Unit One: the Environment
The vision for this unit is to first set the stage of how the environment varies, that life propagates within the environment but always with limits, and that as the environment changes then life has to be able to respond somehow.
This unit will address how we think about traits, niches, and climate change as factors in understanding biology. If done well it sets the rest of the semester up for deeper inquiry into some of these elements of biology. I am likely trying to be too ambitious
August 15 (each day is 75 minutes)
Course mechanics, introduce yourself, name cards, etc. DO NOT TRY TO DO IT ALL TODAY a little bit each time
THERE IS LITERALLY NO WAY FOR YOU TO LEARN EVERYTHING ABOUT BIOLOGY IN ONE OR TWO SEMESTERS. GOAL THIS SEMESTER IS FOR YOU TO LEARN WHERE TO START AS YOU ENCOUNTER DAILY PROBLEMS IN BIOLOGY
What is biology - variation is the law of biology. Diversity is the rule, not homogeneity.
Discuss distributions of traits - height of students, etc. and recognize that the traits of an individual are not defined by the trait distribution, the distribution is defined by the traits of individuals.
- What are traits that distinguish me from what I think of as "normal"?
- Do I think that my location is a trait that lets others make predictions about me?
- How many humans are there on this planet? How many chimpanzees, bonobos?
- Are there mental or psychological traits I have that influence how I learn or interact?
- How do I interpret a bar graph? A histogram? A distribution function?
- (don't forget day 1 cannot do much)
In-class activities and interactions:
Exercises for next class:
A quiz, an introduction to TopHat, a reminder that groups will be settled as of next week.
What does location and the environment tell us about what lives there? Recognize that location is a precise way to refer to the environment - there are multiple deserts, but only one Atacama Desert, and a plant like Boechera lives throughout the Rockies but the environment in New Mexico mountains is still quite different (seasonally, etc.) from that in Montana. That doesn't mean "location" can't change for an individual or a population, but it tells us about what that life has experienced for many generations.
- Where does all of this diversity come from? What creates and influences diversity?
- Can I actually define "stress"? How does that affect how I think about stress in my life?
- What life do I tend to find when there is lots of moisture, rainfall, humidity?
- What life do I tend to think of when there is very little rainfall, it is very dry?
- Traits can be physiological, structural, behavioral, cognitive...
- How do I use field guides or their equivalent to understand traits and distributions?
- What traits do populations of organisms have?
Going back to traits, association with environment, and start talking about fitness. How many offspring will that organism have? How do traits vary among individuals of different species, of the same species? If you find confusing examples, welcome to the world of biology!
- What is a mean, a median, and variance? How are these graphed?
- What is a population? What is a species? To me, anyway!
- Do traits change during the life of an organism? Do traits vary between parents and offspring?
- Could I write a "field guide" entry for an actual field guide, or Wikipedia, or GBIF, or any other such resource? What would I need to know?
- Why are there still organisms we know so little about?
- What environment will likely have the most different types of life in it?
Exercise: take a photo of a moth and identify it using DiscoverLife.org? One exercise each Unit will be a photograph of an organism or habitat. Go out and explore nature. Stand in a river. Find a new plant. Describe it. Your photo and caption are the assignment!
There is variation in every population - a population is something we define using any number of criteria, and within those parameters every individual organism is unique in some way... so if there are cases in OUR MUSEUM of spondylosing ankylistis in dolphins, we should talk in 1104 of genetic - and parasite - and pathogen - variation among individuals OF EVERY SPECIES
And today we are going to put some of these things together. Life reproduces, in varying amount depending on environment, stress, food availability, mate availability (when necessary). So what if the environment in a location starts to change?
- Darwin's 4 tenets of natural selection: the first time
- what is the primary literature? How does this differ from other ways of learning biology?
- Do I know how to find the papers cited in the Barry et al paper? Or papers that cite it?
- What are temporary changes to the environment? What are long-term changes? Are there any consistent patterns?
- What does plasticity mean? What does acclimation mean? What is different about these changes in an organism from what we mean when we talk about adaptation?
