This year's textbook-free Introduction to Biological Anthropology course

The cost of living is ridiculous, but one nice thing about living so close to the beach (besides the beach) is that the semester begins after Labor Day. Many of our students move into vacation homes when the season ends. So although many of you are scrambling to write your syllabi for an August start, we have a bit longer to wallow in procrastination here. It's August, the Sunday of the year.

Since syllabi are on our minds, I thought I'd share mine, once again, because I've changed it, once again.

I get bored reading the same books and I'm ever-hopeful that I can improve my courses. Both of those things mean there's always serious work to be done on the teaching spectrum of this job--something that flies in the face of advice for securing tenure. But what good is that advice if teaching is valued at your institution? And what good is that advice when it's given to a lifelong learner who just cannot imagine heeding it? (I may answer these questions in an upcoming post about my path to being awarded tenure.)

Anyway, this year in APG 201: Human Origins (Introduction to Biological Anthropology; a requirement for majors and a general education course in the natural sciences), we're reading Your Inner Fish again, but we're replacing Paleofantasy with The Incredible Unlikeliness of Being. There is no textbook for good reason. And, as a bonus, students will only spend up to about 30 bucks total on materials.

Yes, I'm sort of chums with, and rather fond of, both books' authors, especially IUB's. But so what? These are fantastic books and complement beautifully not only one another but, most importantly, the material I cover in the classroom.

There will be three quizzes and a research project (focusing on information literacy) that add up to 50% of the course and a notebook that makes up the other 50%. The notebook has all the classroom notes that students take (imperative) and includes their hand-written daily assignments (yes, there are daily assignments) based on the assigned readings/viewings/activities.

Sure, it seems like a lot of grading. There are 120 students in this class, but I  assure you that I am not insane. Number one: I tried the notebook experience last semester and it was hard work but it was manageable. Number two: If I can't teach at a small liberal arts college, I can still act like I do. Students deserve that experience. And so do I.  The grading robots help out with the quizzes (mostly multiple-choice), but otherwise, it's up to me. I don't nit-pick with my red pen, at least not always. They just have to complete the notebook, but very thoughtfully and professionally so, to get credit. But I think it's a much much richer experience if they are encouraged to read along and to think along like this, on their own. And a great way to improve independent reading, writing, and thinking is to have them do it regularly, habitually--just like with sports. Detailed feedback or not, they will improve on these fronts just by practicing them, or they will fail the course for not doing the work. Don't come to practice, get cut from the team. It's so simple, yet so incredibly difficult for far too many with a high school diploma.

Anyway, here's the plan. If it helps you out, I'm honored. If you do something similar it would be encouraging if you could let me know (like if you use no textbook, or if you have them produce a notebook, or if you too rearrange the order of the material, which runs counter to every textbook, all of which put natural selection and genetics right up front and absolutely ruin the evolution learning experience to my mind, as I've written before). The headings for each day (see below) describe that day's lecture/discussion topic and there aren't always readings that address those specifically! I provide quite a bit of information in the form of handouts when that's the case. Also, I have more readings listed here than one might expect for an introductory level, general education course. The saying goes that students should spend three hours outside class for every hour inside class. And I agree. I also think it's a tragedy and, worse, a financial scam (some are $100k in debt... for a state school!) if they're not challenged enough to do much work outside of class. Some of the readings listed are there for students who need help understanding lecture or who missed lecture. That is, some of the readings can be skipped if students are present and engaged with lecture, which draws heavily on them. Of course, the readings that the assignments rest on cannot be skipped. And, of course, my questions based on the readings will improve each semester. Enough rambling, though. Here's the plan:

APG 201: Human origins

Unit 1. OBSERVE. This view of life. Our place in nature.

Big questions: What is the anthropological perspective? What is the scientific approach to understanding human origins? What is a human? What are human traits? How do humans fit on the Tree of Life? What is evolution?

1.1  – Introduction to course* 

*I used to do Dog Origins with my dog, as a metaphor for what we were about to do with humans, but my dog is getting too old and frail and I've got this beautiful new baby so I'm going to use my baby instead and talk about his development and theirs, etc...to set up both the books and the lectures to follow. I don't pass out the syllabus until the end of this first day. We go over it on the second day of class.

Notebook Assignment

·        In-class writing assignment ("What is evolution?")

1.2 – Overview of course

Reading/viewing

·        IUB, Chapter 1: Beginnings - Roberts

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

1.3 – Doing Biological Anthropology                                                 

Reading/viewing

·        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)

http://www.nature.com/scitable/knowledge/library/notes-from-the-field-a-primatologist-s-54334509

·        Expedition Rusinga (video; 8 min) https://www.youtube.com/watch?v=4y1puNyB9e8   

·        The ape in the trees – Dunsworth (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2014/02/the-ape-in-trees.html

·        How Do We Know When Our Ancestors Lost Their Tails? (video; 4 min)

http://video.pbs.org/video/2365211775/

Notebook Assignment

·        In a half-page or more: Why do humans study biological anthropology? And also, why take this course? Be as objective or as personal as you would like with your answer.

1.4 – Scientific process

Reading/viewing

·        How Science Works (video; 10 min):

https://www.youtube.com/watch?v=JH0_xC7q9tU&feature=youtu.be--flowchart

·        Understanding science: How Science Works, pages 1-21; starts here:

http://undsci.berkeley.edu/article/0_0_0/howscienceworks_01

·        Carl Sagan’s Rules for Critical Thinking and Nonsense Detection

https://www.noodle.com/articles/carl-sagans-rules-for-critical-thinking-and-nonsense-detection

·        10 Scientific Ideas That Scientists Wish You Would Stop Misusing

http://io9.com/10-scientific-ideas-that-scientists-wish-you-would-stop-1591309822 

Notebook Assignment

·        Scientific Process worksheet - Located at end of syllabus

·        Osteology and comparative anatomy worksheet - Located at end of syllabus

1.5 – Linnaeus and the Order Primates – NOTEBOOK CHECK

Reading/viewing

·        IUB, Chapter 2: Heads and brains – Roberts

·        Characteristics of Crown Primates – Kirk (Nature Education)

http://www.nature.com/scitable/knowledge/library/characteristics-of-crown-primates-105284416

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

·        Primate Expert worksheet - Located at end of syllabus

1.6 – Primate taxonomy

Reading/viewing

·        IUB, Chapter 3: Skulls and senses – Roberts

·        Many primate video clips –Posted on Sakai

·        Old World monkeys – Lawrence and Cords (Nature Education)

http://www.nature.com/scitable/knowledge/library/old-world-monkeys-83033815

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

·        In a half-page or more: Write about your primate video viewing experience, for example, you might write about what you saw, at face value, or you might want to write about what defied your expectations or what surprised you, or what you would like to learn more about.

