Thursday, September 22, 2016

Chain-ring genetics

If you're a bike rider, as I am, you know that there is a huge market out there trying to lure you into a really, really fancy bike.  Bike prices can easily get well into 4 digits, amazingly, and apparently there are enthusiasts who are willing to pay for them--maybe the thrill of the purchase is itself enough!
In a way, fancy bikes serve as an analogy for broader aspects of our society, as I'll try to illustrate.

I live in a pretty hilly area, and even though I just to bike-path or street-and-sidewalk riding, it's a pretty dramatic range of effort one needs in order to navigate the changing ups and downs.  And my bike, shown in this amateur photo, is a Trek Navigator hybrid, with a 3 x 7 gear cog setup: 3 chain rings in the front, and a 7-cog rear gear set.  That's 21 different gears, and I was happy to buy a bike with such a wide range of pedaling-efficiency options.



The next figure shows the gear ratio range schematically.  For each front chainring (Low, Middle, High), the corresponding line shows the relative gear ratio across the 7 rear cogs:So, in the extreme, if you go up a steep hill you want a front-1/rear-1 choice (the easiest combination, with more pedal rotations per rear wheel rotation, making each rotation easier even if you go slower), and downhill you'd want 3-7 for the opposite effects.
High, Mid, Low gear ratio range  for the 3-front, 7-rear cogs (schematic)

This plethora of gears was an attractive selling point when I bought this bike, which is a good one, but now that it's a few years old, I decided to shop around to see what's on offer these days.  I notice some  3 x 8, 3 x 9, and 2 x 9 front/back cog numbers.  The more expensive bikes tend to have more gears, though one had only 2 chainrings in front--and I wondered about that.  If the rear cogs had the right ratios, there is less weight in the front only having two chainrings, and the shifting will be easier and the shifting mechanism may act more quickly.  But the overall range was less, meaning it might not suit all riders as easily. In any case, there's a lot of techie glitter and salesmanship going on to get you to pony up the $K's for the fancier bikes.  They weigh a few pounds less, too, and so on, as the price goes up.

The bike-tech web sites basically warn you to avoid cross-chaining, which is to set the front chainring to a side of the cluster opposite to the cog set in the rear.  Instead, common advice says, shift to front-rear combinations for which the connecting chain is as close to parallel with the frame as possible.
But if you read a bit more carefully, you can see that some of the cross-chaining evidence, for modern bikes, is not very well established: you may not damage the chain, cog teeth, or be detectably less efficient, after all.  And some of the combinations--where the ranges in the above figure overlap--would never really be used.

So I wondered why one would not just stick with the middle front chainring all the time.  If you do that, the full range of rear cogs can be used without cross-chaining issues.  You don't get all of the bike's range, but you do get most of it.  What would the same ride feel like using only the middle chainring?

I've now tried that by taking my ride today without using the high or low chainring (stupidly, I never had tried that before!).  In going up the very steepest hill, I knew I could find it a tad easier to use the easiest front-rear combination.  Going downhill, I could muster up a bit more speed with the opposite extreme front-rear combination. But basically, the ride was the same.  It was also a bit simpler and involved a lot less coordinated shifting.

I decided I don't need a fancy new bike, after all!

So what does this have to do with genetics?
I was led to write this brief reflection when I thought about how many not really avid bikers have been led by cycle makers to get the most extensive, fanciest gearing (among other options), forking over very much more money, for very little gain, in the process.  Yes, performance is a bit better, but it doesn't really match up to the hype, especially not at the cost, unless you are a bike-racer or off-road biker, or have a yen for the latest-and-greatest and lots of 1%er money to invest in ego toys. The marginal gain per unit cost is minimal.

We're getting a lot of similar marketing for gearing up, so to speak, in our biomedical research and its application.  We're being told how marvelous having lots of chainrings and large rear cog-sets will yield miraculously better health than our old-fashioned ways have done so far.  It's called by flashy impressive or intimidating names like 'next-gen sequencing' or 'Big Data' or 'exome profiling', or 'precision genomic medicine', and that's the analog of Big Gearing (though a lot more costly).  Big Data is for the research community as carbon-fiber frames are for the bicycle industry.  Scientist and general public alike are suckers for slogans promising unbelievably more in the health-research industry from gearing up, much as we are for slogans promising unbelievably better biking.

