is evidence that for the next 500 million years, the young planet was being bombarded by giant asteroids, smallish planets, and lots and lots of comets. This is called the period of great bombardment. Thus scientists speculate that cataclysmic impacts would wipe out any proto-life that may have formed during this time. The bombardment ended about 4 billion years ago, and by 3.8 billion years ago there is compelling evidence of life (chemical signatures of carbon compounds known to be associated only with cellular activity). That's a window of "only" 200 million years. The oldest real fossils date to 3.5 billion years ago.
As we transition from the history and evolution of life on earth, we need to keep a perspective of the original life forms on the planet ... the microbes. Please read the following short exerpt: deep_history_of_life.doc primordial_soup.jpgThe tree of life as represented in 1866 by Ernst Haekel (an "apostle" of Charles Darwin): haeckel1866-1.pdf
The tree of life as represented in the 21st century: tolmmbr2009-3.pdf
A simplified version of the modern tree of life: threedomains.pdf
In the Trees shown above, please note the difference in how the microbes are treated.
The video this week is very personal to me, since it features Carl Woese (https://en.wikipedia.org/wiki/Carl_Woese). In a sense, I was a student of Woese. We corresponded with frequency during the last 4 years of his life. He sent me dozens of his landmark papers on microbial evolution...a field completely overlooked by Darwinian evolution. He also sent me books to read. I read everything he sent, and then we would discuss these books and papers and their implications. It was a mental workout. In 2010, Woese invited me to visit him at the University of Illinois. I spent three nights and 2 full days talking with him, in meetings, getting private presentations, dining, and most memorably, "Carl" took me to the lab where he did his landmark work on the discovery of the Archaea. Several scenes in the video were filmed in this lab. At the time of my visit, Woese was 82 (he never retired), and he explained to me the methods he used to sequence RNA before anyone else was comparing species based on nucleotide sequences. woesebassett.jpg Furthermore, as his guest, my trip was paid for 100% by Woese. Woese introduced me to many of his colleagues, including Norman Pace (https://en.wikipedia.org/wiki/Norman_R._Pace), also featured in the video. Woese died December 30 2012 of pancreatic cancer. The new lab where he worked until he couldn't work any more (October 2012) was later renamed The Carl R. Woese Institute for Genomic Biology http://www.igb.illinois.edu/about/archaea
Abiogenesis, aka Origin of Life, aka Chemical Evolution: This is not biological evolution, which deals only with changes in life over time. Abiogenesis (origin of the first cells) is different. Unlike biological evolution which is an empirical fact, the origin of the first cells is hypothetical and speculative. Nevertheless, we have some brilliant minds working on it, and some progress has been made, but the obstacles in our understanding always come back to ORGANIZATION. You see, if life self-organized from some sort of primordial soup primordial_soup.jpg , we really can't demonstrate self organization. You should be aware that the other two possibilities are not testable. They are: Panspermia (cells came to earth from outer space >3.8 billion years ago), and Supernatural/Divine intervention (which is not testable and for which there is no evidence). In the 1920s, Oparin (Russia) and Haldane (England) both hypothesized that the early earth would have had a very chemically rich atmosphere with lots of energy. They also hypothesized that there would not be NO OXYGEN in this atmosphere (thus a "reducing" atmosphere) because it's too reactive and must be continuously replenished by photosynthesis. Fast forward to the 1950s at the University of Chicago, where Stanly Miller and Harold Urey developed a rudimentary contraption to test the hypothesis of Oparin and Haldane (see figure 17.9, p 447). What they got from these experiments was exciting: For example, these experiments produced some amino acids, nitrogenous bases, and aldehyde sugars. But that leaves a Grand Canyon-sized chasm in understanding how these pieces could have self-assembled. Especially problematic is the evolution of the universal genetic code.
Archived downloads and links
Test 1 Break
More Hardy-Weinberg problems: http://www.k-state.edu/parasitology/biology198/hardwein.html
End of first semester:
Contrasting mitosis and meiosis: 6:45 https://www.youtube.com/watch?v=jjEcHra3484
Meiosis video: 5:30 https://www.youtube.com/watch?v=nMEyeKQClqI
Contrasting mitosis and meiosis: 6:45 https://www.youtube.com/watch?v=jjEcHra3484
Meiosis video: 5:30 https://www.youtube.com/watch?v=nMEyeKQClqI
Videos related to gene expression:
The Crash Course guy covers it all in his own annoying (to me) way, 14 minutes https://www.youtube.com/watch?v=itsb2SqR-R0
Transcription, 2 minutes https://www.youtube.com/watch?v=SMtWvDbfHLo
Translation, 3 minutes https://www.youtube.com/watch?v=TfYf_rPWUdY
Mutations, 6 minutes https://www.youtube.com/watch?v=xYOK-yzUWSI
Test 4 break
I made this crossword puzzle for you: cell_puzzle.pdf
DNA Replication: https://www.youtube.com/watch?v=wcOZHK5bRLs
DNA from Bozeman: https://www.youtube.com/watch?v=q6PP-C4udkA
Inner life of the cell: Harvard biologists made a bunch of computer-animated videos that are incredible. This is some seriously cool stuff. I'll show some short exerts in class as we come to that particular structure/function. You can check it out as you like....it's amazing: https://www.youtube.com/results?search_query=inner+life+of+a+cell
Khan Academy cells: https://www.youtube.com/watch?v=Hmwvj9X4GNY
Features of cells: https://www.youtube.com/watch?v=1Z9pqST72is
Test 3 break:
This is an excellent video overview of cellular respiration: https://www.youtube.com/watch?v=XIJvVCA9RPs
Photosynthesis video from the same production company: https://www.youtube.com/watch?v=QSFUHB8VnD0
Mr. Anderson's photosynthesis video: https://www.youtube.com/watch?v=g78utcLQrJ4
Photosynthesis video game, tutorial, and quiz from Bioman: http://www.biomanbio.com/
Ted Ed's Calvin Cycle video: https://www.youtube.com/watch?v=0UzMaoaXKaM
Test 2 break
This 12 minute video will help you understand the concept and terminology of enzymes. http://www.youtube.com/watch?v=ok9esggzN18
Test 1 break
Water: Hank https://www.youtube.com/watch?v=HVT3Y3_gHGg
ABOUT TEST CORRECTIONS: Because of issues in the past, I'm tightening up my test correction policy. I reserved the right to disregard all submitted test corrections if I find that a student is purposefully attempting to submit phony test corrections. For full credit, please follow these guidelines: ONLY HAND WRITTEN CORRECTIONS WILL BE ACCEPTED FOR CREDIT.
1. Do not: Restate the question and/or answer options as written on the test.
2. Do not: Share your personal reflections on what you were thinking (or not thinking) while you were taking the test.
3. Do not: Say the same thing over and over again.
4. DO: Identify the concept that the question deals with. Use 1/2 page to address that concept using words, labeled diagrams, etc. test_correction_format.doc
5. ALL TEST CORRECTIONS MUST BE HAND WRITTEN/DRAWN, AND LEGIBLE.