1.7 – Locomotion and encephalization         

Reading/viewing

·        IUB, Chapter 4: Speech and gills - Roberts

·        Many primate video clips –Posted on Sakai

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

·        In a half-page or more: Without looking at any resources except for these films, come up with some categories for the different types of primate locomotion, give those categories names and definitions, and list which species in the films fall into which categories you’ve created.

1.8 – Tool use and communication

Reading/viewing

·        IUB, Chapter 5: Spine and segments – Roberts

·        The Human Spark 2 (video; 55 mins)

https://www.youtube.com/watch?v=roqTXf5UNyc&feature=kp

·        Primate locomotion – Gebo (Nature Education)

http://www.nature.com/scitable/knowledge/library/primate-locomotion-105284696

·        Primate Communication – Zuberbuhler (Nature Ed)

http://www.nature.com/scitable/knowledge/library/primate-communication-67560503

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

·        In a half-page or more: Reflect on The Human Spark 2, highlighting something you already knew and also something you learned that was brand new to you. What is the human spark?

1.9 - Diet

Reading/viewing

·        IUB, Chapter 6: Ribs, lungs and hearts– Roberts

·        IUB, Chapter 7: Guts and yolk sacs – Roberts

·        Peace Among Primates – Sapolsky (The Greater Good)

http://greatergood.berkeley.edu/article/item/peace_among_primates

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapters and be sure to include what it’s got to do with human evolution.

·        In a half-page or more: Reflect meaningfully on the article by Sapolsky, relating it to your life is fine but not required.

1.10 - Sociality

Reading/viewing

·        IUB, Chapter 8: Gonads, genitals and gestation – Roberts

·        What Influences the Size of Groups in Which Primates Choose to Live? – Chapman & Teichroeb (Nature Ed)

http://www.nature.com/scitable/knowledge/library/what-influences-the-size-of-groups-in-58068275

·        Primate Sociality and Social Systems – Swedell (Nature Ed)

http://www.nature.com/scitable/knowledge/library/primate-sociality-and-social-systems-58068905

·        Primates in communities – Lambert (Nature Ed)

http://www.nature.com/scitable/knowledge/library/primates-in-communities-the-ecology-of-competitive-59119961

Notebook Assignment

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

1.11 – Evolution and Darwin’s Evidence

Reading/viewing

·        Two chapters from The Autobiography of Charles Darwin: "Voyage…" (p. 71-81 ) and "An account of how several books arose" (p. 116- 135)

http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F1497&pageseq=1

Notebook Assignment

·        In a half-page or more: What circumstances or experiences influenced Darwin's thinking?

1.12 - Phylogeny

Reading/viewing

·        Reading a phylogenetic tree – Baum (Nature Ed)

 http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956

·        Trait Evolution on a Phylogenetic Tree – Baum (Nature Ed)

http://www.nature.com/scitable/topicpage/trait-evolution-on-a-phylogenetic-tree-relatedness-41936

Notebook Assignment

·        Phylogeny worksheet - Located at end of syllabus

1.13 – The modern evidence that Darwin wishes he had

Reading/viewing

·        YIF, Chapter 1: Finding Your Inner Fish - Shubin

·        Amazing Places, Amazing Fossils: Tiktaalik (video; 5 mins)

https://www.youtube.com/watch?v=T2vKlEUX7DI

·        YIF, Chapter 2: Getting a Grip - Shubin

·        The Ancient History of the Human Hand (video; 4 mins)

https://www.youtube.com/watch?v=RUL8hKDdY84

·        IUB, Chapter 9: On the nature of limbs – Roberts

Notebook Assignment

·        In a half-page or more: What does Shubin mean by "your inner fish"? What's the connection between a fish’s fin and your hand? How could you falsify evolutionary theory?

·        In a half-page or more:  Reflect on Roberts’ chapter and be sure to include what it’s got to do with human evolution.

1.14 – Quiz 1– NOTEBOOK CHECK

Unit 2. EXPLAIN and PREDICT. Explaining the similarities and differences. How evolution works.

Big Questions: Why are we like our parents but not exactly? Why are we like other species but not exactly? How did human traits and human variation evolve? How do we know what the last common ancestor (LCA) was like?

2.1 – Inheritance and gene expression, 1

Reading/viewing

·        YIF, Chapter 3: Handy Genes - Shubin

·        YIF, Chapter 4: Teeth Everywhere - Shubin

·        The Evolution of Your Teeth (video; 3 mins) https://www.youtube.com/watch?v=ohq3CoOKEoo

·        YIF, Chapter 5: Getting ahead - Shubin

·        Our Fishy Brain (video; 2.5 mins) http://video.pbs.org/video/2365207797/

·        Developing the Chromosome Theory – O’Connor (Nature Ed)

http://www.nature.com/scitable/topicpage/developing-the-chromosome-theory-164

·        Genetic Recombination – Clancy (Nature Ed)

http://www.nature.com/scitable/topicpage/genetic-recombination-514

·        What is a Gene? Colinearity and Transcription Units – Pray (Nature Ed)

http://www.nature.com/scitable/topicpage/what-is-a-gene-colinearity-and-transcription-430

·        RNA functions – Clancy (Nature Ed)

http://www.nature.com/scitable/topicpage/rna-functions-352

Notebook Assignment

·        In a half-page or more: What did you learn about how to do paleontology from the Shubin chapters? What does he mean by your "inner shark"?

2.2 – Inheritance and gene expression, 2

Reading/viewing

·        YIF, Chapter 6: The Best-Laid (Body) Plans - Shubin

·        YIF, Chapter 7: Adventures in Bodybuilding – Shubin

·        Hox Genes in Development: The Hox Code – Myers (Nature Ed)

·        http://www.nature.com/scitable/topicpage/hox-genes-in-development-the-hox-code-41402

·        Gregor Mendel and the Principles of Inheritance – Miko (Nature Ed)

http://www.nature.com/scitable/topicpage/gregor-mendel-and-the-principles-of-inheritance-593

·        Mendelian Genetics: Patterns of Inheritance and Single-Gene Disorders – Chial (Nature Ed)

http://www.nature.com/scitable/topicpage/mendelian-genetics-patterns-of-inheritance-and-single-966

·        Phenotypic Range of Gene Expression: Environmental Influence – Lobo & Shaw (Nature Ed)

http://www.nature.com/scitable/topicpage/phenotypic-range-of-gene-expression-environmental-influence-581

·        Genetic Dominance: Genotype-Phenotype Relationships – Miko (Nature Ed)

http://www.nature.com/scitable/topicpage/genetic-dominance-genotype-phenotype-relationships-489

·        Pleiotropy: One Gene Can Affect Multiple Traits – Lobo (Nature Ed)

http://www.nature.com/scitable/topicpage/pleiotropy-one-gene-can-affect-multiple-traits-569

·        Polygenic Inheritance and Gene Mapping – Chial (Nature Ed)

http://www.nature.com/scitable/topicpage/polygenic-inheritance-and-gene-mapping-915

Notebook Assignment

·        In a half-page or more: What are Hox genes and, according to Shubin, what do they have to do with linking a fruit fly to you? What is one benefit to being a sponge?