The promotions are always shifting, so to speak, as the science rolls on.

But genetics can be important to our very lives!
The line we are fed by NIH and the research establishment always stresses the vital importance of our Big Data investment.  That is, after all, what 'precision genomic medicine' and wars on cancer and so on suggest they are promising.  It is true that under some circumstances, for some people, large-scale genomic database research may soon, or eventually, lead to more effective treatments of disease. There are already some examples, though how many really required massive genomewide association studies and the like is open to discussion.

As we've noted here many times, there are tons of more clearly genetic, or otherwise-caused, disorders for which the same monetary investment might yield much greater benefit. Most advances still, generally, seem to come from focused research on known, substantial causes.  Lifestyle changes, if our epidemiological data are worth their own huge cost, could much more massively reduce or defer common adult-onset diseases.  And there are a large number of clearly genetic diseases, pediatric and otherwise, for which the actual gene or genes are known.  They often strike at birth or in childhood, and are life-long debilitating,or life-shortening conditions.  They have, in my view, a much stronger and more legitimate claim on research resources.

Nobody wants a disease, genetic or otherwise, not even if it only strikes late in life.  But we should use the gears we have to get up those hills, rather than constantly being promised miracles if we only add another chainring, and then another, and then.....



Friday, August 26, 2016

Is life itself a simulation of life?

It often happens in science that our theory of some area of reality is very precise, but the reality is too complex to work out precisely, or analytically.  This can be when we decide to use computer simulation of that reality to get at least a close approximation to the truth.  When a phenomenon is determined by a precise process, then if we increase the complexity of our simulation, and if the simulation really is simulating the underlying reality, then the more computer power we apply, the closer we get to the truth--that is, our results approach that truth asymptotically.

For example, if you want to predict the rotation of galaxies in space relative to each other, and of the stars within the galaxies, the theories of physics will do the job, in principle. But solving the equations directly the way one does in algebra or calculus is not possible with so many variables.  However, you can use a computer to simulate the movement and get a very good approximation (we've discussed this here, among other places).  Thus, at each time interval, you take the position and motion of each object you want to follow, and those measures of nearby objects, and use Newton's law of gravity to predict the position of the objects one time interval later.

If the motion you simulate doesn't match what you can observe, you suspect you've got something wrong with the theory you are using. In the case of cosmology, one such factor is known as 'dark matter'.  That can be built into models of galactic motion, to get better predictions.  In this way, simulation can tell you something you didn't already know, and because the equations can't be directly solved, simulation is an approach of choice.

In many situations, even if you think that the underlying causal process is deterministic, measurements are imperfect, and you may need to add a random 'noise' factor to each iteration of your simulation.  Each simulation will be slightly 'off' because of this, but you run the same simulation thousands of times, so the effect of the noise evens out, and the average result represents what you are trying to model.

Is life a simulation of life?
Just like other processes that we attempt to simulate, life is a complex reality.  We try to explain it with the very general theory of evolution, and we use genetics to try to explain how complex traits evolve, but there are far too many variables to predict future directions and the like analytically.   This is more than just because of biological complexity however, in part because the fundamental processes of life seem, as far as we can tell, inherently probabilistic (not just a matter of measurement error).  This adds an additional twist that makes life itself seem to be a simulation of its underlying processes.

Life evolves by parents transmitting genes to offspring.  For those genes to be transmitted to the next generation, the offspring have to live long enough, must be able to acquire mates, and must be able to reproduce. Genes vary because mutations arise.  For simplicity's sake, let's say that successful mating requires not falling victim to natural selection before offspring are produced, and that that depends on an organism's traits, and that genes are causally responsible for those traits.  In reality, there are other process to be considered, but these will illustrate our point.

Mutation and surviving natural selection seem to be probabilistic processes.  If we want to simulate life, we have to specify the probability of a mutation along some simulated genome, and the probability that a bearer of the mutation survives and reproduces.  Populations contain thousands of individuals, genomes incur thousands of mutations each generation, and reproductive success involves those same individuals.  This is far too hard to write tractable equations for in most interesting situations, unless we make almost uselessly simplifying assumptions.  So we simulate these phenomena.

