Tuesday, October 8, 2019

Am I at 'risk'? What might that mean?

What does it mean to be 'at risk' of some disease--say, heart disease?  We tend to think it's something like a probability, something that might but won't necessarily happen.  In a sense, except accidents that may have to do with one's job, say, or sex-specific diseases, we are all at risk for every disease.  That is, we could each, in principle, get the disease.  But the average risk isn't usually what we care about: we want to know our specific risk.  What does that mean and how could it be known, or even estimated?

One sense of the idea is that if I am 'at risk', my probability of experiencing the trait is higher than others'.  Perhaps everyone is at some risk, in which case I am not just 'at risk' but want to know what my particular probability of getting the disease is.  And, of course, one can (should--must) ask what 'risk' means--an absolute probability?  a relative probability?  a probability dependent on some criteria that might be changeable, such as diet?  And extrapolation to the future from what past individuals with my measures-of-whatever experienced?

Let's say that someone with certain blood-profile measures (cholesterol, pressure, say) is at higher risk of heart disease, and presumably because of what that measure measured.  That could mean that, based on some past observation, a fraction f of people with the measured 'risk profile' experienced a heart attack in, say, some 5 year period. That does not mean, though it is often carelessly interpreted as meaning, either that all subjects were once at the same probability, p, of getting the disease, or it could mean that a fraction equal to f of people were doomed, and everyone else immune to the disease.  Or it could be some sort of average among people, the net result observed later after all the events have happened.  How can we tell?

There are lots of ways such kinds of risk might be framed, but they will I think necessarily be specific to various measures, that is, apply to persons characterized by the measures on them as individuals:  male, age 70+, cigar smoker, charcoal steak eater, .....

Seems rather straightforward even if, for someone in the 'risk' category, it may be terrifying.  That's a bit odd, since a risk means only some such people will be victims of the possible event.  Which ones? Why not all?  Is everyone in a given category at equal risk?  How can we know--if we even think about these issues?

Time traveling: How such measures, such p's, are determined and how they're used
Risks are something like the probability or chance that an event will occur in the future, given some conditions in the present.  With disease, it may be the probability of experiencing the disease with, or without, employing some preventive measure--medicine, diet, exercise, and so on.  It all sounds straightforward and, one might say 'scientific' since these p's are presumably estimated from data that includes measures of exposure or genotypes, and of subsequent outcomes.

But probability to whom?  Me?  You? Everyone?  Typically, as just noted, there will be various adjustments depending on age, sex, and perhaps other variables.  These are, of course, approximates based on statistical regression studies.  But were all people with the same such profile at equal risk of getting the disorder?  How could we tell?  And a critically important fact is that these are risks that have already been experienced: they are from past data, often reflecting who did in fact get the disease among those having had similar profiles; yet what we most want to know is our risk that is, for our personal, individual future. And to apply some fraction from the past to the future we have to make some, I think fundamental and often unprovable or indeed often very implausible, assumptions, such as that everyone is at the same risk, given their measured risk factors profile.

The only way such time traveling to the future based on the data we have from the past is useful, is if we assume that what is past is prologue, that is, that causal conditions won't change in any relevant way. But even just based on your own experience in our society, isn't that a rather patently naive, or at best wishful-thinking assumption?

Have lifestyle factors changed perceptibly in your lifetime?  They surely have in mine!  And do you seriously think you can predict lifestyle factors that might be relevant 10, 20....50 years from now?  If not, how reasonable can we assume it is to use past exposures to compute future risks? And, this is not to mention the obvious fact that disease rates or risks have clearly changed, usually substantially, since adequate epidemiological and health records have been kept (and the risks vary among populations, too).  This means that extrapolation to the future is, at the very least, resting on strong but untested (and untestable) assumptions.

Naturally, geneticists, obsessed with DNA sequences that are safe to measure without knowing anything except how to read a sequencer, want to ignore these things, and treat genetic variants as absolute causal entities; but history very clearly shows that the lifestyle factors are by far the more important.  After all, in recent history, even during the lifetimes of many or most readers of this post, risks, as well as exposure to risk factors, for late-onset disease have changed a lot.  We have more dietary advice, more health-care interventions, and so on, than we did decades ago, and there's no sign this won't continue.  We also indulge in plenty of, if not more junk-food binging than the past.

So, when 'risk' is made by regression, on group data, measuring only some of the potential variables (and even that inevitably with some measurement error), it is hubris at best to simply extrapolate that past experience to the future.