2.3 – Mutation and gene flow

Reading/viewing

·        YIF, Chapter 8: Making Scents - Shubin

·        YIF, Chapter 9: Vision - Shubin

·        Finding the Origins of Human Color Vision (video; 5 mins)

http://video.pbs.org/video/2365207765/

·        YIF, Chapter 10: Ears - Shubin

·        We Hear with the Bones that Reptiles Eat With (video; 4 mins)

http://video.pbs.org/video/2365207244/

·        Evolution Is Change in the Inherited Traits of a Population through Successive Generations – Forbes and Krimmel (Nature Ed)

http://www.nature.com/scitable/knowledge/library/evolution-is-change-in-the-inherited-traits-15164254

·        Mutations Are the Raw Materials of Evolution – Carlin (Nature Ed)

http://www.nature.com/scitable/knowledge/library/mutations-are-the-raw-materials-of-evolution-17395346  

Notebook Assignment

·        In a half-page or more: After reading the Shubin chapters… Is it fair to say that when you smell something, that something is touching your brain? Why is it called the eyeless gene if you can have it and still have eyes? How does hearing work? What does your ear do besides hear, and how? What does drinking lots of alcohol do to your ears?

·        Scenario building assignment - Located at end of syllabus

2.4 – Genetic drift

Reading/viewing

·        Neutral Theory: The null hypothesis of molecular evolution – Duret (Nature Ed)

http://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839

·        Things Genes Can’t Do – Weiss and Buchanan (Aeon)

http://aeon.co/magazine/nature-and-cosmos/kenneth-weiss-anne-buchanan-genetics/

Notebook Assignment

·        In a half-page or more: Reflect meaningfully on the Weiss and Buchanan article and highlight something that you already knew, but also the things that you learned that are brand new to you.

2.5 – Natural selection

Reading/viewing

·        Negative selection – Loewe (Nature Ed)

 http://www.nature.com/scitable/topicpage/negative-selection-1136

·        On the mythology of natural selection. Part I: Introduction – Weiss (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2014/07/on-mythology-of-natural-selection-part.html

·        On the mythology of natural selection. Part II: Classical Darwinism– Weiss (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2014/07/on-mythology-of-natural-selection-part_16.html

·        Secrets of Charles Darwin’s Breakthrough -  Bauer (Salon)

http://www.salon.com/2015/05/30/secrets_of_charles_darwins_breakthrough_the_real_story_of_how_we_got_to_evolution/

·        Natural selection, genetic drift and gene flow do not act in isolation in natural populations – Andrews (Nature Ed)

http://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648

·        Sexual selection – Brennan (Nature Ed)

http://www.nature.com/scitable/knowledge/library/sexual-selection-13255240

Notebook Assignment

·        Wisdom Teeth worksheet - Located at end of syllabus

2.6 – Malaria resistance and lactase persistence

Reading/viewing

·        Natural Selection: Uncovering Mechanisms of Evolutionary Adaptation to Infectious Disease – Sabeti (Nature Ed)

http://www.nature.com/scitable/topicpage/natural-selection-uncovering-mechanisms-of-evolutionary-adaptation-34539

Notebook Assignment

·        In a half-page or more: How can natural selection explain the prevalence of sickle cell anemia?

2.7 – Building evolutionary scenarios

Reading/viewing

·        Evolution is the only natural explanation – Dunsworth (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2013/06/evolution-is-only-natural-explanation.html

·        The F-words of Evolution  – Dunsworth (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2011/05/f-words-of-evolution.html

·        Another F-word of evolution  – Dunsworth (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2011/05/another-f-word-of-evolution.html

·        Mutation not natural selection drives evolution –  Tarlach (about Nei; Discover Magazine)

http://discovermagazine.com/2014/march/12-mutation-not-natural-selection-drives-evolution

Notebook Assignment

·        Drift vs. Selection worksheet - Located at end of syllabus

·        Looking back at scenario building assignment - Located at end of syllabus

2.8 – Species and speciation

Reading/viewing  

·         Why should we care about species? – Hey (Nature Ed)

http://www.nature.com/scitable/topicpage/why-should-we-care-about-species-4277923

·        Speciation: The origin of new species – Safran (Nature Ed)

http://www.nature.com/scitable/knowledge/library/speciation-the-origin-of-new-species-26230527

·        The maintenance of species diversity – Levine (Nature Ed)

http://www.nature.com/scitable/knowledge/library/the-maintenance-of-species-diversity-13240565

·        Macroevolution: Examples from the Primate World – Clee & Gonder (Nature Ed)

http://www.nature.com/scitable/knowledge/library/macroevolution-examples-from-the-primate-world-96679683

·        Primate Speciation: A Case Study of African Apes – Mitchell & Gonder (Nature Ed)

http://www.nature.com/scitable/knowledge/library/primate-speciation-a-case-study-of-african-96682434

Notebook Assignment

·        In a half-page or more: What are some hypotheses for how or why the African apes, including humans, diverged? Why might genetic divergence and species divergence not occur in sync?

2.9 – Genomics, molecular clocks, and the LCA

Reading/viewing  

·        The Onion Test – Gregory (Genomicron)

http://www.genomicron.evolverzone.com/2007/04/onion-test/

·        The Molecular Clock and Estimating Species Divergence – Ho (Nature Ed)

http://www.nature.com/scitable/topicpage/the-molecular-clock-and-estimating-species-divergence-41971

·        Lice and Human Evolution (video; 11 mins) http://video.pbs.org/video/1790635347/

Notebook Assignment

·        Speciation and molecular clocks worksheet - Located at end of syllabus

2.10 – Quiz 2 – NOTEBOOK CHECK

Unit 3. TEST. Evolving humans, past and present. Ancient evidence for our extinct hominin relatives. Modern human origins and variation. The cultural controversy over evolution.

Big Questions: How did human traits evolve? How and why do humans vary? Should we look to our ancestors as a lifestyle guide? Are we still evolving? Why is human evolution misunderstood and why is it controversial?

3.1 – Fossils, geology, and dating methods

Reading/viewing

·        Planet without apes? – Stanford (Huffington Post)

http://www.huffingtonpost.com/craig-stanford/planet-without-apes_b_1933073.html

·       How to Become a Primate Fossil – Dunsworth (Nature Ed)

http://www.nature.com/scitable/knowledge/library/how-to-become-a-primate-fossil-135630567

Notebook Assignment

·        In a half-page or more: What could lead to a future on Earth without apes? What kinds of evidence would such a process leave behind for future humans to use for explaining why apes went extinct?

