2016's textbook-free Intro to BioAnth course

This is an abridged syllabus for my course this fall. Apologies for any formatting issues, but copying and pasting from Word into Blogger isn't a party. For background on my textbook-free approach and overall philosophy for teaching evolution, please see this post and the links therein.  Cheers to all you learners, teachers, and professors!

Fall 2016

APG 201: Human Origins and Evolution

3 credits

Dr. Holly Dunsworth

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 B4 (information literacy).

Required reading 

• Your Inner Fish by Neil Shubin

• The Incredible Unlikeliness of Being by Alice Roberts

• Additional articles are linked in the syllabus, or posted on our course site on Sakai

Non-required reference

• Biological Anthropology, 3rd Edition by Stanford, et al. (2013, Pearson) – standard textbook (a copy is on reserve at the library, along with Shubin and Roberts)

Quizzes 1, 2, and 3 (15% each); Research Project (15%; a two part exercise in information literacy, evolutionary thinking, and writing); Portfolio (40%; a thin folder or binder containing all the assignments in chronological order.) 

Schedule

Unit 1. Observe and Explain - This view of life. Our place in nature. What is the anthropological perspective? What about the biocultural? 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?

7-Sep       1.1-Introduction to course (reflecting on knowledge to spark semester)

9-Sep 1.2-Overview of course (syllabus, anthropology, etc...)

12-Sep 1.3-Scientific process  

14-Sep 1.4-Linnaeus and the Order Primates 

16-Sep 1.5-Overview of Primate taxonomy; Diet 

19-Sep 1.6-Primate locomotion and encephalization

21-Sep 1.7-Primate tool use and communication

23-Sep 1.8-Primate sociality

26-Sep 1.9-Evolution and Darwin's evidence

28-Sep 1.10-Phylogeny

30-Sep 1.11-no class today

3-Oct 1.12-Modern evidence Darwin wishes he had

5-Oct Quiz 1

Unit 2. Explain and Predict - Explaining the similarities and differences. How evolution works. 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 does evolution occur? How do we know what the last common ancestor (LCA) was like?

7-Oct 2.1-Inheritance and gene expression, 1

10-Oct n/a-Columbus Day, classes do not meet

12-Oct 2.2-Inheritance and gene expression, 2

14-Oct 2.3-Inheritance and gene expression, 3

17-Oct 2.4-Mutation and gene flow

19-Oct 2.5-Natural selection

21-Oct 2.6-More natural selection; Genetic drift

24-Oct 2.7-Malaria resistance and lactase persistence

26-Oct 2.8-Building evolutionary scenarios

28-Oct 2.9- Origins of Bipedalism; Species and speciation 

31-Oct 2.10 -Genomics, molecular clocks, and the LCA

2-Nov Quiz 2 -

Unit 3. Test and Observe - Evolving humans, past and present. Ancient evidence for our extinct hominin relatives. Modern human origins and variation. The cultural controversy over evolution.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? Is evolution racist? Why is human evolution misunderstood and why is it controversial? 

4-Nov 3.1-The LCA and the earliest hominins

7-Nov 3.2-Australopithecus

9-Nov 3.3-Paranthropus  (Research Project Part 1, due to Sakai by 9 am)

11-Nov n/a-Veteran's Day, classes do not meet 

14-Nov 3.4-earliest Homo  

16-Nov 3.5-Homo erectus

18-Nov 3.6-Neanderthals

21-Nov 3.7-Anatomically modern Homo sapiens

23-Nov 3.8-no class today (Research Project Part 2 due to portfolio)

25-Nov n/a-Thanksgiving Break, classes do not meet

28-Nov 3.9-The origins and evolution of human skin color variation

30-Nov 3.10-The origins and evolution of human skin color variation

2-Dec 3.11-The origins and evolution of human skin color variation

5-Dec 3.12-The origins and evolution of human skin color variation

7-Dec 3.13-The origins and evolution of human skin color variation

9-Dec 3.14-Race, racism and the cultural controversy over evolution

12-Dec 3.15-Conclusions (Portfolios due at the start of class today)

14-Dec Quiz 3 (During time of final exam)

Portfolio Assignments and Lecture Resources

1.1   

Assigned Reading/viewing

·        IUB, Chapter 1: Beginnings - Roberts

Portfolio Assignment

·        In-class assignment

Additional resources

·         “Do animals know where babies come from?” by H. Dunsworth (Scientific American)- Located on Sakai

1.2

Assigned Reading/viewing

·        IUB, Chapter 2: Heads and brains – Roberts

Portfolio Assignment

·        Osteology and comparative anatomy worksheet - Located on Sakai

Additional 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)

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/

1.3

Assigned 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 

Portfolio Assignment

·        Scientific Process worksheet - Located on Sakai

1.4

Assigned Reading/viewing

·        Characteristics of Crown Primates – Kirk (Nature Education)

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

Portfolio Assignment

·        Primate Expert worksheet - Located on Sakai

1.5

Reading/viewing

·        Many primate video clips –Posted on Sakai

Portfolio Assignment

·        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. Also: 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.

Additional resources

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

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

1.6      

Assigned Reading/viewing

·        IUB, Chapter 3: Skulls and senses – Roberts

Portfolio 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.

Additional resources

·        Primate locomotion – Gebo (Nature Education)

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

1.7

Assigned Reading/viewing

·        IUB, Chapter 4: Speech and gills - Roberts

Portfolio 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.