We could feel much more positive if these issues were addressed directly, rather than generally being ignored.  This would mean that those routinely computing future risks (based on genotype or whatever) by simply extending past risks to the future....would be confronted with the problem and forced to think more carefully and more circumspectly about biomedical risks and what they mean--and don't mean.  That would be both a scientific and a public service, and far more honest than what we have today (though 'honest' implies the probable counterfactual that the scientists making the predictions understand what they are doing). This applies, of course, to the very notion of 'precision genomic' medicine.

But if you think about it even just a little, it is easy to see that risk is a risky concept, an assumption about the nature of causes and about the degree that we have measured or understand them, and about their degree of context-specificity and about the past's translatability to the future.

Can the prospect of getting some disease be truly probabilistic, in which, say, everyone in a given risk class has the same probability of getting the disease--or is that just a gross oversimplification, an average of past cases, due to lack of knowledge about causation on our part?  This is a key, if perhaps almost unanswerable--perhaps inherently philosophical--question, one that has no 'answer' in the usual sense.  Unfortunately, experts are not paid to express the realities of such doubts, even if they think about them.  We want answers!

But perhaps since the proper answer involves unknowable facts about the future, there are none, and the past is all that we have.  At least we should acknowledge the uncertainties that plague predictions.



Monday, September 23, 2019

This year’s textbook-free Human Origins and Evolution syllabus


You are a Homo sapiens. We are all Homo sapiens.
And no Homo sapiens who doesn’t know their species will be given a final letter grade for this course.

APG 201 (3 credits)
Human Origins and Evolution

Dr. Holly Dunsworth

Acknowledgments: For contributing to this course and syllabus through their lovely influence, I am grateful to Jeffrey Kurland, Alan Walker, Pat Shipman, Jim Wood, Susan Antón, Briana Pobiner, Paul Beardsley, Anne Buchanan, and Ken Weiss. And I’m grateful to all the authors of the texts referenced here.


Course description
The biocultural evolution of humans. An investigation into humankind’s place in nature, including a review of the living primates, human genetics and development, evolutionary theory, and the human fossil record. Fulfills both the General Education outcomes A1 (STEM knowledge) and C3 (Diversity and Inclusion)

This is your origins story. To write it, we will learn from biological and evolutionary anthropologists, who study human and nonhuman primate biology, behavior, diversity, adaptation and evolution in order to better understand the human species and explain how we arrived at our current condition: Incessantly chattering, naked, culturally dependent, big-brained, bipedal creatures who are diverse in appearance and culture and inhabit nearly all types of habitats on Earth. Along our journey we will ask ourselves how we know what we know. We will also address, head-on why so much of this material is culturally controversial. The science of human evolution and its dissemination into the popular imagination has a long history of racism and sexism. In this course we will address that history and the stigma it attached to human origins by identifying bad evolutionary thinking, misconceptions, and the misapplications of that thinking. Class time will be spent on lectures (with robust handouts), activities, and discussions where we take back our species’ shared origins story and make it one that’s fit for all humankind.

Required materials
1.       The Incredible Unlikeliness of Being by Alice Roberts 
2.       Moleskine Classic Collection, hardcover, Ruled Notebook, 240 pages, 5 x 8 1/4 inch

ASSESSMENT

Book of Origins Check
During the designated week, early in the semester, each student will meet briefly with me to show me the initial progress they’ve made on their Book of Origins.

Quizzes 1, 2, and 3
These are take-home quizzes where students are free to consult class resources. Quizzes will consist of multiple-choice, short answer, and essay. They are passed out in class and submitted in class, there is no opportunity to obtain quizzes late or submit late quizzes for any points unless students have an excused absence as defined by the university handbook. This way, course attendance and participation is all wrapped up in quiz scores, which will benefit from regular attendance and participation.

Thanks, Evolution! Project –OPTIONAL EXTRA CREDIT
This is a journey to the evolutionary origins of something for which you are grateful. It is a hunt for high-quality, appropriate scientific/scholarly evidence in the literature (via Google Scholar) and a short bit of science writing. By the end of this project you will not write *the* one true correct version of an entity’s origins; you will write a sound scientific and scholarly origins story (for something meaningful to you). If you choose to do this assignment, you submit it in class at which time you present your research to the class in a one-minute (175 word max) ‘lightning talk’ without any visuals, just your spoken words. A full set of instructions, helpful guidelines, and grading rubric will be provided separately in class. Again, this is completely optional extra credit.