3.2 – The primate fossil record; Origins of bipedalism

Reading/viewing

·        Dating Rocks and Fossils Using Geologic Methods – Peppe (Nature Ed)

http://www.nature.com/scitable/knowledge/library/dating-rocks-and-fossils-using-geologic-methods-107924044

Notebook Assignment

·        Geology worksheet - Located at end of syllabus

3.3 – Sahelanthropus, Orrorin, Ardipithecus - NOTEBOOK CHECK

Reading/viewing

·        Desktop Diaries: Tim White (video; 7 mi– Posted on Sakai)

http://www.sciencefriday.com/video/08/09/2013/desktop-diaries-tim-white.html

·        Ancient Human Ancestors: Walking in the woods (video; 4 mins)

http://video.pbs.org/video/2365207936/

·        Lucy (video; 5 mins) https://www.youtube.com/watch?v=m8Lkk6u-wQM

·        Trowelblazers (blog): http://trowelblazers.tumblr.com/

·        An Unsuitable Job for a Woman (blog): http://www.ellencurrano.me/blog/

·        Overview of hominin evolution – Pontzer (Nature Ed)

http://www.nature.com/scitable/knowledge/library/overview-of-hominin-evolution-89010983

·        The Earliest Hominins: Sahelanthropus, Orrorin, and Ardipithecus - Su (Nature Ed):

http://www.nature.com/scitable/knowledge/library/the-earliest-hominins-sahelanthropus-orrorin-and-ardipithecus-67648286  

Notebook Assignment

·        In a half-page or more: Go to each of the blogs above (Trowelblazers and An Unsuitable…), choose one woman from each and briefly discuss her contribution to scientific knowledge of the world.

3.4 – Australopithecus and Paranthropus

Reading/viewing

·        Lucy: A marvelous specimen – Schrein (Nature Ed)

http://www.nature.com/scitable/knowledge/library/lucy-a-marvelous-specimen-135716086

·        The "Robust" Australopiths – Constantino (Nature Ed)

http://www.nature.com/scitable/knowledge/library/the-robust-australopiths-84076648Notebook Notebook Assignment

·        In a half-page or more: Describe something monumental (either for paleoanthropology or for you personally) to be learned or realized thanks to Lucy.

3.5 – The first stone tool makers and Homo habilis

Reading/viewing

·        Ancient Hands, Ancient Tools (video; 5 mins) https://www.youtube.com/watch?v=5_ew9J8lpwo

·        A Primer on Paleolithic Technology – Ferraro (Nature Ed)

http://www.nature.com/scitable/knowledge/library/a-primer-on-paleolithic-technology-83034489

·        Evidence for Meat-Eating by Early Humans – Pobiner (Nature Ed)

http://www.nature.com/scitable/knowledge/library/evidence-for-meat-eating-by-early-humans-103874273

·        Archaeologists officially declare collective sigh over “Paleo Diet”

http://hells-ditch.com/2012/08/archaeologists-officially-declare-collective-sigh-over-paleo-diet/

Notebook Assignment

·        In a half-page or more:  What are the academic criticisms of the paleo diet? Can you name something at the grocery store that could count as "paleo"? Why did I ask this question?

3.6 – Homo erectus

Reading/viewing

·        Homo erectus - A Bigger, Smarter, Faster Hominin Lineage – Van Arsdale (Nature Ed)

http://www.nature.com/scitable/knowledge/library/homo-erectus-a-bigger-smarter-97879043

Notebook Assignment

·        In a half page or more: Make the case for Homo erectus being our species’ direct ancestor, as opposed to a more distant relative like the robust australopiths/Paranthropus.

3.7– Neanderthals

Reading/viewing

·        Archaic Homo sapiens – Bae (Nature Ed)

http://www.nature.com/scitable/knowledge/library/archaic-homo-sapiens-103852137

·        What happened to the Neanderthals? – Harvati (Nature Ed)

http://www.nature.com/scitable/knowledge/library/what-happened-to-the-neanderthals-68245020

·        Neanderthal Behavior – Monnier (Nature Ed)

http://www.nature.com/scitable/knowledge/library/neanderthal-behavior-59267999

Notebook Assignment

·        In a half-page or more: What happened to the Neanderthals?

3.8 - Anatomically modern Homo sapiens - RESEARCH PROJECT DUE

Reading/viewing

·        The Transition to Modern Behavior – Wurz (Nature Ed)

 http://www.nature.com/scitable/knowledge/library/the-transition-to-modern-behavior-86614339

Notebook Assignment

·        the printed parts of the Research Project will go here for day 3.8

3.9 – Models of human origins and geographic dispersal

Reading/viewing

·        The Neanderthal Inside Us (video; 4 mins)

http://www.nytimes.com/video/science/100000002887069/science-profile-svante-paabo.html?playlistId=100000002891080

·        Anthropological genetics: Inferring the history of our species through the analysis of DNA – Hodgson & Disotell (Evolution: Education and Outreach)

http://link.springer.com/article/10.1007%2Fs12052-010-0262-9#page-1

·        Testing models of modern human origins with archaeology and anatomy – Tryon & Bailey (Nature Ed)

http://www.nature.com/scitable/knowledge/library/testing-models-of-modern-human-origins-with-96639156

·        Human Evolutionary Tree – Adams (Nature Ed)

http://www.nature.com/scitable/topicpage/human-evolutionary-tree-417

·        Paternity Testing: Blood Types and DNA – Adams (Nature Ed)

http://www.nature.com/scitable/topicpage/paternity-testing-blood-types-and-dna-374

Notebook Assignment

·        In a half-page or more: Choose two models for human origins and dispersal and compare and contrast them.

3.10 -  Race and evolution’s P.R. problem

Reading/viewing

·        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

Notebook Assignment

·        In a half-page or more: Why was Ota Benga brought to the U.S.? Why was Ota Benga brought to the Bronx Zoo? Regarding issues that Ota Benga’s story raised, what do religious and evolutionary perspectives have in common? Why doesn’t a story like Ota Benga’s take place today?

3.11 – Skin pigmentation

Reading/viewing

·        Understanding Race: http://www.understandingrace.org/

·        In the Name of Darwin – Kevles (PBS) http://www.pbs.org/wgbh/evolution/darwin/nameof/

·        Human Skin Color Variation (NMNH): http://humanorigins.si.edu/evidence/genetics/skin-color

·        Human Races May Have Biological Meaning, But Races Mean Nothing About Humanity – Khan (Discover blogs)

http://blogs.discovermagazine.com/crux/2012/05/02/human-races-may-have-biological-meaning-but-races-mean-nothing-about-humanity/#.U5XBl_ldWSo

·        Are humans hard-wired for racial prejudice?  - Sapolsky (LA Times)

http://www.latimes.com/news/opinion/opinionla/la-oe-sapolsky-brain-and-race-20130728-story.html

Notebook Assignment

·        Peruse the whole Understanding Race site then take the quiz and prove that you completed it by listing the correct answers. (just letters is fine)

·        In a half-page or more: Why is evolution controversial?