Additional resources

·        Primate Communication – Zuberbuhler (Nature Ed)

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

1.8

Assigned Reading/viewing

·        The Human Spark 2 (video; 55 mins)

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

Portfolio Assignment

·        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?

Additional resources

·        Peace Among Primates – Sapolsky (The Greater Good)

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

·        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

1.9

Assigned  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

Portfolio Assignment

·        In a half-page or more: According to your impression of Darwin’s writings, what circumstances or experiences influenced Darwin's thinking?

1.10

Assigned 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

Portfolio Assignment

·        Phylogeny worksheet - Located on Sakai

1.11

Assigned  Reading/viewing

·        IUB, Chapter 5: Spine and segments – Roberts

Portfolio 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.

1.12

Assigned Reading/viewing

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

·        YIF, Chapter 2: Getting a Grip - Shubin

Portfolio 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?

Additional resources

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

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

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

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

2.1

Assigned Reading/viewing

·        YIF, Chapter 3: Handy Genes – Shubin

Portfolio Assignment

·        In a half-page or more: What the heck is this Sonic hedgehog thing that Shubin’s talking about?

2.2

Assigned Reading/viewing

·        YIF, Chapter 4: Teeth Everywhere – Shubin

Portfolio Assignment

·        In a half-page or more: Teeth make better fossils than bones and so they preserve more often and fill up the fossil record. If you want to do paleontology, you need to get excited about teeth. Why are teeth exciting?

Additional resources

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

·        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

2.3

Assigned reading/viewing

·        YIF, Chapter 5: Getting ahead – Shubin

Portfolio Assignment

·        In a half-page or more: What does Shubin mean by your "inner shark"?

Additional resources

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

·        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

2.4

Assigned Reading/viewing

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

·        YIF, Chapter 7: Adventures in Bodybuilding – Shubin

Portfolio 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?

Additional resources

·        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

2.5

Portfolio Assignment

·        Scenario building assignment (Part 1) - Located on Sakai

Additional Resources

·        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

2.6

Portfolio Assignment

·        Wisdom tooth assignment - Located on Sakai

Additional Resources

·        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

·        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/

2.7

Portfolio Assignment

·        Scenario building assignment (Part 2) - Located on Sakai

Additional resources

·        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

2.8

Assigned 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

Portfolio Assignment

·        Scenario building assignment (Part 3) - Located on Sakai

Additional resources

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

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

2.9

Assigned Reading/viewing

·        YIF, Chapter 8: Making Scents - Shubin

·        YIF, Chapter 9: Vision - Shubin

·        YIF, Chapter 10: Ears – Shubin

Portfolio 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?

Additional resources

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

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

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

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

·        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

2.10

Assigned Reading/viewing

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

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

Portfolio 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.

Additional resources

·        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/

·        Planet without apes? – Stanford (Huffington Post)

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

3.1

Reading/viewing

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

Portfolio 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.

Additional resources

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

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

·        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

·        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/

·        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 

3.2

Reading/viewing

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

Portfolio 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.

Additional resources

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

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

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

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

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

3.3

·        By 9 am this morning, upload Research Project Part 1 to Sakai (so there is nothing to do today for your Portfolio)

Additional resources

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

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

3.4

Assigned Reading/viewing

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

Portfolio 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.

Additional resources

·        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/

3.5

Reading/viewing

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

Portfolio 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.

Additional resources

·        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

3.6

Reading/viewing

·        IUB, Chapter 10: Hip to Toe – Roberts

Portfolio 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.

Additional resources

·        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

3.7

Reading/viewing

·        IUB, Chapter 11: Shoulders and Thumbs – Roberts

Portfolio 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

Additional resources

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

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

·        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

3.8

Portfolio Assignment

·        Print Research Project Part 2 and include it here

3.9

Assigned reading/viewing

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

Portfolio Assignment

·        Peruse the whole site then take the Human Variation Quiz at Understanding Race and record the correct answers (just the letters suffice).
(Plus whatever we accomplished in class in the Skin Color workbook and any homework I assigned to do with it.)

Additional Resources

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

3.10

Portfolio Assignment

·        In a half-page or more: Describe all the factors you can think of that contributed to the skin color you have today, right now. Would you be answering this question, in this course, if your skin color were different? Why or why not?

(Plus whatever we accomplished in class in the Skin Color workbook and any homework I assigned to do with it.)

3.11

Assigned reading/viewing

·        Humans never stopped evolving – Hawks (The Scientist)

http://www.the-scientist.com/?articles.view/articleNo/46651/title/humans-never-stopped-evolving/

Portfolio Assignment

·        In a half-page or more: Are we still evolving? Why is this a question?
(Plus whatever we accomplished in class in the Skin Color workbook and any homework I assigned to do with it.)

Additional resources

·        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

3.12

Portfolio Assignment

·        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.
(Plus whatever we accomplished in class in the Skin Color workbook and any homework I assigned to do with it.)

3.13

Portfolio Assignment

·        The complete student workbook for the Smithsonian’s “Evolution of Human Skin Color” curriculum (as much as we covered in class from days 3.9-3.13) - You should have already obtained and printed the workbook from Sakai for classroom work starting on 3.9. Here's where it lives publicly: http://humanorigins.si.edu/education/teaching-evolution-through-human-examples

3.14

Assigned 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

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

·         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

Portfolio Assignment

·        In a half-page or more: What’s the link between racism and evolution? Is Ota Benga’s treatment justified by evolutionary theory? Is evolutionary theory racist?