How, basically, do we do this?  Here, generically and simplified, but illustrating the issues, is the typical way (and the way taken by my own elaborate simulation program, called ForSim which is freely available):

For each individual in a simulated population, each generation, we draw a random number based on an assumed mutation rate, and add the resulting number and location of mutations to the genotype of the individual.  Then for each resulting simulated genotype, we draw a random number from the probability that such a genotype reproduces, and either remove or keep the individual depending on the result.  We keep doing this for thousands of generations, and see what happens.  As an example, the box lists some of the parameter values one specifies for a program like ForSim.



Sometimes, if the simulation is accurate enough, the probability and other values we assume look like what ecologists or geneticists believe is going on in their field site or laboratory.  In the case of humans, however, we have little such data, so we make a guess at what we think might have been the case during our evolution.  Often these things are empirically estimated one at a time, but their real values affect each other in  many ways.  This is, of course, very far from the situation in physics, described above!  Still, we at least have a computer-based way to approximate our idea of evolutionary and genetic processes.

We run this for many, usually many thousand generations, and see the trait and genomic causal pattern that results (we've blogged about some of these issues here, among other posts).  This is a simulation since it seems to follow the principles we think are responsible for evolution and genetic function.  However, there is a major difference.

Unlike simulations in astronomy, life really does seem to involve random draws for probabilistic processes.  In that sense, life looks like it is, itself, a simulation of these processes.  The random draws it makes are not just practical estimates of some underlying phenomenon, but manifestation of the actual probabilistic nature of the phenomenon.

This is important, because when we simulate a process, we know that its probabilistic component can lead to different results each time through.  And yet, life itself is a one-time run of those processes. In that sense, life is a simulation but we can only guess at the underlying causal values (like mutation and survival rates) from the single set of data: what actually happened its one time through.  Of course, we can test various examples, like looking at mutation rates in bacteria or in some samples of people, but these involve many problems and are at best general estimates from samples, often artificial or simplified samples.

But wait!  Is life a simulation after all?  If not, what is life?
I don't want us to be bogged down in pure semantics here, but I think the answer is that in a very profound way, life is not a simulation in the sense we're discussing.  For the relevant variables, life is not based on an underlying theoretical process in the usual sense, of whose parameters we use random numbers to approximate in simulations.

For example, we evaluate biological data in terms of 'the' mutation rate in genomes from parent to offspring.  But in fact, we know there is no such thing as 'the' mutation rate, one that applies to each nucleotide as it is replicated from one generation to the next, and from which each actual mutation is a random draw.  The observed rate of mutation at a given location in a given sample of a given species' genomes depends among other things on the sex, the particular nucleotides surrounding the site in question (and hence all sites along the DNA string), and the nature of the mutation-detection proteins coded by that individual's genome, and mutagen levels in the environment.  In our theory, and in our simulations, we assume an average rate, and that the variation from that average will, so to speak, 'average out' in our simulations.

But I think that is fundamentally wrong. In life, every condition today is a branch-point for the future. The functional implications of a mutation here and now, depend on the local circumstances, and that is built into the production of the future local generations.  Life in fact does not 'average' over the genome and over individuals does not in fact generate what life does, but in a sense the opposite.  Each event has its own local dynamics and contingencies, but the effect of those conditions affects the rates of events in the future.  Everywhere it's different, and we have no theory about how different, especially over evolutionary time.

Indeed, one might say that the most fundamental single characteristic of life is that the variation generated here today is screened here today and not anyplace else or any time else.  In that sense, each mutation is not drawn from the same distribution.  The underlying causal properties vary everywhere and all the time.  Sometimes the difference may be slight, but we can't count on that being true and, importantly, we have no way of knowing when and to what extent it's true.

The same applies to foxes and rabbits. Every time a fox chases a rabbit, the conditions (including the genotypes of the fox and rabbit) differ. The chance aspect of whether it's caught or not are not the same each time, the success 'rate' is not drawn from a single, fixed distribution.  In reality, each chase is unique.

After the fact, we can look back at net results, and it's all too tempting to think of what we see as a steady, deterministic process with a bit of random noise thrown in.  But that's not an accurate way to think, because we don't know how inaccurate it is, when each event is to some (un-prespecified) extent unique.  Overall, life is not, in fact, drawing from an underlying distribution.  It is ad hoc by its very nature and that's what makes life different from other physical phenomena.