Book of Origins– Due last day of class, in class
Your book is your origins story. You will write this book over the course of the semester and keep it when our course is over. Your book is not your notebook. You will need a separate notebook for taking class notes and for organizing handouts and worksheets; your book is something else. Your book is due on the last day of class and will be graded and returned to you at the time of the final exam (which is not a final exam, see below). Your book is your creation and the content includes your assignments entered in preparation for that day’s class meeting as well as all information that you find meaningful and wish to enter that’s transcribed from your classroom lecture notes, handouts, worksheets, etc.  Assignments (e.g. 1.1, 1.2, 1.3, etc…. ) that go into the notebook are listed on the schedule and the details of each assignment are located in the long version of this syllabus posted on Sakai. Assignments are choreographed readings and activities that you do outside of class, timed to maximize your engagement with the in-class course material and your mastery of it. Some will ask you to respond to a reading with words or drawings. Others will involve watching films or performing interactive activities on-line. Still others guide you to perform specific exercises in preparation for in-class activities. If the assignment asks you to write something, you must write in your own words. If you want to include quotes in your book, please do but they are in addition to any assignment that is to be completed in your own words. You need to fill at least one page, at minimum, for each assignment to get full credit for its completion. Grading is based mostly on whether you completed the assignments thoughtfully and professionally, not whether you completed them entirely correctly. In other words, you earn full credit for each assignment by putting forth the effort to complete it—as long as it’s a solid effort, is mostly accurate, and earnestly attempts to answer the questions that are asked!  I grade this way because these assignments are often struggles that I’m asking you to face on your own ahead of in-class discussion.  Errors in the assignments are therefore tolerated but systematic/egregious inaccuracies are not. Your book’s overall grade will be based on completion of assignments, effort, clarity/legibility, organization, and additional content you have added above and beyond the bare minimum you are asked to include in each assignment. There are more pages than there are assignments and that space is best used, rather than left as empty space. So, the overall grade takes into consideration how thoughtful you are in creating your book, curating materials beyond merely entering complete assignments. Be sure to number your pages so that you can provide a table of contents. 

Racism and Sexism Project  - Due at the time of the final, in class
This is a written assignment due at the time of the final exam, and instead of an exam, our time will be spent sharing out with small groups and the entire class. It is a multi-part short-essay assignment that should reflect much of what you accomplished over the semester and especially during the last weeks. If done well, my feedback will be to urge you to share this assignment with your people and online.  Leading up to this project’s deadline, we will use class time to prepare. A full set of instructions, helpful guidelines, and grading rubric will be provided separately in class.



Assignments that go into your Book of Origins
(and non-required “resources” that support/complement the material)

These assignments, which must each fill at least one page of your book, are due to yourself before class on the day listed on the syllabus. Using the assigned materials, answer the questions for the assignments by writing, drawing, sketching, collaging, pasting pics, etc in any format that works. “Assigned” links are crucial to answering the question for that day’s assignment. Do not even do that day’s assignment if you have not read/viewed the assigned links. “Resources” are not assigned, but are provided as support for the assignment and/or the course content in class. They will be especially helpful if you do not understand something, have missed class, or wish to learn more. Dr. Dunsworth will be helpful in all three of those circumstances too, so contact her as well.


A Tale of Your Origins and Evolution 
With chapters of our course titled according to to Propp's Morphology of the Folktale via Misia Landau's  Narratives of Human Evolution

Chapter 1: Initial Situation. Setting your story in motion as only  humans can; anthropology; the scientific process; taxonomy; the Order Primates; observing the natural world and determining our place in it; evolution (change over time in lineages that share common ancestors); phylogeny; species and speciation; fossils and fossilization

1.1 Write and/or draw at least one page of answers to the following: What is evolution? What do you know about human evolution? What are you interested in learning about evolution and/or human evolution? You must translate any and all answers to these questions that you wrote on day 1 of class into your book for 1.1.

1.2 The Scientific Process! First, choose one of the following well-known and established observations:
a)     Children from low income homes show evidence of malnutrition.
b)     In most humans, the right humerus (upper arm bone) is larger than the left one.
c)      Chimpanzees living in zoos tend to be overweight compared to their relatives living in the wild.

Next, without using anything but your own mind, offer up two different hypotheses to explain that one observation. Briefly describe how you would test these hypotheses. Include discussion of the methods and variables for obtaining evidence and the kinds of evidence that you would need to find to both refute and to support each hypothesis. 
Assigned
·         How Science Works (video; 10 min):
·         Understanding science: How Science Works, pages 1-21; starts here:
Resources
·         What is it like to be a biological anthropologist? A Field Paleontologist's Point of View – Su (Nature Education) http://www.nature.com/scitable/knowledge/library/what-is-it-like-to-be-a-59719064
·         Notes from the Field: A Primatologist's Point of View – Morgan (Nature Education)
·         Expedition Rusinga (video; 8 min) https://www.youtube.com/watch?v=4y1puNyB9e8  
·         Carl Sagan’s Rules for Critical Thinking and Nonsense Detection
·         10 Scientific Ideas That Scientists Wish You Would Stop Misusing
·         Surprise! Semen is required