3.15 – SUBMIT ENTIRE PORTFOLIO (including this assignment) AT THE START OF CLASS TODAY

Reading/viewing

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

·        IUB, Chapter 12: 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

Portfolio Assignments

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

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.

You are a Homo sapiens. We are all Homo sapiens. 

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

Confessions of a Contrarian

If you care about some area of human life, and you look at it closely, it probably won't take you long to become a contrarian about it: to know it is to see its weaknesses.  Our fallibilities as a species are everywhere to be found. We could just accept that and motor along, or we can recognize, react, and resist!  Unfortunately, the older you get and perhaps the more secure (so you can afford to criticize), the more flaws you may see and the more you may wish to try to change them.

That often means criticizing, in part because better ways of doing things may not be obvious, thus suggesting positive changes not so easy.  Of course, established parts of society resist change.  The 'in's' usually want to protect their privilege, resources, and status quo.  The young may not see the issues or may be intimidated by the structures because it's risky to critique them (making it harder to get jobs, grants, etc.).  Resistance is difficult and often doesn't work.

But if you've read much of what we have to say here on MT, you know that I, at least, feel that pointing out problems is important, despite the obstacles.  Change often means mass, and often grass-roots, resistance.  But first, it requires recognition of the problems and that often in turn requires repetition.  If something is worth saying, and it's something people don't want to hear because it may threaten comfortable business-as-usual, it's worth repeating.  I do that sort of repetition here, but usually in the context of reasons for my view and/or thoughts about how to change things.

Some may see this as contrarian.  To that, I must plead guilty.

We here are not the only ones to note what is going on in terms of funding, careers in science, hyperbole in science reporting, PhDs without jobs or careers, but lots of debt, well into their 30's, the huge locked-in funding system of well-heeled, locked-in un-killable projects, universities hungry for more graduate students even though this mainly is for their own bragging rights (since the students aren't getting jobs), and so on.  These are real problems worth crabbing about.

Also, the inertia of science is such that, at present, we are ever-increasing the size and duration of projects that essentially just do the same thing as has been done for years before, with only minor tweaks in technology and major increases in scale, as if scale is a good substitute for thought--indeed, it's often presented that way, in the common implicit or even sometimes explicit boasting about hypothesis-free science.

Albert Einstein is often credited (falsely, apparently) with defining insanity as continuing to do the same thing and hoping the result will be different.   Even showing deep flaws in what is going on is often presented as a reason for doing even more of the same--for example, the commentary and article by Lek et al. in the 18 August issue of Nature.  Similar points can be made about the highly publicized issues of statistical inference that we've posted about before.  Nobody wants to, or perhaps knows how to, or dares to say that what we're doing is continuing along a path of wishful-thinking. Science is an Establishment that is naturally inertial and resists change.  But I believe the problems need to be pointed out.

Wendell Berry; Wikipedia (photo by By Guy Mendes) 

It may take a contrarian to assert this point of view.  Doing so may be in vain, but it isn't pointless and repetition does not make it false.  Our concern here on MT is about science and its position in society (I can be contrarian about other things, too!).  I try to be responsible in presenting my view, and to explain and to justify it. I am afraid I don't do it with eloquence.  But the poet-contrarian Wendell Berry, whom I have had the privilege of meeting a few times, does, having expressed contrariness quite well, as you can see on the OnBeing blogsite, and here's their link to Wendell reading it himself.  The poem begins, "I am done with apologies. If contrariness is my/inheritance and destiny, so be it. If it is my mission/to go in at exits and come out at entrances, so be it."  I won't complain if you leave here to go read the rest.

All those little LGP (Little Green People) out there: A space fantasy

Ah, yes, the highly publicized, if not hyped, search for planets with life 'out there'!  A promotor's dream, because how can you ever falsify the idea that we're not in this alone?  NASA and other funding-hungry semi-sci-fi agencies continue to drop hints about habitable planets and so on.  You know the patter, and the promises almost as flagrant as those of 'precision' genomic medicine.

Well, forget the hype, promise and 'artist' impressions, and let's take a little look at what is in a sense being promised.....

First, let's go back to Aristotle's time and before, and imagine space as a crystal sphere in which the Earth is centered. That is, what we can see is the encircling sky dome.  There we peer into the stars, galaxies, and so on.

Now let us suppose that there really is 'life' out there, and as a short-cut for our purposes here let's further suppose that what we mean by 'life' is living organisms that are advanced enough to use and/or transmit electromagnetic waves strong enough to reach Earth detectably.  Now, to make the SETI (search for extra-terrestrial intelligence) effort easier, let's imagine that these particular emanations can be discriminated from all other sources of electromagnetic radiation in the skies, like light from stars, microwave background from the Big Bang, and so forth--that is, so we can specifically visualize the life-signals' beams by their being green.  I pick green so we can think of them as being (intentional or not, but at least direct evidence) from the Little Green People (LGP) that are out there--if any of them are. That we exist suggests that thinking that life of interesting sorts exists elsewhere is not particularly surprising, and it must have many forms we might not even recognize.

So, let's grant NASA's and the ESL's (and sci-fi writers) wishes and assume that not just life but LGP are out there.  Indeed, let's make our effort to contact them really, really easy, and simply assume that there are millions of planets, even just in the visible universe, that have such LGPs on them.  That's at least plausible; whether it's probable can't be said because we have no way to evaluate what 'probable' would mean.