3.12 – The cultural controversy over evolution

Reading/viewing

·        Does Evolutionary Theory Need a Rethink? (Nature)

http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

·        You'd have to be science illiterate to think "believe in evolution" measures science literacy –Kahan (The Cultural Cognition Project)

http://www.culturalcognition.net/blog/2014/5/24/weekend-update-youd-have-to-be-science-illiterate-to-think-b.html

·        Even Atheists Intuitively Believe in a Creator – Jacobs (Pacific Standard)

http://www.psmag.com/nature-and-technology/even-atheists-intuitively-believe-in-a-creator

·        We are not the boss of natural selection – Dunsworth (io9)

http://io9.com/we-are-not-the-boss-of-natural-selection-it-is-unpwnab-1325126849

Notebook Assignment

·        In a half page or more: Why is evolution controversial?

·        In a half-page or more: Are we still evolving? Why did I ask this question?

3.13 – Building evolutionary scenarios

Notebook Assignment

·        Revise your research project essay to make it excellent

·        In a half-page or more: After re-reading the essay you wrote in class on Day 1.1 ("What is evolution?") compose a letter to yourself highlighting what you were right about and what you were wrong about or what was incomplete about your answer based on what you learned this semester.

3.14 - Quiz 3

3.15 – Conclusion to course – NOTEBOOK CHECK

Reading/viewing

·        YIF, Chapter 11: The Meaning of It All – Shubin

·        IUB, The Making of Us - Roberts

·        Evolution reduces the meaning of life to survival and reproduction... Is that bad? – Dunsworth (The Mermaid’s Tale)

http://ecodevoevo.blogspot.com/2012/06/evolution-reduces-meaning-of-life-to.html

Notebook Assignment

·        In a half-page or more: Briefly describe what you learned this semester. And, reflect on what you're still left wondering and how you could find the answers to your remaining questions.

·        In a half-page or more: Can an evolutionary perspective have a positive impact on someone’s life? Explain why you answered yes or no.

Final Exam Time Slot: No final exam: Instead, discuss notebook and course with Dr. Dunsworth and receive grade in person between 8 am-noon today in Chafee 132.

Extra credit!!! Make a time machine then go back to the start of the semester, attend classes, take notes, read all of the things, think about all of the things, complete the assignments, and study for the quizzes.

How many diseases does it take to map a SNP? Fifteen years on

Ken and I are here in Finland, preparing to teach a week of Logical Reasoning in Human Genetics with Joe Terwilliger and colleagues.  Not statistical methods, not laboratory techniques, not the latest way to analyze sequence data.  Concepts, logical reasoning.

Ken and Joe have been reasoning logically for a long time.  They've taught this course together in many places, and they wrote at least one logically reasoned paper 15 years ago.  That paper was published in Nature Genetics.  That journal shortly afterwards made an editorial policy decision to be the loudspeaker for genetic association studies (GWAS), and would be unlikely in the extreme to publish such a view today.  But Joe often says that it could, and probably should be published again, with very few wording changes.  (He also says that if overhead projectors were still available, he'd give the same talks he gave in 1995, since the issues in human genetics haven't changed.  We have lots more data, but no fundamentally new concepts or insights regarding SNP associations and complex traits.  In fairness, though, he does update his slides -- he adds photos of the latest places he has traveled.  Looking forward to photos of Crimea this week.)

The 2000 paper was called, "How many diseases does it take to map a SNP?"  They began:

There are more than a few parallels between the California gold rush and today's frenetic drive towards linkage disequilibrium (LD) mapping based on single-nucleotide polymorphisms (SNPs). This is fuelled by a faith that the genetic determinants of complex traits are tractable, and that knowledge of genetic variation will materially improve the diagnosis, treatment or prevention of a substantial fraction of cases of the diseases that constitute the major public health burden of industrialized nations. Much of the enthusiasm is based on the hope that the marginal effects of common allelic variants account for a substantial proportion of the population risk for such diseases in a usefully predictive way. A main area of effort has been to develop better molecular and statistical technologies often evaluated by the question: how many SNPs (or other markers) do we need to map genes for complex diseases? We think the question is inappropriately posed, as the problem may be one primarily of biology rather than technology.

Today, emphasis is more on ever larger sample sizes to find rare alleles, since common alleles turned out not to be the magical answer, but the issues are the same.  The problem is biological, rather than one of sample size. And not only do we have at least as much causal complexity due to environmental factors, but to the mix have been added the comparable complex 'genetic' causal factors as epigenetic modification of DNA affecting gene expression, and the potential contributions of highly complex microbiome.

The idea of mapping diseases from SNPs is that markers will be near the disease allele.  But, there are problems with this, as GWAS are successfully showing.

If traits do not strongly predict underlying genotypes, that is, if P(GP|Ph) is small, linkage and LD mapping may have very low power or may not work at all. As an extreme example, one's genotype cannot be reliably determined by merely stepping on the bathroom scale! But even if this could be done, there is a widespread but invalid belief that because something can be mapped (that is, P(GP|Ph) is high), the causal predictive power of the genotype (P(Ph|GP); Fig 1, blue arrow) will also be high. In fact, we have surprisingly little data on this latter topic, which requires extensive sampling from the general population, rather than patients. Note that the opposite can also be untrue—that is, if P(Ph|GP) is high it does not mean P(GP|Ph) will be high, as in genetically heterogeneous mendelian disorders such as retinitis pigmentosa. It is important to note that when we speak of P(Ph|GP) in this context, we speak of the marginal mode of inheritance, which is only valid for consideration of singletons, and relatives will not have independent and identically distributed penetrances (even without assuming epistasis or gene-environment interactions) because the other genetic and environmental factors are also correlated among them! Similar arguments can be made about detectance, P(GP|Ph), which must always be a function of the ascertainment, something that is often overlooked in the literature when investigators make comparisons of power for different study designs

 Figure 1. Schematic model of trait aetiology.
The phenotype under study, Ph, is influenced by diverse genetic, environmental and cultural factors (with interactions indicated in simplified form). Genetic factors may include many loci of small or large effect, G_Pi, and polygenic background. Marker genotypes, Gx, are near to (and hopefully correlated with) genetic factor, G_p, that affects the phenotype. Genetic epidemiology tries to correlate G_x with Ph to localize G_p. Above the diagram, the horizontal lines represent different copies of a chromosome; vertical hash marks show marker loci in and around the gene, G_p, affecting the trait. The red P_i are the chromosomal locations of aetiologically relevant variants, relative to Ph.

Other inconvenient biological issues, mentioned in the paper, include that linkage disequilibrium is stochastic, and this has implications for the use of SNPs in disease mapping, that regulatory rather than protein coding sites often affect disease risk, and these are generally impossible to identify (see below), that late-onset chronic diseases are much more complex than the clearly genetic pediatric disease, that the most effective disease mapping and association studies are done in "selective samples of individuals or families at high risk relative to the average risk in the population, and from populations with unusual histories" (hence, Joe's eclectic and interesting travelogue), etiology tends to be very heterogeneous, phenotype can't predict genotype and vice versa, environmental effects can be significant, but are unpredictable and often impossible to identify, and so on.

