Learning Objectives: 

• Nitrogen is an essential element to life on Earth
• Nitrogen is found in every section of DNA and in every component of proteins (Amino Acids). 
• Nitrogen, like other essential elements, is ‘cycled’ through Nature, undergoing a series of chemical reactions along the way. 
• Nitrogen is abundant in Nature, but is usually ‘tied up’ in a Triple Bonded molecule (N2) and not accessible to living creatures. 

New Assignments: 

• The Gift of Salmon
• Spring Semester_new beginnings

Clark was out on the first day of classes, students read and annotated the article: The Gift of Salmon (see link to .pdf at left). This article describes how salmon migrations UP STREAM actually bring much needed nutrients deep into the continent and provide as much as 40% of the Nitrogen that forests require to grow. As a consequence of the decline of Salmon populations, interior forests have many fewer nutrients to draw from. 

Additionally, students reflected on their Final Exam from last semester, and were given a handout asking them to compare the Review guide for the Final with the actual test. (highlighting that the test came DIRECTLY from the review guide, and that cramming for the exam .. and using Chapt GTP to look up answers, is no substitute for engaging with the class lectures and activities along the way). 

On Thursday, Clark began his lecture on the Nitrogen Cycle: The Nitrogen cycle_part1_what is it. Students were encouraged to take notes. 

Learning Objectives: 

• Nitrogen Cycle and processes. 
• Forms of Nitrogen (NOx, N2O, NH3, etc.)
• Fixation, Nitrification, DeNitrification, Ammonification, Assimilation

New Assignments: 

• Nitrogen Cycle Activity Stations (students were to ‘color in’ one per student)
• Nitrogen cycle flow chart
• Poster Project. Students used their flow charts to create a poster illustrating the path and events of their Nitrogen atoms. 

This week began with a continuation of last week’s lecture on the Nitrogen Cycle ( The Nitrogen cycle_part2_enters life ) including coloring time (each student was given ONE station for the next day’s out-door activity to color in).. On Tuesday, we went outside with students hanging their station/posters up on trees and then rolling dice to determine which path their Nitrogen happened to follow. Working in teams of 2-3, they moved through various ‘steps’ in the Nitrogen cycle, documenting both the form the Nitrogen would take as well as the chemical process involved (Fixation is the process in which Gaseous Nitrogen, N2 is broken up and reforms into NOx, for example). From this sequence of steps, student then created artistic posters illustrating the various events which took place to their particular “Nitrogen Cycle”. 

Learning Objectives: 

• Double Helix nature of the DNA molecule and ‘DNA backbone’ consisting of Sugar and Phosphate groups.
• Molecular Diagram of Nitrogenous Bases which, as organic compounds, leave the Carbon Atoms out.
• How A ‘goes to’ T and C ‘goes to’ G. and that those letters are used as short-hand for the names of those bases.

New Assignments: 

• Video Notes: The Genetic Revolution

Monday was a holiday (Martin Luther King day). On Tuesday, we reviewed the various courses that students might sign up for in their Junior Year. Clark then gave students time (~30 minutes) to work on finishing up their Nitrogen Cycle posters from last week. We then stepped into a short discussion introducing where Genetic Engineering is at today with that conversation being an introduction into the documentary: The Genetic Revolution. (we watched the first 20 minutes) Students were required to take notes which will be collected once we finish the video on Thursday.

Thursday discussion: Introduction to structure of DNA molecule.  Using the websites below as talking points, students were encouraged to draw sketches of their own while Clark discussed covalent bonds (as being very strong) and hydrogen bonds (as being very week). Also focused on, was the molecular structure of the Nitrogenous bases vs the Phosphate groups vs the Deoxyribose molecules.. as well as the structure of alcohols during the lab on Extracting DNA from Strawberries.

• • Structure of a Nucleotide
  • Comparison of Deoxyribose to Ribose
  • Hydrogen bonds in water
  • Hydrogen bonds in DNA

Learning Objectives: 

• Genome vs Gene vs DNA
• Example Genes include: FOXP2, BRCA and SRY gene
• DNA Replication takes place with Enzymes Helicase and DNA Polymerase
• Karyotype.
• pGlo Plasmid

New Assignments: 

Transcribe and Translate Simulation. Students were required to document their ‘journey’ through this simulation including writing down the sequences of events, the names of the nucleotides, how they paired up at different parts of the process and the names of the Amino Acids which finally formed the ‘primary structure’ of a developing protein. 