1.3 For all  four great apes (orangutans, gorillas, bonobos, chimpanzees), use at least one page (that’s one page for each ape) to answer the following questions.  Complete sentences are not necessary and neither are the numbers, as long as the info is there.  Pictures and figures are fine too. Get your information from these excellent websites:
Assigned
    Animal Diversity Web: http://animaldiversity.ummz.umich.edu /
    Primate Factsheets: http://pin.primate.wisc.edu/factsheets
    Encyclopedia of Life: http://eol.org/
    Time Tree: http://www.timetree.org/

1.      [paste or draw a picture of the ape]
2.      What is the species? (for gorillas and orangutans, choose one, but note the others)
3.      Where does it live on Earth?
4.      What is the range of its habitat? Describe the nature of the habitat.
5.      Is your primate nocturnal, diurnal, or crepuscular?
6.      What does it eat?
7.      How does it move about? 
8.      How does it socialize? (i.e. solitary? groups?...)
9.      How does it raise offspring? (i.e. solitary? groups?...)
10. Body size (both kg/g and lb/oz)? Are male and female different?
11. What does it look like? Color? Fur?
12. What are its threats to survival? 
13. At what point in the past (millions of years ago) did it share a most recent (aka “last”) common ancestor with humans? (go to www.timetree.org to find out)
Resources
·         Characteristics of Crown Primates – Kirk (Nature Education)
·         Old World monkeys – Lawrence and Cords (Nature Education)

1.4 Write and/or draw in at least one page what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Two chapters from The Autobiography of Charles Darwin: "Voyage…" (p. 71-81 ) and "An account of how several books arose" (p. 116- 135)

1.5 Write and/or draw in at least one page what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Beginnings (chapter 1)
Resources
·         Reading a phylogenetic tree – Baum (Nature Ed)
·         Trait Evolution on a Phylogenetic Tree – Baum (Nature Ed)
·         Human Evolutionary Tree – Adams (Nature Ed)
·         Human evolution is more a muddy delta than a branching tree—Hawks (Aeon)
https://aeon.co/ideas/human-evolution-is-more-a-muddy-delta-than-a-branching-tree

1.6 Using the table of primates and their traits, draw the Human, Baboon, Squirrel Monkey, and Baboon lines on the figure (which you should transfer into a page in your book). Make sure to draw arrows where traits changed. Trees are hypotheses, as long as they are logically based on the information, they are not incorrect. There is more than one correct answer.

Resources
·         Monkeys all the way down – Dunsworth (Sapiens)

1.7- Write and/or draw in at least one page what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Heads and brains (2)
Resources
·         Our Fishy Brain (video; 2.5 mins) http://video.pbs.org/video/2365207797/
·         Planet without apes? – Stanford (Huffington Post)
·         Primate Speciation: A Case Study of African Apes – Mitchell & Gonder (Nature Ed)
·         Why should we care about species? – Hey (Nature Ed)
·         Speciation: The origin of new species – Safran (Nature Ed)
·         The maintenance of species diversity – Levine (Nature Ed)
·         Macroevolution: Examples from the Primate World – Clee & Gonder (Nature Ed)

1.8 Go to http://www.eskeletons.org/ and based on what you see, draw the os coxa (half of the pelvis) of a chimpanzee and a human, in at least one page. Describe the similarities and differences in anatomy between chimp and human pelves/pelvises (do not worry about applying technical jargon). What kinds of behavioral differences might correlate with the anatomical differences in the pelvis and why? Go to http://www.eskeletons.org/ and based on what you see, draw the skull  (including teeth) of a chimpanzee and a human, in at least one page. Describe the similarities and differences in anatomy between chimp and human skulls and teeth (do not worry about applying technical jargon). What kinds of behavioral differences might correlate with the anatomical differences in skulls and teeth and why?

Resources
·         Amazing Places, Amazing Fossils: Tiktaalik (video; 5 mins) https://www.youtube.com/watch?v=T2vKlEUX7DI
·         How to Become a Primate Fossil – Dunsworth (Nature Ed)
·         Dating Rocks and Fossils Using Geologic Methods – Peppe (Nature Ed)
·         Overview of hominin evolution – Pontzer (Nature Ed)


Chapter 2: Hero. The origins of sex; how eggs and sperm get made and how they make you; mutation; gene flow; natural selection; genetic drift and other evolutionary processes

2.1Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.

Assigned
·         When Did Sex Become Fun? – Dunsworth (Sapiens)

2.2 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.