The figure very schematically suggests what I mean.  The ring around the Earth represents what we can see today. Again, we assume we can discriminate the 'green' radiation from all the other radiation coming in.  The length of each arrow represents the length of time the civilization out there was sending a signal, and let's allow these to be for millions of years (note I'm being very generous: for example, any human-sent signal emanating from Earth would only be about 100 years' long, since radio signaling is only that old).  The place of origin will usually millions or billions of light years away, way, way, way beyond this figure, and the signal has taken that number of years getting here, as it's doing just now when we see it.  After the end of an arrow, that civilization was no longer sending, probably no longer exists, but we don't know that until the end of the signal arrives.  Before the arrowhead, the civilization hadn't developed appropriate signaling technology, so we can't know it is (or was) there.   Incoming signals outside of that ring are not yet visible to us--we don't know they're on their way here and have no way to know those LGP civilizations even exist.

The green-dappled sky
OK, envision our celestial globe, with its hundreds of billions of stars in the Milky Way, and the hundreds of billions of similar galaxies we know are in the heavens, again, just considering our 14 billion year old universe's visible horizon, which is I think tens of billions of light-years in diameter. If life is here on Earth, why not all over the place out there?  There are similar environments, presumably, in countless planets.  At any given moment, we would see green dots on the celestial sphere wherever an LGP signal was incoming.

So, let's say, just to be as favorable to the LGP search as possible, that we see a million such dots. That's not implausible, and let us assume, again to be generous, that each emitting population actively disseminates electromagnetic radiation for a million years, from the time they developed the technology until they evolved on to extinction or disinterest or whatever.

This should mean rich hunting grounds.  But I think it does no such thing.

By far most, if not essentially all such LGP emanations will be from more than a million light years away from Earth.  That means that by the time we can detect them, the emanations will have stopped and the people probably become extinct (many reasons, such as their local star blew up, they evolved to some other species, they damaged their environment beyond sustainability, they overpopulated themselves into starvation....).  And of course, we have no idea just by seeing a dot whether it's one of those, or one from a still-living source.

Even if such a source were still viable, and even if we guess right about which one that may be at the time we mount an expedition or sent a 'Hello!' message, it would likely take 'us' so long to reach them, with either generations of astronauts in transit or just a radio signal, that the LGP would be done-for by the time we or our signal got there.  A manned expedition would take hugely more generations than have ever existed for our species, of course.  And, of course, no matter how clever they were, the LGP wouldn't be able to detect us for millions of years after we sent our message to them, assuming they were still alive at that time so distant from when we received their emanation.  And, of course, we'd be extinct or would have polluted the Earth out of life, by the time any such contact occurred.

So, it is essentially hopeless to wave around vague suggestions of finding 'life in space'.  In fact, most of the universe isn't just a few millions of light years away from us, it's billions of them.  Even hinting at connecting with LGP borders on fraud by those who want our attention, and funds, to explore these possibilities.

The hopeful (sort-of) side
However, there is, surprisingly (sort of), a hopeful side.  That's because if there in fact are LGP out there, most of their signals won't be visible to us at any given time.  Millions or billions or even trillions of little green dots may be approaching us from any or all directions, but just haven't gotten here yet.  That would only be expected if we can see a million of them at our particular time today.

Out of all of those incoming signals, maybe some are close enough to us to constitute something to be excited about....except that once we see their blip, it will at best have been sent at the beginning of their signal-generating lifespan and we'll have no idea how long ago that happened, and hence whether they're still there and sending, so we can't know how long the blip will keep appearing, and most of the time the signal will be millions if not billions of years old, and as above, the senders long-gone.

If some movie or video game outfit develops a real tele-transporter or wormhole traversing system, we might dream of going 'there', wherever there is.  Even then, we'll have to choose which of the million green dot sources to travel to, and just hope the senders are still there.  Of course, they're not really green, so choosing light blips to pursue won't be easy!

There are enough fascinating things about space, and enough real, not imaginary, needs right here on our green earth.  We should keep fantasies to the world of fiction.

Many more words are extinct than those we get to read

I'm starting a new human evolution book project. Technically I've already started it but I've got the greenlight from my agent so it's for real. 

So much writing, at least for me, is just exploratory, organizational vomit that I never times infinity wish to see on the printed page. 

But, here, let me show you my vomit from this morning:

High heels are sexy because they change a woman’s posture so that her boobs and butt stick out and that’s attractive because boobs and butts and because waist hip ratio. 

Wait, no, they’re sexy because they make a person taller and taller is universally attractive. 

What if they’re a handicap or a fitness indicator like a risky bird call or a peacock’s tail? The hampered, painful locomotion signals to potential mates how badass the high heel wearer is. “We will have badass kids!” say high heels. 

source

Or they keep women from being able to escape too quickly if ambushed by aroused men, but that’s too macabre for me to consider further and pisses me off. 

How about, they’re sexy because we decided they are. Culture is weird and powerful: neck lengthening rings, circumcision, Taco Bell. 

Or they’re sexy because they make a woman’s feet look small for her height and this is sexy because … Fibonacci? (Must do calculations.) I don’t know. "Hold me closer tiny footed," isn’t how the song goes. 