Monday was a quick introduction to DNA vs Genes vs Genome. The idea that our Genome is divided into 23 sets of Chromosomes was introduced as shown in the Human Karyotype. (note: This sequence illustrates how the long DNA molecule is ‘packaged’ to fit inside the cell nucleus). Along the way we discussed a few of the more interesting genes including BRC, SRY and FOXp2. (the breast cancer gene, the ‘male’ gene and the gene which allows humans and other animals to ‘learn’ how to vocalize.

A major discussion topic of this week is DNA Transcription and Translation. This is the sequence of biological events which actually brings ‘genes to life’. See this video with Professor Dave explaining the basics. 

Also of interest, was this detailed introduction to DNA replication video, which highlights the structure of DNA and the enzymes responsible for replication. This one is interesting because of the level of detail provided with the ‘molecular machinery’. 

Learning Objectives: 

• The BioRad genetic engineering experiment. 
• The major genes included in the pGlo plasmid.
• Control genes (in this case, ara’c’.and how they operate

New Assignments: 

This week was focused on the BioRad lab of inserting a genetically modified plasmid into samples of E. Coli bacteria with the intent of seeing the GFP gene ‘in action’. This gene, when ‘turned on’ will create a protein which, when exposed to UV light, will ‘light up like a day-glow’ highlighter. Note: Clark also has a genetically modified fish in his tank called a GlowFish which also has this gene. The lab activity took all of the class period on Tuesday and 1/2 of the period on Thursday. With the remaining time, we watched the Sci-Fi thriller, GATTACA which takes place in the ‘not too distant future’ and imagines a world divided into Genetically Superior people and the “invalids” , people who’s parents were too poor to ‘design’ their babies. 

Learning Objectives: 

• Review of Transcription and Translation including reading “codon tables’.
• Introduction to Viruses and bacteriophages. 

New Assignments: 

• Using AI to decode the human genome

The week began with our final installment of our BioRad lab, to see if any student groups had sample colonies which had produced the GFP gene into their populations.. (we turned out the lights and Clark walked around with his handy, pocket UV light source).. We then finished up the film Gattaca from last week.

On Tuesday, class began with a review of all that we had learned in the last few weeks regarding how Genes actually become proteins.. Transcription and Translation were key terms of the day.

We then stepped into these three, interesting videos introducing Viruses and how they related to our studies of genetics. 1. What is a Virus? 2: Dr. Dave gets detailed! 3: What are Bacteriophages.

Learning Objectives: 

• Enzymes as complex proteins and their functions

New Assignments: 

• evolution of the eye
• Enzymes and Hydrogen Peroxide – CER – Google Docs

Monday students talked to Clark about missing assignments and used class time to complete missing work and/or work on their extra credit notes for the upcoming Test on Thursday. 

Tuesday we did a lab investigating the behavior of enzymes including one called Catalase. 

Thursday was the test. After the test, students were encouraged to use any extra time to read and annotate the article: The Evolution of eyes began with just one. 

Learning Objectives: 

• The genetics of inheritance.
• Haploid vs Diploid cells
• Meiosis vs mitosis. 

New Assignments: 

• Video: The Family on All fours (extra credit for notes taken)
• PTC testing
• Meiosis Poster Project: Students are to watch this video on Meiosis and create a multi-panel poster illustrating the various steps of Meiosis. 

Additional Resources: 

• PTC The genetics of bitter taste

Monday we watched the first half of the video: The Family on all fours. This video follows scientists as they discuss a family in Turkey which has a number of children who walk like ‘dogs’.. and explores the possibilities of ancient genes which might have a role.

Tuesday We finished the video and began a conversation about how we have TWO sets of genes, one set from mom and a second set from Dad. The value in this is that if one set is damaged for some reason, we have a ‘back up’ set which will still work (unless you get two, damaged copies). And whereas some genes are neccisary for survival (how to produce hemoglobin, for example) other genes are not, and can vary widely in their expression.. One gene of interest, is the gene that allows us to detect bitter taste.