- If the environment changes, what are 4 ways that organisms may respond to that?
Barry et al 1995 from the journal Science
So now we will get into evidence that things are changing in a linear direction. We don't have to deal with whether it is anthropogenic; though I think that is likely we are going to focus on Biology! Today we will work with maps and species distributions, and try to determine what could happen in the next few decades in the southeastern United States. Right now the idea is to make an in-class project using DiscoverLife or GBIF, they can find a species just found to the north of here and see if there are records in GMNH... but gotta bring this back to scale! I probably have to do a lot of leg work to make this functional.
Idotea metallica, traits include temperature at which it can reproduce - crossing the Atlantic was normal, reproducing in the North Sea was not!
- why are models so useful in science?
- how can i explain "climate velocity"?
and this news story
this is too much to read all at once
Today they will learn about modeling; zombie models, weather models, climate models. Tetraclita moving up the coast of California.
Note that if predictions are right, and species move northward as the planet warms, what happened when it was last really cool? Fundulus heteroclitus, others, with distributions suggesting they were pushed down, and then back up into Chesapeake.
How do we know distributions are changing (spatial, histograms, etc.)? What shifting baseline data do we have (birds, corals, cherry blossoms, ice, and so on)? How, very basically, are hypotheses tested that two distributions are different?
- Science serves our planet by making predictions or forecasts.
- A model is a way of putting things we know about together, systematically, to help make these predictions.
- Why does a light surface like snow or ice reflect more of the sun's energy than ocean or land? Why is this important for biology?
- Biological signs of a changing climate, changing planet: can I remember TWO for the exam, and for when I am asked? (We will learn more)
- Testing for distribution changes - not the math, but the rationale
Exercise for next class: listen to this podcast https://gimletmedia.com/climatechange and study for the exam in these 3 ways:
Finishing models, returning to traits, returning to acclimation, to stress, to fitness, to distributions, to change. A big wrap-up of what we have learned.
- Describe 3 traits that vary within a species or population, and 3 traits that distinguish species or populations from one another
- Can I describe stress in terms of energy, survival, or other quantifiable ways?
- Why are maps useful for describing a population or species?
- If the environment changes, what can happen to the distribution of a species?
- What data that you can see, count, or observe can tell you that the environment is changing in a consistent way over the past century?
- Why do scientists develop "models" to describe life on this planet?
- What resources could I use to know more about an organism that I see?
Exercise for next class: study for the exam in these 3 ways:
1. think about and write how you respond to this cartoon
September 7 - EXAM ONE
Today the students will all take the exam individually as well as in their groups
Diversity and the function of diversity
We've talked about variation in traits within and among groups of organisms, now more about form and function. What are these things, in so many colors and shapes, DOING, and what can we learn from them, how do we interact with them? This is where I figure we get into plants as capturing energy, animals consuming energy, mushrooms returning energy to the soil - microbes doing all the same things, effectively, at a smaller scale. Some notes in Evernote on this.
Big picture - life exists as things that contain nucleic acids and can replicate those nucleic acids somehow. Viruses even, as parasites. Single cells or multicellular, which raises an interesting question of how cells identify each other as same or different? Same or different?
immune system is just "same or different" so we learn from things like how mice and elephants and trout AND humans use smell as a cue in immune sensitivity for mating
We learn why fungi are difficult to eliminate as infections (self-self recognition, easiest when "other" is very different)
- How do I interpret a phylogenetic tree?
- Why is it important that life contains nucleic acids (mode of passing information)?
- What evidence is there for endosymbiosis? (They contain their own genomes)
- Are all single-celled organisms prokaryotes? What is my favorite single-celled organism, probably?
- What does phylogeny help us in terms of understanding immunity?
Reading: the immune system chapter in free book? Yes, chapter 4 and chapter 9
Plants and algae - photosynthesis and how that works, why it is important, origins in endosymbiosis, eukaryotes
Reading: Chapter 5 and 6
Animals that eat Plants
Reading: Chapters 6 and 7
Animals that photosynthesize?