Assigned
·         Roberts: Skulls and Senses (3)
Resources
·         Finding the Origins of Human Color Vision (video; 5 mins) http://video.pbs.org/video/2365207765/
·         The Evolution of Your Teeth (video; 3 mins) https://www.youtube.com/watch?v=ohq3CoOKEoo
·         Gregor Mendel and the Principles of Inheritance – Miko (Nature Ed)
·         Mendelian Genetics: Patterns of Inheritance and Single-Gene Disorders – Chial (Nature Ed)
·         Developing the Chromosome Theory – O’Connor (Nature Ed)
·         Genetic Recombination – Clancy (Nature Ed)

2.3  Without looking anything up (except to see better pictures of the primates), write an answer for each of the questions below. In other words, come up with a hypothesis (a good guess) to explain the evolution of each of the four phenomena. These are evolutionary scenarios that you are writing.  This is brainstorming, so have no fear, but be clear.
1.      How did the mandrill get that colorful face? What about the rear (which looks like the face)?
2.      How did the colobus monkey (a leaf-eater or foliovore) get a long, specialized gut?
3.      How did silverback gorillas become twice as big as females?
4.      How did humans become “naked”? (i.e. how did we cease to be as furry as the other primates)?
Resources
·         What is a Gene? Colinearity and Transcription Units – Pray (Nature Ed)
·         RNA functions – Clancy (Nature Ed)
·         Phenotypic Range of Gene Expression: Environmental Influence – Lobo & Shaw (Nature Ed)
·         Genetic Dominance: Genotype-Phenotype Relationships – Miko (Nature Ed)
·         Pleiotropy: One Gene Can Affect Multiple Traits – Lobo (Nature Ed)
·         Polygenic Inheritance and Gene Mapping – Chial (Nature Ed)

2.4 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Things Genes Can’t Do – Weiss and Buchanan (Aeon)
Resources
·         Mutation not natural selection drives evolution –  Tarlach (about Nei; Discover Magazine)
·         Evolution Is Change in the Inherited Traits of a Population through Successive Generations – Forbes and Krimmel (Nature Ed)
·         Mutations Are the Raw Materials of Evolution – Carlin (Nature Ed)

2.5 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Speech and gills (4)
Resources
·         Secrets of Charles Darwin’s Breakthrough -  Bauer (Salon)
·         Natural selection, genetic drift and gene flow do not act in isolation in natural populations – Andrews (Nature Ed)
·         Evolution is the only natural explanation and it’s all we need – Dunsworth (The Mermaid’s Tale)
·         Negative selection – Loewe (Nature Ed)
·         On the mythology of natural selection. Part I: Introduction – Weiss (The Mermaid’s Tale)
·         On the mythology of natural selection. Part II: Classical Darwinism– Weiss (The Mermaid’s Tale)
·         Natural Selection: Uncovering Mechanisms of Evolutionary Adaptation to Infectious Disease – Sabeti (Nature Ed)

2.6 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Spines and segments (5)
Resources
·         Neutral Theory: The null hypothesis of molecular evolution – Duret (Nature Ed)


Chapter 3: Change. Gestational development; ontogeny and phylogeny; genomics; evo-devo; molecular clocks and the 'Last Common Ancestor'

3.1 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Ribs Lungs and Hearts (6)
Resources
·         The Onion Test – Gregory (Genomicron)
·         The Molecular Clock and Estimating Species Divergence – Ho (Nature Ed)

3.2 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Guts and Yolk Sacs (7)
Resources
·         Hox Genes in Development: The Hox Code – Myers (Nature Ed)
·         We Hear with the Bones that Reptiles Eat With (video; 4 mins) http://video.pbs.org/video/2365207244/
·         How Do We Know When Our Ancestors Lost Their Tails? (video; 4 min) http://video.pbs.org/video/2365211775/

3.3 Look back at what you wrote for 2.3, for each of your evolutionary scenarios (i.e. your answers to the questions1, 2, 3, and 4), describe which evolutionary mechanisms (discussed in class) that you hypothesized were at work in each of your scenarios. You probably didn’t use all the terms and ideas we used in class but you may have been getting at some of them. .
1.      [list the mechanisms you used, even if you didn’t write the official terms at the time]
2.      [list the mechanisms you used, even if you didn’t write the official terms at the time]
3.      [list the mechanisms you used, even if you didn’t write the official terms at the time]
4.      [list the mechanisms you used, even if you didn’t write the official terms at the time]

Next, rewrite each of the four explanations you wrote back in 2.4. Make them more scientifically accurate, using only the four main mechanisms of evolution that we discussed in class and those terms: mutation, gene flow, genetic drift, and natural selection. You may need to just change a few words or you may need to completely revise the entire answer, it depends on what you originally wrote.  Important! Banned words for your scenarios include: Need(s/ed/ing), want(s/ed/ing), try(s/ed/ing), best, most, and fittest.