But, wait, high heels change a woman’s locomotion. Women who walk in them have an exaggerated female-stereotyped gait. Ask those biomechanists who said so. That’s why heels are sexy, then, they heighten femininity and project its signal further out across the savannah, and into the gaze of more men for longer in each of their numerous salivating minds. 

But why are swinging hips sexy? Because they’re opposite of a man’s? 

But there’s something else that heels do to gait. They make a person unstable, careful, as if they're just learning to walk. One slips into those torture slippers and they're suddenly precious, adorable, in need of rapt attention. Like a toddler, walking for the very first time. 

The idea’s out there, somewhere, that heels make a woman helpless and that’s attractive to men who want to rescue women. This toddler idea is just a fraction of a degree away from that one. Is male attraction to helpless women the same thing that drives them to be doting fathers? Gawd. If that’s true, that means I shouldn’t be as annoyed when they want to rescue full grown women, and when full grown women want to be rescued, because, after all, it’s just good fatherly mojo. But, we’re not babies, dammit. 

High heels. Sexy for so many reasons, but also because they make women into babies and, hey, wait a second...

We don’t think babies are sexy. What the bleep am I talking about? Back up: what we prefer in babies can be preferred in adults for fundamentally similar reasons but those preferences can result in different outcomes. 

Attractive helpless babies get cared for and not sexualized (too much) and attractive helpless women do too but that affection includes bleeping. 

It all makes perfect sense. How on earth did our lineage survive this long without high heels?

FAS - Fishy Association Studies

           

                                  On Saturday, July 19, 1879, the brilliant opera 

                                  composer, Richard Wagner, "had a bad night; 

                                  he thinks that...he ate too much trout."  

                                             Quoted from Cosima Wagner's Diary, Vol. II, 1878-83.

As I was reading Cosima Wagner's doting diary of life with her famous husband, I chanced across the above quote that seemed an appropriate, if snarky, way to frame today's post. The incident she related exemplifies how we routinely assign causation even to one-off events in daily life. Science, on the other hand, purports to be about causation of a deeper sort, with some sufficient form of regularity or replicability.

Cause and effect can be elusive concepts, especially difficult to winnow out from observations in the complex living world.  We've hammered on about this on MT over the years.  The best science at least tries to collect adequate evidence in order to infer causation in credible rather than casual ways. There are, for example, likely to be lots of reasons, other than eating trout, that could explain why a cranky genius like Wagner had a bad night.  It is all too easy to over-interpret associations in causal terms.

By such thinking, the above figures (from Wikimedia commons) might be interpreted as having the following predictive power:
     One fish = bad night
     Two fish = total insomnia
     Many fish = hours of nightmarish dissonance called Tristan und Isolde!

Too often, we salivate over GWAS (genomewide association studies) results as if they justify ever-bigger and longer studies.  But equally too often, these are FAS, fishy association studies.  That is what we get when the science community doesn't pay heed to the serious and often fundamental difficulties in determining causation that may well undermine their findings and the advice so blithely proffered to the public.

We are not the only ones who have been writing that the current enumerative, 'Big Data', approach to biomedical and even behavior genetic causation leaves, to say the least, much to be desired.  Among other issues, there's too much asserting conclusions on inadequate evidence, and not enough recognition of when assertions are effectively not that much more robust than saying one 'ate too much trout'.  Weak statistical associations, so typically the result of these association studies, are not the same as demonstrations of causation.

The idea of mapping complex traits by huge genomewide case-control or population sample studies is a captivating one for biomedical researchers.  It's mechanical, perfectly designed to be done by huge computer database analysis by people who may never have seen the inside of a wet lab (e.g., programmers and 'informatics' or statistical specialists who have little serious critical understanding of the underlying biology).  It's often largely thought-free, because that makes the results safe to publish, safe for getting more grants, and so on; but more than being 'captivating' it is 'capturing'.... a hog-trough's share of research resources.

The promise, not even always carefully hedged with escape-words lest it be shown to be wrong, is that from your genome your future biomedical (and behavioral) traits can be known.  A recent article in the July 28 issue of the Journal of the American Medical Association (JAMA), Joyner et al. describes the stubborn persistence of under-performing but costly research that becomes entrenched, a perpetuation that NIH's misnomered 'precision based genomic medicine' continues or even expands upon. Below is our riff on the article, but it's open-source so you can read the points they make and judge for yourself if we have the right 'take' on what they say.  It is one of many articles that have been making similar points....in case anyone is listening.

The problem is complex causation
The underlying basic problem is the complex nature of causation of 'complex' traits, like many if not most behavioral or chronic or late-onset diseases. The word complex, long-used for such traits, refers not to identified causes but to the fact that the outcomes clearly did not have simple, identified causes.  It seemed clear that their causation was due mainly to countless combinations of many individually small causal factors, some of which were inherited; but the specifics were usually unknown. Computer and various DNA technologies made it possible, in principle, to identify and sort through huge numbers of possible causes or at least statistically associated factors, including DNA sequence variants.  But underlying this source for this approach has been the idea, always a myth really, that identifying some enumerated set of causes in a statistical sample would allow accurate prediction of outcomes.  This has proven not to be the case nearly as generally as has been promised.

To me, the push to do large-scale huge-sample, survey-based genomewide risk analysis was at least partly justified, at least in principle, years ago when there might have been some doubt about the nature of the causal biology underlying complex traits, including the increasingly common chronic disease problems that our aging population faces.  But the results are in, and in fact have been in for quite a long time.  Moreover, and a credit to the validity of the science, is that the results support what we had good reason to know for a long time.  The results show that this approach is not, or at least clearly no longer the optimal way to do science in this area or contribute to improving public health (and much of the same applies to evolutionary biology as well).