Whole genome sequencing will not be a general miracle cure.  Exome sequencing can sometimes find  coding variants that have strong effects because we know how to identify exomes and how to read their code.  But many if not most mapped sites for complex traits, as might be expected, are in regulatory regions.  Yet we are still quite inept at identifying regulatory regions, for many reasons not least having to do with their complexity and fluidity among individuals and populations.  So whole genome sequencing will likely have to be analyzed by using markers, as in GWAS, and that will not automatically show us where key regulatory affects are located or how they work.  If these are too heterogeneous, they'll vary hugely, so that mapping will still face the complexity problem.  Time will tell what transpires.

The problems faced in treating complex diseases as if they were Mendel's peas show, without invoking the term in its faddish sense, that 'complexity' is a subject that needs its own operating framework, a new twenty-first rather than nineteenth—or even twentieth—century genetics.

So, if the data are better and less costly now than 15 years ago, the basic issues haven't changed.  

Logical Reasoning (we hope!) in Finland

On  Monday we begin an instance of our 5-day mini-course on conceptual issues in human genetics. We did this last August in Helsinki, Finland, where we have ongoing collaborations.  We've done the course in Finland several times over the years, and in Madrid, Berlin, and Venezuela.  This year, by request of parties in Finland, it will be offered in Oulu, along the northwest coast of the country.  The students are largely, but not only, from Finland.  Others are typically from various EU and sometimes other, countries.  It is a series of talks by us, Joe Terwilliger (close friend of Kim Il Ung, and itinerant tuba player and Abe Lincoln impersonator), Markus Perola a serious Finnish physician and genetics researcher, Tero Hiekkalinna, a computer person and, for some reason, Pabst beer fanatic, and Johannes Kettunen, whom we've not yet met but is part of the relevant Finnish genetic research establishment.

The objective is not to give lectures on modern technologies and details, but to discuss the conceptual issues in evolutionary and biomedical genetics, the nature of approaches, study designs and inferential logic, including topics in the philosophy of science that relate to how we evaluate data to draw conclusions and modify our understanding.

The students are usually graduate students, post-docs, and research or medical professionals. This is for discussion--no exams!  The resulting interactions have always been interesting and we assume they will be so again this year.

We'll post about this course if or as issues relevant to MT readers arise.

Dim MT

Things have been slow on the MT this summer.  Ken and I have been preparing for this year's "Logical Reasoning in Human Genetics" course, happening next week in Oulu, Finland and Holly and I have been working hard on a book.  So, Ken and I probably won't be posting much again until the end of August, but it looks like Holly is gearing up to do some blogging while we're gone, so check back for some exquisite Holly-ness.

Oulu, Finland, from gofinland.org

Wordsworth(less), but interesting

I am a fan of William Wordsworth's poetry.  In particular, he was one of the leaders of a naturalism movement, that changed poetry from rather formal or even stuffy, difficult-structured material laced if not laden with arcane references to the classics or the Bible, that only the desperately intellectual could actually read.  Some of it, like Milton's Paradise Lost, is great (with an annotated edition!), but most of it is just difficult.

By contrast Wordsworth strolled through Nature, especially of his native England and its peaceful, scenic Lake District, and wrote in a simpler, ordinary-language way about the splendors, trials, and beauties of what he saw.  Most of his works are very fine, in my particular view.  So, to pass some time, I decided to read a poem called Peter Bell.  It was published in 1819.  Unfortunately, I agree with many critics, especially of his own time, that this was a real loser.  It's corny and implausible to the extreme.  However,  its Prologue, though hardly related to what followed, provided a very interesting description of what was known of cosmology at the time, an imaginary voyage into space. In light of recent space ventures, and images from what's really out there, rather than just the imagination, I thought this Prologue would be interesting to post, on a lazy summer's day:

Peter Bell

William Wordsworth, 1819

Prologue

There's something in a flying horse, 
There's something in a huge balloon; 
But through the clouds I'll never float 
Until I have a little Boat, 
Shaped like the crescent-moon. 

And now I 'have' a little Boat, 
In shape a very crescent-moon 
Fast through the clouds my boat can sail; 
But if perchance your faith should fail, 
Look up--and you shall see me soon! 

The woods, my Friends, are round you roaring, 
Rocking and roaring like a sea; 
The noise of danger's in your ears, 
And ye have all a thousand fears 
Both for my little Boat and me! 

Meanwhile untroubled I admire 
The pointed horns of my canoe; 
And, did not pity touch my breast, 
To see how ye are all distrest, 
Till my ribs ached, I'd laugh at you! 

Away we go, my Boat and I-- 
Frail man ne'er sate in such another; 
Whether among the winds we strive, 
Or deep into the clouds we dive, 
Each is contented with the other. 

Away we go--and what care we 
For treasons, tumults, and for wars? 
We are as calm in our delight 
As is the crescent-moon so bright 
Among the scattered stars. 

Up goes my Boat among the stars 
Through many a breathless field of light, 
Through many a long blue field of ether, 
Leaving ten thousand stars beneath her: 
Up goes my little Boat so bright! 

The Crab, the Scorpion, and the Bull-- 
We pry among them all; have shot 
High o'er the red-haired race of Mars, 
Covered from top to toe with scars; 
Such company I like it not! 

The towns in Saturn are decayed, 
And melancholy Spectres throng them;-- 
The Pleiads, that appear to kiss 
Each other in the vast abyss, 
With joy I sail among them. 

Swift Mercury resounds with mirth, 
Great Jove is full of stately bowers; 
But these, and all that they contain, 
What are they to that tiny grain, 
That little Earth of ours? 

Then back to Earth, the dear green Earth:-- 
Whole ages if I here should roam, 
The world for my remarks and me 
Would not a whit the better be; 
I've left my heart at home. 

See! there she is, the matchless Earth! 
There spreads the famed Pacific Ocean! 
Old Andes thrusts yon craggy spear 
Through the grey clouds; the Alps are here, 
Like waters in commotion! 

Yon tawny slip is Libya's sands; 
That silver thread the river Dnieper! 
And look, where clothed in brightest green 
Is a sweet Isle, of isles the Queen; 
Ye fairies, from all evil keep her! 

And see the town where I was born! 
Around those happy fields we span 
In boyish gambols;--I was lost 
Where I have been, but on this coast 
I feel I am a man. 

Never did fifty things at once 
Appear so lovely, never, never;-- 
How tunefully the forests ring! 
To hear the earth's soft murmuring 
Thus could I hang for ever! 