On Thursday, we stepped into the conversation of how ‘sex cells’ form from each parent (sperm and egg).. first by considering the fact that sex cell are Haploid which then come together form a Diploid Zygote. This video introduces this concept. We then began the topic of how these Haploid cells are produced during Meiosis. 

New Assignments: 

SP Strawberry DNA Extraction Lab. This lab had students first crushing and then extracting DNA from strawberries, which appeared as white filaments floating in the alcohol layer.

Article: Oldest Human Genomes Reveal how a small group burst out of Africa. Students were given a ‘hard copy’ of this article to Annotate during class time.

New Assignments: 

• Class DNA model building project/activity. Each student in the class chose one of the Nucleotides shown in here. After being given a piece of card-stock, the students copied the nucleotide onto the cardstock, providing mirror images on both side. (note: a nucleotide contains a phosphorus group, a sugar and a nitrogenous base!).

Weekly activities and discussion.

•  
• The Wooly Mammoth will live again! 

What are enzymes? (explained along with exploring DNA replication)

What are Amino Acids 

From DNA to Protein

New Assignments: 

• To Benu and Back. An overview of the mission to a near-Earth asteroid. Students were to follow along and answer questions on the guided question worksheet: OSIRIS-REx mission question sheet
• Another short video with better graphics (but less science).
•  

This week began with a discussion of the space mission OSIRIS-REx which was an amazing engineering feat in, and of itself. The aspect that was most relevant to our class, was the discovery of the ‘building blocks of life’ on the Asteroid, bolstering the theory that Amino Acids occur naturally in our Solar System, and are not limited to Earth.

Next, we delved into VIruses and how different they are from bacteria. Also discussed was what ‘bird flu’ meant, and that all ‘flu’s’ are fundamentally, Bird flus. Students watched the three short video clips at left and were instructed to take notes while Clark added his overlay of commentary.

• Meiosis
• Mitosis
• Haploid vs diploid
• Dominant vs recessive alleles.
• review guide for test 1_spring 2025
• NOTE! Students who construct a page of notes based on the Review guide, will receive extra credit on the test for doing so. This is not for using during the test, but simply as evidence that the student studied for the test. Must be hand written and address topic described on the Review Guide

• Notes on the video: Fresh!  This film considers our industrialized food production system

• student notes_Feb12_haploid

The last major topic of the week was an introduction to Dominant and Recessive Alleles and the processes of Meiosis and Mitosis in creating haploid or diploid daughter cells. As part of this discussion, students tasted PTC paper to determine if they carried the gene which allows a person to taste it.

• Proteins gain their function based on their 3-dimensional shape
• Genes are turned ‘on’ by chemical signals.
• Synthetic Chemicals in the environment can mimic natural hormones and cause disruptions to body systems.

• Video Notes: 10 Americans. Students watched a short film by the Environmental Working Group describing the results of blood tests done on ten, random Americans. Students were to respond to questions on this guided questions sheet.10 Americans question sheet
• Interpretive Poster assignment. After reading the article here: studies link chemicals to genital development  Students worked in pairs to create posters which detailed recent experiments done to explore the effects of two, common plastic additives on human reproductive systems. (endocrine disruptors).

Discussion: How protein folding gives them shape and function.

This week was centered on “the test” for the end of the first marking period. (see review guide posted in previous weeks).

• Plasmids vs Chromosomes
• Genes are ‘translated’ into Proteins which give the creatures “traits”.
• The pGlo Plasmid as an engineered Gene for sale.
• student notes_pGlo1
• student notes_pGlo2
• student notes_pGlo3

• pGLO_day1 worksheet. Students used this handout to predict how inserting the pGlo gene would affect the growth of the bacteria.
• pGLO_predictions after inserting pGlo. Students used this handout to compare their results with their predictions

This week we jumped into the long awaited pGlo plasmid transformation lab. In this lab experiment, students were provided with samples of e. Coli bacteria that have been genetically modified to remove all pathogenic traits. We then ‘heat shock’ them and introduce a custom engineered Plasmid which gives the bacteria resistance to antibiotics (ampilcilin in our case) and one which creates a protein which glows under black light.. Lots of fun.. once you get past the odors..

• Meiosis and sex cell segragation.
• Punnett Squares
• Inheritance.