1.      How did the mandrill get that colorful face? What about the rear?
2.      How did the colobus monkey get a long, specialized gut?
3.      How did silverback gorillas become twice as big as females?
4.      How did humans become “naked”? (i.e. how did we cease to be as furry as the other primates)?

Chapter 4: Departure. When to get born and why it's so difficult.

4.1 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Gonads, genitals, and gestation (8)

4.2 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Labor Pains and Helpless Infants: Eve or Evolution? (Part 1) – Dunsworth (Sapiens)
·         Labor Pains and Helpless Infants: Eve or Evolution? (Part 2) – Dunsworth (Sapiens)

Chapter 5: Test. When you were a big-brained, seemingly helpless baby; milk and lactase persistence; origins of bipedalism; origins of language.

5.1 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: On the Nature of Limbs (9)
Resources
·         Overview of hominin evolution – Pontzer (Nature Ed)
·         The Smithsonian Human Origins website
http://humanorigins.si.edu/evidence/human-fossils
·         Primate locomotion – Gebo (Nature Education)
·         Ardi-Ardipithecus ramidus and human evolution ((video; 3:33 mins) https://www.youtube.com/watch?v=S5c5syi0124
·         Ancient Human Ancestors: Walking in the woods (video; 4 mins)
·         The Earliest Hominins: Sahelanthropus, Orrorin, and Ardipithecus - Su (Nature Ed):

5.2 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Hip to Toe (10)
Resources
·         Lucy (video; 5 mins) https://www.youtube.com/watch?v=m8Lkk6u-wQM
·         Lucy: A marvelous specimen – Schrein (Nature Ed)

5.3 Using resources and assignments in this syllabus and from class notes and handouts, make page-sized informational, fact-filled baseball-like cards for “Ardi” and “Lucy.”  You must use at least one page for each. Why do these individuals and species matter? What is interesting? What do we know? What don’t we know? How do they relate to you? How do you relate to them?

5.4 Using resources and assignments in this syllabus and from class notes and handouts, make page-sized informational, fact-filled baseball-like cards for the “Nariokotome (Homo erectus) boy” and a Neanderthal of your choice (may even be composite individual that you name).  You must use at least one page for each. Why do these individuals and species matter? What is interesting? What do we know? What don’t we know? How do they relate to you? How do you relate to them?

Chapter 6: Donor. Development of adult brain,origins of human sociality, and development of 'secondary sex traits' 

6.1 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Peace Among Primates – Sapolsky (The Greater Good)
Resources
·         Sexual selection – Brennan (Nature Ed)
·         What Influences the Size of Groups in Which Primates Choose to Live? – Chapman & Teichroeb (Nature Ed)
·         Primate Sociality and Social Systems – Swedell (Nature Ed)
·         Primates in communities – Lambert (Nature Ed)
·         Why is no one interested in vagina size? – Dunsworth (New York Mag)
https://www.thecut.com/2015/12/why-is-no-one-interested-in-vagina-size.html

6.2  React to the Whiten et al paper in at least one page. To help, try miming each of the behaviors in Table 2 noting some that are familiar to you as a human who behaves as a human, and some that aren’t.
Assigned (pdf will be passed out in class as well)
·         "Cultures in chimpanzees" by Whiten, Goodall, et al., Nature 1999

Resources
·         Primate Communication – Zuberbuhler (Nature Ed)
6.3  Read on and then answer questions A and B after reading:
Remember…
       Most of us were taught incorrectly or led, wrongly, to believe that ‘evolution’ = ‘natural selection’ and that all evolution occurs through natural selection. This leads us to see every evolutionary scenario, all the way from fairy tale ones to the most scientifically legitimate ones, as natural selection. This is, of course, not a correct understanding of evolution.
       Natural selection can result in new adaptations or in the elimination of bad traits. The former is “positive” selection, the latter is “negative” and is always occurring no matter what. Positive selection does happen but is not easy to test, since natural selection occurs via differential reproductive success, but “survival of the luckiest” alleles via genetic drift can look exactly the same by increasing and decreasing allele frequencies just by chance. The difference between the two is that, in a selection scenario, the trait that’s evolving is causing the differential reproduction (whether enhancing or inhibiting, even if ever so slightly affecting it slowly over time), but in a genetic drift scenario the trait is randomly “drifting” to lower or higher frequencies merely due to chance (unlinked to the trait in question) effects on differential reproduction and chance passing of one allele or the other to offspring. Like selection, drift can completely fix or completely eliminate traits. Genetic drift is always occurring, and so is negative selection to some degree (filtering out mutations that prevent survival and reproduction) and positive selection to some degree (increasing the prevalence of mutations, new or old, that enhance survival and reproduction).