"Shame on you!" cried my little Boat, 
"Was ever such a homesick Loon, 
Within a living Boat to sit, 
And make no better use of it; 
A Boat twin-sister of the crescent-moon! 

"Ne'er in the breast of full-grown Poet 
Fluttered so faint a heart before;-- 
Was it the music of the spheres 
That overpowered your mortal ears? 
--Such din shall trouble them no more. 

"These nether precincts do not lack 
Charms of their own;--then come with me; 
I want a comrade, and for you 
There's nothing that I would not do; 
Nought is there that you shall not see. 

"Haste! and above Siberian snows 
We'll sport amid the boreal morning; 
Will mingle with her lustres gliding 
Among the stars, the stars now hiding, 
And now the stars adorning. 

"I know the secrets of a land 
Where human foot did never stray; 
Fair is that land as evening skies, 
And cool, though in the depth it lies 
Of burning Africa. 0 

"Or we'll into the realm of Faery, 
Among the lovely shades of things; 
The shadowy forms of mountains bare, 
And streams, and bowers, and ladies fair, 
The shades of palaces and kings! 

"Or, if you thirst with hardy zeal 
Less quiet regions to explore, 
Prompt voyage shall to you reveal 
How earth and heaven are taught to feel 
The might of magic lore!" 

"My little vagrant Form of light, 
My gay and beautiful Canoe, 
Well have you played your friendly part; 
As kindly take what from my heart 
Experience forces--then adieu! 

"Temptation lurks among your words; 
But, while these pleasures you're pursuing 
Without impediment or let, 
No wonder if you quite forget 
What on the earth is doing. 

"There was a time when all mankind 
Did listen with a faith sincere 
To tuneful tongues in mystery versed; 
'Then' Poets fearlessly rehearsed 
The wonders of a wild career. 

"Go--(but the world's a sleepy world, 
And 'tis, I fear, an age too late) 
Take with you some ambitious Youth! 
For, restless Wanderer! I, in truth, 
Am all unfit to be your mate. 

"Long have I loved what I behold, 
The night that calms, the day that cheers; 
The common growth of mother-earth 
Suffices me--her tears, her mirth, 
Her humblest mirth and tears. 

"The dragon's wing, the magic ring, 
I shall not covet for my dower, 
If I along that lowly way 
With sympathetic heart may stray, 
And with a soul of power. 

"These given, what more need I desire 
To stir, to soothe, or elevate? 
What nobler marvels than the mind 
May in life's daily prospect find, 
May find or there create? 

"A potent wand doth Sorrow wield; 
What spell so strong as guilty Fear! 
Repentance is a tender Sprite; 
If aught on earth have heavenly might, 
'Tis lodged within her silent tear. 

"But grant my wishes,--let us now 
Descend from this ethereal height; 
Then take thy way, adventurous Skiff, 
More daring far than Hippogriff, 
And be thy own delight! 

"To the stone-table in my garden, 
Loved haunt of many a summer hour, 
The Squire is come: his daughter Bess 
Beside him in the cool recess 
Sits blooming like a flower. 

"With these are many more convened; 
They know not I have been so far;-- 
I see them there, in number nine, 
Beneath the spreading Weymouth-pine! 
I see them--there they are! 

"There sits the Vicar and his Dame; 
And there my good friend, Stephen Otter; 
And, ere the light of evening fail, 
To them I must relate the Tale 
Of Peter Bell the Potter." 

Off flew the Boat--away she flees, 
Spurning her freight with indignation! 
And I, as well as I was able, 
On two poor legs, toward my stone-table 
Limped on with sore vexation. 

"O, here he is!" cried little Bess-- 
She saw me at the garden-door; 
"We've waited anxiously and long," 
They cried, and all around me throng, 
Full nine of them or more! 

"Reproach me not--your fears be still-- 
Be thankful we again have met;-- 
Resume, my Friends! within the shade 
Your seats, and quickly shall be paid 
The well-remembered debt." 

I spake with faltering voice, like one 
Not wholly rescued from the pale 
Of a wild dream, or worse illusion; 
But, straight, to cover my confusion, 
Began the promised Tale. 

Heart disease - the 7.5% solution?

Statins are in the news again, and not just because of the new PCSK9-based drugs, at least one of which is likely to be approved by the FDA this week, probably for a small class of at-risk patients.  These drugs will drive LDL cholesterol levels through the floor, while generating an estimated 17.8 billion for pharma by the year 2023 (and that's before we even know whether they will reduce risk of heart attack and stroke).

No, this is about your run-of-the-mill class of LDL-lowering statins.  In late 2013, the American Heart Association and the American College of Cardiology recommended new guidelines for determining who should be on statins.

• anyone who has cardiovascular disease, including angina (chest pain with exercise or stress), a previous heart attack or stroke, or other related conditions

• anyone with a very high level of harmful LDL cholesterol (generally an LDL above greater than 190 milligrams per deciliter of blood [mg/dL])

• anyone with diabetes between the ages of 40 and 75 years

• anyone with a greater than 7.5% chance of having a heart attack or stroke or developing other form of cardiovascular disease in the next 10 years.

Risk score is based on the ASCVD calculator, which uses basic data (age, sex, total cholesterol, HDL cholesterol, systolic blood pressure, and smoking and diabetes status) to calculate risk.  Unlike the previous Adult Treatment Panel III (ATP III) guidelines which were based on a target LDL level and risk factors determined by the long-term Framingham heart disease study (using the Framingham Risk Calculator), these new guidelines were based on a risk profile.  With these new guidelines, it was thought that about 13 million additional Americans would benefit from statins, for a total of a third of all Americans.

A study published in the Journal of the American Medical Association last week asks whether these guidelines were better at identifying at-risk individuals than the old ATP III guidelines.  The prospective study followed up 2435 people from the Framingham study who had never taken statins.  Based on the ATP III guidelines, 14% would have been 'eligible' compared with 39%, based on the 2013 guidelines.

The median follow-up was 9.4 (interquartile range, 8.1-10.1) years. There were a total of 74 (3.0%) incident CVD events (40 nonfatal myocardial infarctions, 31 nonfatal strokes, and 3 with fatal CHD) and 43 (1.8%) incident CHD events (40 nonfatal myocardial infarctions and 3 with fatal CHD).

Among those eligible for statin treatment by the ATP III guidelines, 6.9% (24/348) developed incident CVD compared with 2.4% (50/2087) among noneligible participants (HR, 3.1; 95% CI, 1.9-5.0; P less than .001). Applying the ACC/AHA guidelines, among those eligible for statin treatment, 6.3% (59/941) developed incident CVD compared with only 1.0% (15/1494) among those not eligible (HR, 6.8; 95% CI, 3.8-11.9; P less than .001). Therefore, the HR of having incident CVD among statin-eligible vs noneligible participants was significantly higher when applying the ACC/AHA guidelines’ statin eligibility criteria compared with the ATP III guidelines (P less than .001).