• Text book reading and video review. Students reviewed pages 231-241 in the text book to introduce themselves to the terminology of gamete formation
• Video: Meiosis. This video lays out with animation and discussion, the sequences described in the text book (above)
• Punnett Squares and probability of inheriting a recessive trait. (Double_the_Muscle-_Genotype_and_probability_worksheet). This was done in table groups after discussing the ‘double muscle’ cow. The double muscle cow.. is that because of a failed ‘stop’ gene.
• Marin Water Job descriptions (main page) ( careers page) (Salary Page) For extra credit, students identified two (2) job titles which sounded interesting, and wrote a short summary of the job description along with the monthly, starting salary.

This week wrapped up our pGlo set of labs with students seeing for themselves whether or not their colonies of E. Coli had successfully incorporated the pGlo plasmid. Where we left off last week was by adding arabinose sugarwater to our petri-dishes in hopes that the ‘ara’c’ gene would kick in, triggering the GFP gene, which actually produces the protein which glows under black light..

Midweek, we stepped into the discussion of how are genes are passed on during sexual reproduction. We began with a quick review of pages 231-241 in the text book, just to familiarize ourselves with the terminology, and then we viewed a 12 minute, animated video highlighting the process of the Gonads producing our sex cells (Gametes). Students were to take one-page of notes to summarize the process.

• An Introduction to Stop Motion Studio (using Legos), This video is helpful in describing the many features of the app..
• Using Stop Motion Studio to create a racing car video. This video is helpful in offering tips on making your video interesting (including adding sound effects).
• How to use WeVideo video editor.

• Article; Mutated DNA Restored to Normal in Gene Therapy Advance
• meiosis stop motion video project
• For extra credit: Marin Water Job descriptions (main page) ( careers page) (Salary Page) , students identified two (2) job titles which sounded interesting, and wrote a short summary of the job description and why they thought this job was interesting to them.. Also required: look at the salary page and identify the starting, monthly salary. (due by Friday, March 21)

Short discussion: Careers in ecology, science and environmental engineering! Clark first reminded students of the extra-credit opportunities for simply taking a look at the MMWD website careers (and salaries!) page.. (see New Assignments at left).. and then highlighted a Summer Internship opportunity at Pepperwood Nature Reserve, just North East of Santa Rosa (check out this link for information) 

This week began with an introduction to Stop Motion film making as a way tell stories. Several websites were shown to the class showing the tools and techniques to create stop motion films. An Introduction to Stop Motion Studio (using legos), and Using Stop Motion Studio to create a racing car video. Also of interest: Foil, and Man, two, animated shorts using stop motion techniques to tell stories.

Gene editing using CRISPR

• Mendelian genetics
• Punnett Squares and Di-hybrid crosses.

New Assignments:

• History of Gregor Mendel (students followed along with this worksheet: gregor mendel).
• DiHybrid Punnett square practice. Dihybrid Practice. Students worked on four scenarios in which two ‘parents’ created gametes and then off spring. In addition to responding to prompts, students are to: a) draw colored pictures of two parents illustrating the Traits described and b) convert probabilities from (number) / 16 to percentages.. c) Use Coin tosses for crosses where there is a 50/50 chance of a cross actually appearing (ten tosses to determine ACTUAL numbers).

(notes for next year: Have a worksheet which asked students to tabulate class data.. perhaps place them all on a central table from largest to smallest.. ask the question, do large pods always have large seeds? Do Large pods always have many seeds? Do Small pods always have small seeds? etc.) Also redo DiHybrid worksheet to include more interesting combinations and instructions to draw sketches of parents (phenotype)

Weekly activities and discussion.

This week began with giving students a full block period to get a good start on their Meiosis Video Project..

We then stepped into a bit of history on Mendelian Genetics.. (Gregor Mendel, the ‘Father of Genetics”)  While stopping the video to discuss, Clark passed out to each student, an English Pea pod to examine. We measured, counted, etc. the peas inside to observe the diversity of traits.

Next we stepped back to way in which Mendel predicted the probability of certain traits appearing in offspring, the Punnett Square. Clark first began with a cartoon characterization of two people, one with straight (up) hair and the other with flat (horizontal) hair. This of course is due to Genes (on chromosomes) and the fact that people can have different Alleles. Clark introduced the standard practice of using symbols (letters) to represent alleles and how we can use Punnett squares to predict the probability of various Phenotypes based on genotypes. click these to see students notes of the discussion. student notes_dihybrid_1 student notes_dihybrid_2 student notes_dihybrid_3

• Mendelian genetics
• Punnett Squares and Di-hybrid crosses.