Read this blurb from a website below about a very common perception of human evolution:
_______________________________________________________________________________
Wisdom teeth might be lost as people continue to evolve
Why the modern diet may make wisdom teeth unnecessary
About 25 to 35 per cent of people will never get their wisdom teeth
By: Astrid Lange Toronto Star Library, Published on Tue Jun 25 2013
Wisdom teeth are the third and final set of molars that most people get in their late teens or early 20s. But not everyone does — the American Dental Association estimates that about 25 to 35 per cent of people will never get their wisdom teeth. Another 30 per cent will only get 1 to 3 of them. Anthropologists believe wisdom teeth evolved due to our ancestors’ diet of coarse, rough food — leaves, roots, nuts and meat — which required more chewing power and resulted in excessive wear of the teeth. Since people are no longer ripping apart meat with their teeth and the modern diet is made of softer foods, wisdom teeth have become less useful. In fact, some experts believe we are on an evolutionary track to losing them altogether.
_____________________________________________________________________________________

A.    Briefly explain the evolutionary mechanism behind the evolutionary scenario for future wisdom tooth loss that the author of the blurb alludes to. In other words, think about what the writer is really hypothesizing for future human evolution and rephrase his explanation, but scientifically, in terms of all or just some of the four main mechanisms of evolution that we discussed in class which are mutation, gene flow, genetic drift, and selection. Important! Banned words for your scenario include: Need(s/ed/ing), want(s/ed/ing), try(s/ed/ing), best, most and fittest.
B.    Write out an alternative scenario where natural selection is responsible for the loss of wisdom teeth in our future selves. If it’s not obvious, this will be a significantly different scenario from what the writer has imagined in the blurb and from what you wrote in response to ‘a.’ Important! Banned words for your scenario include: Need(s/ed/ing), want(s/ed/ing), try(s/ed/ing), best, most, and fittest.

Chapter 7: Transformation. Adulthood: the joys; Origins of tool use and the relationship to dietary evolution

7.1 Take this quiz and in at least one page write and/or draw what you found to be meaningful, significant, or noteworthy about the experience.
Assigned
Resources
·         Dietary Detective: Smithsonian Scientist Briana Pobiner https://www.si.edu/object/yt_VYSw0EWwNhw

7.2 Write and/or draw what you found to be meaningful, significant, or noteworthy in the readings. If struggling to identify that information, then pull out what you have questions about, what you’d like to learn more about, what you’re uncertain about, what surprised you, what relates to other material we have already covered in the course, or what may relate to what you anticipate we will cover down the road.
Assigned
·         Roberts: Shoulders and Thumbs (11)
Resources
·         Ancient Hands, Ancient Tools (video; 5 mins) https://www.youtube.com/watch?v=5_ew9J8lpwo
·         The Ancient History of the Human Hand (video; 4 mins) https://www.youtube.com/watch?v=RUL8hKDdY84
·         A Primer on Paleolithic Technology – Ferraro (Nature Ed)
·         Evidence for Meat-Eating by Early Humans – Pobiner (Nature Ed)
·         Archaeologists officially declare collective sigh over “Paleo Diet”
·         Homo erectus - A Bigger, Smarter, Faster Hominin Lineage – Van Arsdale (Nature Ed)
·         The "Robust" Australopiths – Constantino (Nature Ed)
·         Neanderthal Behavior – Monnier (Nature Ed)



Chapter 8: Test Again. Adulthood: the oys; Removing the  racism and sexism from scientific explanations for, and consequent popular beliefs about,  human biological variation

8.1 Have you taken a genetic ancestry test? Do you know much about your ancestry? How many generations back do you know about? What is the idea that Terrell says ancestry tests are keeping alive? How are they doing that? What do you take away as significant from the video about Neanderthal DNA?
Assigned
·         Ancestry Tests Pose a Threat to Our Social Fabric: Commercial DNA testing isn’t just harmless entertainment. It’s keeping alive ideas that deserve to die – Terrell (Sapiens) https://www.sapiens.org/technology/dna-test-ethnicity/
·         The Neanderthal Inside Us (video; 4 mins)
Resources
·         Archaic Homo sapiens – Bae (Nature Ed)
·         What happened to the Neanderthals? – Harvati (Nature Ed)
·         The Transition to Modern Behavior – Wurz (Nature Ed)
·         Testing models of modern human origins with archaeology and anatomy – Tryon & Bailey (Nature Ed)