That is, according to this study, the 2013 ACC/AHA guidelines identified more people at risk of heart disease than the ATP III guidelines.  That's presumably progress in understanding heart disease risk, and so a good thing. (Does anyone else find the use of the word 'eligible' odd, though?  Like statins are a reward for passing the risk threshold?)

But why don't they ask about family history?  That is one of the most useful bits of data a physician can have about a patient's risk of heart disease (and other things).  Is it too cynical to suggest that acknowledging its usefulness might diminish the importance of what has been learned from the Framingham study?

Less cynically, one reason, though we don't know if the various investigators considered it in this way, is that family history integrates all factors, including those that are being specifically measured (like blood pressure, LDL levels, and so on). Whether they are genetic or environmental, they went into determining whether the relative had heart disease.  So counting family history and LDL, or for that matter, weight and BMI, also not included, may be redundant to an unknown extent.  For risk factors, this would perhaps inflate the apparent risk, but for protective factors the opposite.  But family history is debatably the best single factor, perhaps as important as all the test-battery factors.  At least, it's important to consider why that alone, or that somehow corrected for redundancy, should be a part of all of this.

So, apparently we don't know more about the causes of ASCVD now than we did before 2013, we're just evaluating what we know differently.  So, assuming that statins really do reduce risk of ASCVD, that more people are 'eligible' is thought to be a good thing.  Though, as the JAMA commentary on this article notes in urging increased treatment with statins, "Although a 10-year ASCVD risk threshold of 7.5% or higher might initially seem to be a low threshold, many, indeed most, CVD events occur among the low-risk members of the population."

Wait!  "Low-risk" is defined by us, based on what we know about heart disease!  Our understanding is clearly wrong if all these 'low-risk' people are really high-risk!  Not to mention that there's clearly a huge false-positive pool if a risk estimate of 7.5 out of 100 makes a person eligible for statins!  That means that 92.5 of those 100 people are taking statins even though they weren't going to have a stroke or heart attack.  And, all this means, at least to me, that we really don't understand what causes heart attacks or stroke. The Framingham study identified cholesterol, particularly LDL, as a risk factor, but we're not really sure why, and we don't know what levels are in fact most risky, and people with low LDL can have heart attacks, too.  Statins may or may not work by reducing LDL cholesterol, and lower LDL cholesterol may or may not reduce risk.

And, statins can have serious side effects -- physical as well as the cost burden.  So, if of 100 people taking statins a large majority weren't going to have heart attacks anyway, statins are causing a lot of unnecessary side effects without preventing disease.  Though, to be fair, physicians can't predict the future, and must do their best with the information they have.  They don't know who will or won't have a heart attack, because epidemiology hasn't given them enough information.  They've got to treat people with 7.5% risk as if they are at 100% risk of disease.

So, it's not physicians who are failing here, it's epidemiologists.  But I'll even be fair to epidemiologists -- it's the methods, based on population data and probability (which may not even exist; see our series of posts on this starting here), that are failing.  Epidemiologists are doing their best with what they've got.  We don't know precisely what causes heart attacks, but to prevent them, we've got to treat people with low risk as though they are at high risk, and that's because some people at low risk really are at high risk.

No one has 7.5% of a heart attack.  They have 0% or 100% of a heart attack. Figuring out who is in which group is currently impossible.  What we do know for certain is that putting everyone on statins, as though they have 100% risk is very good for the pharmaceutical companies that make them, and good for people whose heart attack or stroke was prevented, even if we will never know which people these were, and unnecessary and even harmful for everyone else.

This is a lousy way to do medicine.  But it's currently the only way we've got.

The wonder of it all

We've expressed our skepticism about aspects of the Pluto mission, as well as many other aspects of our own science (genetics and evolution).  Still, there's the wonder of it all, and two verses come to mind, that you may have been assigned to read in school: 

The World is Too Much With Us  (William Wordsworth)

The world is too much with us; late and soon,

Getting and spending, we lay waste our powers;—

Little we see in Nature that is ours;

We have given our hearts away, a sordid boon!

This Sea that bares her bosom to the moon;

The winds that will be howling at all hours,

And are up-gathered now like sleeping flowers;

For this, for everything, we are out of tune;

It moves us not. Great God! I’d rather be

A Pagan suckled in a creed outworn;

So might I, standing on this pleasant lea,

Have glimpses that would make me less forlorn;

Have sight of Proteus rising from the sea;

Or hear old Triton blow his wreathèd horn.

   -------------------

When I Heard the Learn'd Astronomer (Walt Whitman)

When I heard the learn’d astronomer,

When the proofs, the figures, were ranged in columns before me,

When I was shown the charts and diagrams, to add, divide, and measure them,

When I sitting heard the astronomer where he lectured with much applause in the lecture-room,

How soon unaccountable I became tired and sick,

Till rising and gliding out I wander’d off by myself,

In the mystical moist night-air, and from time to time,

Look’d up in perfect silence at the stars.

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.....And I guess we'll finish with another by Wordsworth, a more contemplative view of the subtleties involved:

Star-Gazers
What crowd is this? what have we here! we must not pass it by;
A Telescope upon its frame, and pointed to the sky:
Long is it as a barber's pole, or mast of little boat,
Some little pleasure-skiff, that doth on Thames's waters float.

The Showman chooses well his place, 'tis Leicester's busy Square;
And is as happy in his night, for the heavens are blue and fair;
Calm, though impatient, is the crowd; each stands ready with the fee,
And envies him that's looking;--what an insight must it be!

Yet, Showman, where can lie the cause? Shall thy Implement have blame,
A boaster, that when he is tried, fails, and is put to shame? 
Or is it good as others are, and be their eyes in fault?
Their eyes, or minds? or, finally, is yon resplendent vault?

Is nothing of that radiant pomp so good as we have here?
Or gives a thing but small delight that never can be dear?
The silver moon with all her vales, and hills of mightiest fame,
Doth she betray us when they're seen? or are they but a name?

Or is it rather that Conceit rapacious is and strong,
And bounty never yields so much but it seems to do her wrong?
Or is it, that when human Souls a journey long have had
And are returned into themselves, they cannot but be sad? 

Or must we be constrained to think that these Spectators rude,
Poor in estate, of manners base, men of the multitude,
Have souls which never yet have risen, and therefore prostrate lie?
No, no, this cannot be;--men thirst for power and majesty!

Does, then, a deep and earnest thought the blissful mind employ
Of him who gazes, or has gazed? a grave and steady joy,
That doth reject all show of pride, admits no outward sign,
Because not of this noisy world, but silent and divine!

Whatever be the cause, 'tis sure that they who pry and pore
Seem to meet with little gain, seem less happy than before: 
One after One they take their turn, nor have I one espied
That doth not slackly go away, as if dissatisfied. 

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As these verses suggest, regardless of any other issues, there is no mistaking the wonders of Nature out there, or up there, and thinking about what it all is, and means.