• EPA changes rules See original article here:
• Lactase_Pedigrees_Patterns_Inheritance_Student (note: Students were only given pages 2-5 in class to work on).
• Living on one dollar: This video explores how very poor people living on one dollar a day. Students were to take one page of notes.

The above activity, based on Lactose intolerance, started with an overview of the evolution of mammals. Mammals by definition, have mammary glands which produce milk. To return to evolutionary biology for a moment, we reviewed the evolution of mammals including a) the first mammals b) monotremes c) Marsupials and d) placental mammals. The key point was that mammals by design are able to digest milk, but usually with a cut-off date (i.e., most mammals stop producing Lactase at a certain age and so are forced to find food for themselves).. Humans though, in some groups, evolved an ability to continue digesting milk, as described in this video: Got Lactase?

Clark reviewed in detail, example 2 on the packet of Dihybrid crosses from last week. We first reviewed how genotype leads to phenotype, and then gamete formation. The central point of the review however, was to first recognize that there are often several combinations of genes (genotypes) which lead to phenotypes. And based on this, determining the probability of a particular phenotype emerging as an offspring. Clark then showed how tossing coins could be used to model the traits passed from parent to child (we used quarters and dimes to represent the traits that a male might pass on, and nickels and pennies to model the traits that a female might pass on, with heads representing the dominant allele, and tails representing the recessive allele. Students were asked to ‘toss the coins” sixteen times to see how the probability predicted by the punnett square matched up with the ‘coin toss’.. (noting that a 3/16 probability doesn’t mean that 3/6 toss will automatically end up being true).

Learning Objectives: 

• Geologic Eras
• First land plants (eg liverworts) Ordovician period
• Horsetail/ Ferns Devonian Period

Additional Resources

• Fossils of first land plants discovered in Argentina

New Assignments:

• Lets plant a garden! Student groups were each given a pot, soil and a variety of plants to start our Spring Garden project!
• Review Guide for next week’s unit test: review guide for Test 2_Spring semester

Weekly activities and discussion.

• The Mesoamerican Milpa
• Overview of plant evolution: David Attenborough
• First Land plants and mushrooms
• Video (start) The Martian. 
• close up of Mars from latest REAL rover and an exploration of the ‘insane technology’ of the rover. 

For next week: 

• Devonian plants
• Cladogram of plants
• jumping spores of horset
• ail ferns
• The definitive overview of plant evolution

Learning Objectives: 

New Assignments:

• The Gift of Salmon. Students were to annotae the article and respond to the prompts. (click here to see original article on-line) 
• Review Guide for next week’s unit test: review guide for Test 2_Spring semester

Weekly activities and discussion.

• This week was mostly focused on starting our garden project and studying for the upcoming test. (this Thurs/Fri)

• Nitrogen cycling was introduced with the article: The gift of Salmon and will be expanded on during following weeks.

Learning Objectives: 

• Nitrogen as a vital element for growth
• Nitrogen cycles through Earth’s systems.

New Assignments:

• Article: When the world ran on Guano (When The Western World Ran on Guano for students to annotate) 
• Nitrogen Cycling activity and Poster project. Students first ‘rolled the dice’ to see what path they might take if they were living life as a Nitrogen Atom. Based on the path they took through the Biosphere, they then created a poster depicting the various ‘stops’ they would make (eg, atmosphere down to soil, up into plants, then into animals, etc). Each step of the process included an event (lightning breaks up atmospheric N2 into NOx) and a molecular form (NO2, for example). 

Weekly activities and discussion.

• A comparison of the real, international space station vs the Hermes space ship depicted in The Martian
•  

Learning Objectives: 

• Evolution of Plants: First land plants, first seed Plants
• Conifers and cones

New Assignments:

• Paleozoic highlights. This review guide introduced students to the Periods which comprise the Paleozoic including Cambrian up to Permian. Each of the periods had something interesting happening (first fish, first land plants, first fish with backbones, etc.) Periods of the Paleozoic
• Oil in the Forest
• Learning to Concentrate (this lab activity reviewed concepts of concentration as a mass ratio and had students converting to decimal equivalents and ppm). Also, the lab introduced the concept of a ‘serial dilution’ which we will see again next week. 