·         Anthropological genetics: Inferring the history of our species through the analysis of DNA – Hodgson & Disotell (Evolution: Education and Outreach)
·         Paternity Testing: Blood Types and DNA – Adams (Nature Ed)
·         Colonialism and narratives of human origins in Asia and Africa— Athreya and Ackerman
·         #WakandanSTEM: Teaching the evolution of skin color—Lasisi
8.2 React meaningfully to the readings and make sure to address the following: What’s the link between racism and evolutionary theory and what do you think about it?
Assigned
·         From the Belgian Congo to the Bronx Zoo (NPR): http://www.npr.org/templates/story/story.php?storyId=5787947
·         A True and Faithful Account of Mr. Ota Benga the Pygmy, Written by M. Berman, Zookeeper – Mansbach
http://adammansbach.com/other/otabenga.html (Note! This is a fictional account based on the real history.)
·         How to write about Africa – Wainaina (Granta):  https://granta.com/how-to-write-about-africa/
·         For Decades, Our Coverage Was Racist. To Rise Above Our Past, We Must Acknowledge It: We asked a preeminent historian to investigate our coverage of people of color in the U.S. and abroad. Here’s what he found—Goldberg (NatGeo)
8.3 What is race? What is racism? Choose one of Marks’ ten facts and explain why it’s important to you.
Assigned
·         Chapter 15: Ten Facts about human variation – Marks (Human Evolutionary Biology)
                https://webpages.uncc.edu/~jmarks/pubs/tenfacts.pdf (copy and past that URL, direct link may not work)

Resources
·         In the Name of Darwin – Kevles (PBS) http://www.pbs.org/wgbh/evolution/darwin/nameof/
·         Why be against Darwin? https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajpa.22163
·         Human Skin Color Variation (NMNH): http://humanorigins.si.edu/evidence/genetics/skin-color
·         There's no such thing as a 'pure' European—or anyone else – Gibbons (Science)
·         Frederick Douglass’s fight against scientific racism – Herschthal (NYT)
·         The unwelcome revival of race science—Evans  (The Guardian)
·         A lot of Southern whites are a little bit black – Ingraham (Washington Post)
·         There’s No Scientific Basis for Race—It's a Made-Up Label: It's been used to define and separate people for millennia. But the concept of race is not grounded in genetics—Kolbert (NatGeo) https://www.nationalgeographic.com/magazine/2018/04/race-genetics-science-africa/
·         On the Origin of White Power – Johnson (SciAm blogs)
·         White People Are Noticing Something New: Their Own Whiteness—Bazelon (The New York Times) https://www.nytimes.com/2018/06/13/magazine/white-people-are-noticing-something-new-their-own-whiteness.html
·         Surprise! Africans are not all the same (or why we need diversity in science) – Lasisi
·         Why white supremacists are chugging milk (and why geneticists are alarmed) – Harmon (NYT)

8.4 What is the difference between sex and gender? What does it mean to say that sex is a spectrum? How has old/bad science encouraged people to deem women “inferior”? Does cutting edge biology impact gender expression and gender stereotypes? What does this mean to you?
Assigned
·         Sex Redefined – Ainsworth (Nature)
·         The book that fights sexism with science – review of Saini’s book (Guardian)
Resources
·         How the alt-right’s sexism lures men into white supremacy – Romano (Vox)
https://www.vox.com/culture/2016/12/14/13576192/alt-right-sexism-recruitment
·         How Donald Trump Got Human Evolution Wrong – Dunsworth (Washington Post)
8.5 How does racism affect a person’s health? Racism affects everyone, so how does racism affect you?
Assigned
·         Everyday discrimination raises women’s blood pressure – Yong (The Atlantic)
·         Being black in America can be hazardous to your health – Khazan (The Atlantic) https://www.theatlantic.com/magazine/archive/2018/07/being-black-in-america-can-be-hazardous-to-your-health/561740/
Resources
·         Why America’s Black Mothers and Babies Are in a Life-or-Death Crisis - Villarosa (The New York Times) https://www.nytimes.com/2018/04/11/magazine/black-mothers-babies-death-maternal-mortality.html
·         The labor of racism –Davis (Anthrodendum) https://anthrodendum.org/2018/05/07/the-labor-of-racism/
·    Against Human Nature—Ingold

Chapter 9: Triumph. Aging, wisdom, and reflection

9.1 Look back at day 1.1. Write a letter to yourself on day 1.1. Tell yourself what you got right, what you got wrong, what you left out. Now from where you stand on 9.1 today, identify an idea or concept that emerged from the course that’s important to you now. Next, identify a question that emerged from the course that’s important to you now, describe the steps you took to find an answer (web search, google scholar, etc), and whether or not you found a satisfying answer, and whether you still have questions.

Resources
·         Roberts: The Making of Us (12)

***BOOKS ARE DUE IN CLASS TODAY***

Racism and Sexism projects are due at the time of the final, in a few days…. See you then!