I think it fair to say that I was making these points, in print, in prominent places, starting as long ago as nearly 30 years, in books and journal articles (and more recently here on MT), that is, ever since the relevant actual data were beginning to appear.  But neither I nor my collaborators were the original discoverers of this insight: instead, the basic truth has been known in principle and in many empirical experimental (such as agricultural breeding) and observational contexts, for nearly a century! Struggling with the inheritance of causal elements ('genes' as they were generically known), the 1930s' 'modern synthesis' of evolutionary biology reconciled (1) Darwin's idea of gradual evolution, mainly of quantitative traits, with the experimental evidence of the quantitative nature of their inheritance, and (2) the discrete nature of inheritance of discrete causal elements first systematically demonstrated by Mendel for selected 2-state traits.  That was a powerful understanding but in too many ways it has thoughtlessly been taken to imply that all traits, not just genes, are usefully 'Mendelian', due to substantial, enumerable, strongly causal genetic agents.  That has always been the exception, not the rule.

A view is possible that is not wholly cynical 
We have been outspoken about the sociocultural aspect of modern research, which can be understood by what one might call the FTM (Follow the Money) approach, in some ways a better way to understand where we are than looking at the science itself.  Who has what to gain by the current approaches?  Our understanding is aided by realizing that the science is presented to us by scientists and journalists, supplier industries and bureaucrats, who have vested interests that are served by promoting that way of doing business.

FTM isn't the only useful perspective, however.  A less cynical, and yet still appropriate way to look at this is in terms of diminishing returns.  The investment in the current way of doing science in this (and other areas) is part of our culture.  From a scientific point of view, the first forays into a new way or approach, or a theoretical idea, yield quick and, by definition, new results.  Eventually, it becomes more routine and the per-study yield diminishes. We asymptotically approach what we can glean from the approach.  Eventually some chance insight will yield some forms of better and more powerful approaches, whatever they'll be.

If current approaches were just yielding low-cost incremental gain, or were being done in well-off investigators' basement labs, it would be a normal course of scientific-history, and nobody would have reason to complain.  But that isn't how it works these days.  These days understanding via FTM is important: the science establishment's hands are in all our pockets, and we should expect more in return than the satisfaction that the trough has been feeding many very nice careers (including mine), in universities, journalism, and so on.  How, when, and where a properly increased expectation of science for societal benefits will be fulfilled is not predictable, because facts are elusive and Nature often opaque.  However, simply more-of-the-same, at its current costs, with continuing entrenched justification, isn't the best way for public resources to be used.

There will always be a place for 'big data' resources.  A unified system of online biomedical records would save a lot of excess repeat-testing and other clinical costs, if every doctor you consult could access those records.  The records could potentially be used for research purposes, to the (limited) extent that they could be informative.  For a variety of conditions that would be very useful and cost-effective indeed; but most of those would be relatively rare.

Continuing to pour research funds into the idea that ever more 'data' will lead to dramatic improvements of 'precision' medicine is far more about the health of entrenched university labs and investigators than that of the general citizenry. Focused laboratory work that is more rigorously supported by theory or definitive experiment, with some accountability (but no expectations nor promises of miracles) is in order, given what the GWAS etc. era, plus a century of evolutionary genetics, has shown. There are countless areas, especially many serious early onset diseases, for which we have a focused, persuasive, meaningful understanding of causation and where resources should now be invested more heavily.

Intentionally open-ended beetle collecting ventures joined at the hip to promises of 'precision' without those promising even knowing what that word means (but hinting that it means 'perfection'), or glorifying the occasional seriously good findings as if they are typical or as though more focussed, less open-ended research wouldn't be a better investment, is not a legitimate approach.  Yet that is largely what is going on today.  The scientists, at least the smart ones, know this very well and say so (in confidence, of course).

Understanding complex causation is complex, and we have to face up to that.  We can't demand inexpensive or instant or even predictable answers.  These are inconvenient facts few want to face up to.  But we and others have said this ad nauseam before, so here we wanted to point out the current JAMA paper as yet another formal and prominently published realization of the costly inertia in which we are embedded, and by highly capable authors. In any aspect of society, not just science, prying resources loose from the hands of a small elite is never easy, even when there are other ways to use those resources that might have better payoff for all of us.

Usually, such resource reallocation seems to require some major new and imminent external threat, or some unpredicted discovery, which I think is far more likely to come from some smaller operation where thinking was more important than cranking out yet another mass-scale statistical survey of Big Data sausage.  Still, every push against wasteful inertia, like the Joyner et al. JAMA paper,  helps. Indeed, those many whose careers are entrapped by that part of the System have the skills and neuronal power to do something better if circumstances enabled it to happen more readily.  To encourage that, perhaps we should stop paying so much attention to Fishy stories.

In Memoriam: Al Knudsen, a modest, under-recognized founder of cancer genetics (and more)

My first job was a young faculty member was in the Graduate School of Biomedical Sciences, at the University of Texas Health Science Center in Houston.  Our small Center for Demographic and Population Genetics was part of the Graduate School, and it was small enough that we got to know, and interact with, the Dean.  And what a dean he was!

The great, and good Al Knudsen (1922-2016).  Google images.