Phytoplankton, zooplankton - most numerous by far
Animals eat animals
Reading: Chapters 7 and 11
Focus on traits that tend to dictate role: stinging tentacles to subdue prey, venom, etc. - distinct from poison that PROTECTS prey... also carnassial teeth in Carnivores,
and then the marsupials that somehow manage to be all these things as well (herbivores, omnivores, carnivores)
Fungi eats anything
Reading chapters 5 and Ocean Giants
paper, to consider size of all multicellular organisms including huge fungi, aspen trees, individual redwoods,
Talking about scale, talking about log distributions, talking about role of fungi in returning nutrients to soil and directly interacting with plants in symbiosis, importance for agriculture, for forestry, distinction between soil and dirt
Microbes do everything too and what do we gain from this?
are viruses alive? transposable elements? what is life?
Big picture prior to exam, roles in an ecosystem, symbionts, parasites, pathogens, hosts, predators, consumers, producers, one big ecosystem
October 5 - EXAM TWO
Exercises to consider:
- fungal bingo, edible or not, things that could confuse with, TRAITS!
- photo exercise this unit perhaps a mushroom
- reading this paper on ocean giants https://peerj.com/articles/715/
WHY learn about animals that you may never see in real life, or that seem so obscure?
We study sponges in part because they are guts
and so on.... we know that getting rid of fungal infections is difficult because they are more closely related to animals than other forms of life.
Chapters 12-15 in the book will be our focus
which means we need to talk about measuring DENSITY, what is PROBABILITY, how do we MARK individuals to determine how many?
What are habitats? ecosystems? Communities? Populations? Biomes?
Exercises to consider:
- photo exercise this unit is a plant that is changing for autumn
- Not being able to see all at once how would you identify how many turtles in the pond between Warnell and Ecology? How many fish?
Back to traits - how do traits tell us about function in an ecosystem? What are ecosystem services?
What does nutrient cycling tell us about what an ecosystem requires?
Rio Grande Silvery Minnows - algivores - change with dams and water diversion, the bosque cottonwoods also imperiled, what organisms function for algivory - introduced suckers
food webs and control: Pisaster and Bob Paine
hosts and parasites
Wrap it up be mindful of this weekend being party weekend
October 31 - Halloween-themed EXAM THREE
Natural Selection, how mutations become substitutions, phylogeny
We want to be able to understand the film "Genes to Ecosystems" requires coming back to trait diversity as a heritable component within and among populations of organisms.
What are mutations, what are substitutions? How do we infer these rates? How does this help us interpret phylogeny, and generate phylogeny?
how mutations become substitutions - use in-class and out of class simulations? Trevor Bedford etcetera simply to visualize
then an admission of why phylogeny is interesting - we don't know it! we infer it! we use fossil data, morphology, DNA, all of these traits contribute to a pretty good idea of how Mammals or Birds are related to one another at certain time scales...
How does natural selection affect that rate? MHC (balancing) as an unusual example we've talked about briefly. Natural selection works through successful reproduction nothing more.
read: Sandwalk Adventures by Jay Hosler
Darwin's Four Postulates again
HIV as an example
viruses and tremendous numbers, talk about mutation as an event per reproduction
you should use Hosler for Darwin - they will remember the 4 postulates better because we have already been over it once, then unit 4 they will see these concepts again.
just make it a required $15 text for unit 4
Four tenets of Darwin's model for natural selection, each one a testable hypothesis:
- more are born than can possibly survive
- individuals are variable in many ways
- some of this variation is heritable
- so some individuals will have more offspring than others as a consequence.
A model is so we can predict things...
God is a wonderful belief. Any god. Fine. But not a means of predicting how the world works. Science is only as good as its predictions. (?)
antibiotic resistance; costs and tradeoffs
November 28 LAST CLASS
lets regroup what we knew!
Exercises to consider:
Final exam period Dec 7-13 we will have graded presentations by groups of their projects?? Maybe just the top 10 groups, so they may not want to present but they compete for the opportunity to do so because those have better grades but then there will be bickering about that...