Weekly activities and discussion.

• A comparison of the real, international space station vs the Hermes space https://response.restoration.noaa.gov/remembering-cosco-busan-overview-2007-oil-spill
• ship depicted in The Martian
• Bioremedation was introduced as a way to repair damaged and polluted ecosystems. Several examples were given of interesting examples in which plants or mushrooms were used to clean up toxic waste.
  • Cosco Busan accident. Using human hair and mushrooms to break down toxic hydrocarbons
  • Using Mushrooms to clean up oil pits in El Salvador

Learning Objectives: 

• Coral reefs as critical ecosystems. 
• Coral reefs in distress with climate change. 
• Copper is toxic to aquatic ecosystems. 

New Assignments:

• creating a toxic copper solution
• video_Blue Planet Coral Reefs
• impact of copper on aquatic ecosystems
• Video: Chasing Coral (students were to take a page of notes)

Weekly activities and discussion.

• This week began with an introduction to Coral reefs as complex ecosystems. Corals themselves are interesting animals which, essentially live primarily like plants (growing stems out of Calcium Carbonate) and feeding off of the sugars produced by (blue-green) algae living inside their body tissues. (98% of their ‘food’ comes from the algae) and only at night, putting out their tentacles to feed). They are much like Sea Anemone.. (related to Jelly Fish, in fact).. and also put out the GFP that we saw in our recent pGlo lab. To start off the discussion, we watched the original Blue Planet episode on Coral Reefs. (first 30 minutes on Mon/Tues).. with the guided question sheet here:
• The end of the week had students attempting to create a predefined concentration solution and then using professional Copper Concentration test kits to measure their work. We then watched a new documentary called Chasing Coral (first half). Students were to take notes on the film. 

Learning Objectives: 

• How to convert from ppm to decimal equivelents
• How to calculate how many grams total there are in a copper solution with a known concentration
• How to use the Copper test kits to measure directly, copper concentrations.
• Introduction to Population Dynamics

New Assignments:

• Easter’s End reading and worksheet:
• Poster Assignment here: easter’s end student worksheet

Weekly activities and discussion.

• This week took students in a new direction as we considered the ecological footprint of humanity through time. The first example is of the people of Easter Island, who thrived for generations before completely destroying the islands fragile ecosystems.
• Students first read an article titled: Easter’s end and based on the reading first answered a few, key questions and then worked in pairs to create an illustrated timeline of events depicting the rise and fall of the populations of Easter Ishttps://www.cnn.com/interactive/2021/07/saving-californias-kelp-forests-cte-spc/land.
• Population Dynamics: The example of Kelp Forests was given as a community of creatures which interact and depend on each other. Clark listed a set of creatures in the kelp forest (kelp, sea-otters, sea-urchins, fish, etc.).. and highlighted that due to over hunting of Sea-otters and the recent Marine Heat waves which killed off much of the Star Fish, the Sea Urchin populations have exploded which, in turn, has led to a massive destruction of the kelp itself, which are the foundation of the entire ecosystem. CNN special report: Collapse of Kelp Forests

Learning Objectives: 

• Healthy Diet (and unconscious choices we make)
• Ultra-processed foods (and how they affect our moods and mental health) 

New Assignments:

• The Link between processed foods and mental health
• Handout of above article for students: ultra processed foods
• Notes Page for lecture on Healthy Diet (this was the last page of the article/handout on Ultra Processed foods that Clark handed out). notes on Healthy Diet

Weekly activities and discussion.

• This week introduced Healthy Diet as something to consider. The basic premise Clark made was that many of our thoughts are ‘unconscious” . Examples include who we seek out as a mate, which is unconsciously based on the faces, sounds and smells of our parents. When it comes to food however, many of our tastes (seeking out sweet things, salty things and fatty things) are a direct result of evolution, which taught us to seek these things out because they were exceedingly rare in nature.
• healthy diet ppt slides

Additional Resources:

• Video: The Vagus Nerve 
• Free range? Grass Fed? 
• Germs in your gut are talking to your brain