It was a small graduate school, so Dr Knudsen still was active in research, cancer research. One of the first talks I heard down there in Houston, when I still didn't have my first pair of cowboy boots, y'all, was an interesting idea about the causes of cancer.

Radiation was a known carcinogen, as were some chemicals, and there were various ideas about how carcinogenesis worked at the gene level. The basic idea was that these agents caused genetic mutations that led cells to misbehave, and though abnormal, escape detection by the immune system. More mutations meant more cancer risk, and this was consistent with 'multi-hit' ideas of cancer. More mutations took longer to accumulate, which was consistent with the increasing risk of cancer with age.  But genetics was still very rudimentary then, compared to now, direct testing primitive at best. And there were some curious exceptions.  An interesting fact was that some cancers seemed familial, arising in close relatives, and typically at earlier ages than the sporadic versions of what seemed to be the same type of tumor.  Why?

One example was the eye cancer retinoblastoma which arose in children or young adults, mostly in isolated cases; but there were affected families in which Rb was often present at birth.  Knudsen's idea was that in affected families one harmful allele was being transmitted, but the disease did not arise until a second mutation occurred.  Al published a quantitative mutational model of the onset age pattern in a PNAS paper in 1971, just before I myself had arrived in Houston, but by chance I had heard him present his work at the time of my job interview.

The basic idea was a 2-hit hypothesis, in which you could inherit one Rb mutation, and then only had to 'wait' for some one of your embryonic retinal cells to suffer the bad luck of a hit in the normal copy in order for a cancer to develop.  That waiting time accounted for the earlier onset of familial cases, because they only had to 'wait' for one mutation, whereas sporadic cases needed to experience two Rb hits in the same cell lineage.

This was a profound insight.  It allowed for cancer genetic findings, in which some forms of cancer clustered in families (e.g., some breast and colorectal cancers). Yet most cases were sporadic.  It was shown roughly at that time, by clever work in those crude days of human genetics, that tumors were clonal--the tumor, even when it had spread, was the descendant of a single aberrant (mutated) cell.

It did not take long for this sort of thinking, along with various methods for detection, to find the Rb gene....and other genes related to cancer.  This eventually included genomewide tests for loss of detectable variation based on microsatellite sites, continued to confirm the idea, far beyond those types of cancer that seem to be caused largely by changes in a single gene. The idea of somatic mutation caused by environmental factors, was complemented by the idea that it is common to inherit genotypes that are partially altered but insufficient by themselves to cause cancer, so that the tumor only arises later in life, after environmentally-caused (or stochastic) further mutations occur.

Knudsen's basically 2-hit idea was quickly generalized to 'multi-hit' models of cancer, and the discovery that cancers in a given individual were clonal led to models in which combinations of inherited mutations (present in every cell) and those that occurred somatically, seemed to account for the basic biology of cancer.  Many of the individual genes whose mutation puts a person at very elevated risk of one or more forms of cancer have since been identified, and newer technology has allowed their functional nature (and reason for their role in cancer) to be found.  Some are involved in DNA repair or control of cell division, and it's understandable why their mutational loss is dangerous.

The sources of variation in these genes may vary, but cancer as a combination of inherited and somatically generated mutations is a, if not the, prevailing general model for its biological nature and epidemiology, and shows why tumors are somatic evolutionary phenomena at the gene level.  But his nugget of an idea triggered much broader work in human genetics that, once technology caught up to the challenge, led to our understanding (and, too often, convenient ignoring) of the role of combined inherited and somatically induced variation as a major cause of the common, complex disorders for which genomewide mapping has become a routine approach.

I was still in Houston when Dr Knudsen moved to the Fox Chase Cancer Center in Philadelphia.  We missed him, but over the following decades he continued to contribute to the understanding of cancer.  His inspiring, gentle, and generous nature was an exception in the snake-pit that has become so common in the 'business model' of so many biomedical research circles.

Al's foundational work earned him many honors.  But he didn't get one that I think he richly deserved: his quiet, transformative role in understanding cancer, and the much broader impact on human genetics that followed as a result, deserved a Nobel Prize.

When scientific theory constrains

It's good from time to time to reflect on how we know what we think we know.  And to remember that, as it has been in any time in history, much of what we now think is true will sooner or later be found to be false or, often, only inaccurately or partially correct.  Some of this is because values change -- not so long ago homosexuality was considered to be an illness, e.g.  Some is because of new discoveries -- when archaea were first discovered they were thought to be exotic microbes that inhabited extreme environments but now they're known to live in all environments, even in and on us. And of course these are just two of countless examples.

But what we think we know can be influenced by our assumptions about what we think is true, too. It's all too easy to look at data and interpret it in a way that makes sense to us, even if there are multiple possible interpretations.  This can be a particular problem in social science, when we've got a favorite theory and the data can be seen to confirm it; this is perhaps easiest to notice if you yourself aren't wedded to any of the theories.  But it's also true in biology. It is understandable that we want to assert that we now know something, and are rewarded for insight and discoveries, rather than more humbly hesitating to make claims.

Charitable giving
The other day I was listening to the BBC Radio 4 program Analysis on the charitable impulse.  Why do people give to charity?  It turns out that a lot of psychological research has been done on this, to the point that charities are now able to manipulate us into giving.  If you call your favorite NPR station to donate during a fund drive, e.g., if you're told that the caller just before you gave a lot of money, you're more likely to make a larger donation than if you're told the previous caller pledged a small amount.

A 1931 advertisement for the British charity, Barnardo's Homes; Wikipedia

Or, if an advertisement pictures one child, and tells us the story of that one child, we're more likely to donate than if we're told about 30,000 needy children.  This works even if we're told the story of two children, one after the other.  But, according to one of the researchers, if we're shown two children at once, and told that if we give, the money will randomly go to just one of the children, we're less likely to give.  This researcher interpreted this to mean that two is too many.

But there seem to me to be other possible interpretations given that the experiment changes more than one variable.  Perhaps it's that we don't like the idea that someone else will choose who gets our money.  Or that we feel uncomfortable knowing that we've helped only one child when two are needy.  But surely something other than that two is too many, given that in 2004 so many people around the world donated so much money to organizations helping tsunami victims that many had to start turning down donations.  These were anonymous victims, in great numbers.  Though, as the program noted, people weren't nearly as generous to the great number of victims of the earthquake in Nepal in 2015, with no obvious explanation.

The researcher did seem to be wedded to his one vs too many interpretation, despite the contradictory data.  In fact, I would suggest that the methods, given what were presented, don't allow him to legitimately draw any conclusion.  Yet he readily did.

Thinness microbes?
The Food Programme on BBC Radio 4 is on to the microbiome in a big way.  Two recent episodes (here and here) explore the connection between gut microbes, food, and health and the program promises to update us as new understanding develops.  As we all know by now, the microbiome, the bug intimates that accompany us through life, in and on our body, may affect our health, our weight, our behavior, and perhaps much more.  Or not.

Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus aureus on Tryptic Soy Agar.  Wikipedia

Obesity, asthma, atopy, periodontal health, rheumatoid arthritis, Parkinson's, Alzheimer's, autism, and many many more conditions have been linked with, or are suggested to be linked with, in one way or another, our microbiome.  Perhaps we're hosting the wrong microbes, or not a diverse enough set of microbes, or we wipe the good ones out with antibiotics along with the bad, or with alcohol, and what we eat may have a lot to do with this.

One of the researchers interviewed for the program was experimenting with a set of identical twins in Scotland.  He varied their diets having them eat, for example, lots of junk food and alcohol, or a very fibrous diet, and documented changes in their gut microbiomes which apparently can change pretty quickly with changes in diet.  The most diverse microbiome was associated with the high fiber diet. Researchers seem to feel that diversity is good.

Along with a lot of enthusiasm and hype, though, mostly what we've got in microbiome research so far is correlations.  Thin people tend to have a different set of microbes than obese people, and people with a given neurological disease might statistically share a specific subset of microbes.  But this tells us nothing about cause and effect -- which came first, the microbiome or the condition?  And because the microbiome can change quickly and often, how long and how consistently would an organism have to reside in our gut before it causes a disease?

There was some discussion of probiotics in the second program, the assumption being that controlling our microbiome affects our health.  Perhaps we'll soon have probiotic yogurt or kefir or even a pill that keeps us thin, or prevents Alzheimer's disease.  Indeed, this was the logical conclusion from all the preceding discussion.

But one of the researchers, inadvertently I think, suggested that perhaps this reductionist conclusion was unwarranted.  He cautioned that thinking about probiotic pills rather than lifestyle might be counterproductive.  But except for factors with large effects such as smoking, the effect of "lifestyle" on health is rarely obvious.  We know that poverty, for example, is associated with ill health, but it's not so easy to tease out how and why.  And, if the microbiome really does directly influence our health, as so many are promising, the only interesting relevant thing about lifestyle would be how it changes our microbiomic makeup.  Otherwise, we're talking about complexity, multiple factors with small effects -- genes, environmental factors, diet, and so on, and all bets about probiotics and "the thinness microbiome" are off.  But, the caution was, to my mind, an important warning about the problem of assuming we know what we think we know; in this case, that the microbiome is the ultimate cause of disease.

The problem of theory
These are just two examples of the problem of assumption-driven science. They are fairly trivial, but if you are primed to notice, you'll see it all around you. Social science research is essentially the interpretation of observational data from within a theoretical framework. Psychologists might interpret observations from the perspective of behavioral, or cognitive, or biological psychology, e.g., and anthropologists, at least historically, from, say, a functionalist or materialist or biological or post-modernist perspective. Even physicists interpret data based on whether they are string theorists or particle physicists.

And biologists' theoretical framework? I would suggest that two big assumptions that biologists make are reductionism and let's call it biological uniformitarianism. We believe we can reduce causation to a single factor, and we assume that we can extrapolate our findings from the mouse or zebrafish we're working on to other mice, fish and species, or from one or some people to all people. That is, we assume invariance rather than that what we can expect is variation. There is plenty of evidence to show that by now we should know better.

True, most biologists would probably say that evolutionary theory is their theoretical framework, and many would add that traits are here because they're adaptive, because of natural selection. Evolution does connect people to each other and people to other species, it has done so by working on differences, not replicated identity, and there is no rule for the nature or number of those differences or for extrapolating from one species or individual to another. We know nothing to contradict evolutionary theory, but that every trait is adaptive is an assumption, and a pervasive one.

Theory and assumption can guide us, but they can also improperly constrain how we think about our data, which is why it's good to remind ourselves from time to time to think about how we know what we think we know. As scientists we should always be challenging and testing our assumptions and theories, not depending on them to tell us that we're right.