Life, and we who partake of it, are unique. The fact of local, contingent uniqueness is an important reason that the study of life eludes much of what makes modern physical science work.  The latter's methods and concepts assume replicable law-like underlying regularity. That's the kind of thing we attempt to model, or simulate, by treating phenomena like mutation as if they are draws from some basic underlying causal distribution. But life's underlying regularity is its irregularity.

This means that one of the best ways we have of dealing with complex phenomena of life, simulating them by computer, smoothes over the very underlying process that we want to understand.  In that sense, strangely, life appears to be a simulation but is even more elusive than that.  To a great extent, except by some very broad generalities that are often too broad to be very useful, life isn't the way we simulate it, and doesn't even simulate itself in that way.

What would be a better approach to understanding life?  The next generation will have to discover that.

Thursday, August 25, 2016

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)
·        Notes from the Field: A Primatologist's Point of View – Morgan (Nature Education)
·        Expedition Rusinga (video; 8 min) https://www.youtube.com/watch?v=4y1puNyB9e8  
·        The ape in the trees – Dunsworth (The Mermaid’s Tale)
·        How Do We Know When Our Ancestors Lost Their Tails? (video; 4 min)

1.3
Assigned Reading/viewing
·        How Science Works (video; 10 min):
·        Understanding science: How Science Works, pages 1-21; starts here:
·        Carl Sagan’s Rules for Critical Thinking and Nonsense Detection
·        10 Scientific Ideas That Scientists Wish You Would Stop Misusing
Portfolio Assignment
·        Scientific Process worksheet - Located on Sakai

1.4
Assigned Reading/viewing
·        Characteristics of Crown Primates – Kirk (Nature Education)
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)


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)

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)

1.8
Assigned Reading/viewing
·        The Human Spark 2 (video; 55 mins)
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)
·        What Influences the Size of Groups in Which Primates Choose to Live? – Chapman & Teichroeb (Nature Ed)
·        Primate Sociality and Social Systems – Swedell (Nature Ed)
·        Primates in communities – Lambert (Nature Ed)

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)
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)
·        Trait Evolution on a Phylogenetic Tree – Baum (Nature Ed)
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)
·        The Ancient History of the Human Hand (video; 4 mins)


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)
·        Genetic Recombination – Clancy (Nature Ed)
·        What is a Gene? Colinearity and Transcription Units – Pray (Nature Ed)
·        RNA functions – Clancy (Nature Ed)

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)
·        Gregor Mendel and the Principles of Inheritance – Miko (Nature Ed)
·        Mendelian Genetics: Patterns of Inheritance and Single-Gene Disorders – Chial (Nature Ed)
·        Phenotypic Range of Gene Expression: Environmental Influence – Lobo & Shaw (Nature Ed)
·        Genetic Dominance: Genotype-Phenotype Relationships – Miko (Nature Ed)
·        Pleiotropy: One Gene Can Affect Multiple Traits – Lobo (Nature Ed)
·        Polygenic Inheritance and Gene Mapping – Chial (Nature Ed)

2.4
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)
·        Mutations Are the Raw Materials of Evolution – Carlin (Nature Ed)

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)
·        Sexual selection – Brennan (Nature Ed)

2.6
Portfolio Assignment
·        Wisdom tooth assignment - Located on Sakai
Additional Resources
·        Neutral Theory: The null hypothesis of molecular evolution – Duret (Nature Ed)
·        Negative selection – Loewe (Nature Ed)
·        On the mythology of natural selection. Part I: Introduction – Weiss (The Mermaid’s Tale)
·        On the mythology of natural selection. Part II: Classical Darwinism– Weiss (The Mermaid’s Tale)
·        Secrets of Charles Darwin’s Breakthrough -  Bauer (Salon)

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)

2.8
Assigned reading/viewing
·        Evolution is the only natural explanation – Dunsworth (The Mermaid’s Tale)
·        The F-words of Evolution  – Dunsworth (The Mermaid’s Tale)
·        Another F-word of evolution  – Dunsworth (The Mermaid’s Tale)
Portfolio Assignment
·        Scenario building assignment (Part 3) - Located on Sakai
Additional resources
·        Mutation not natural selection drives evolution –  Tarlach (about Nei; Discover Magazine)

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)
·        We Hear with the Bones that Reptiles Eat With (video; 4 mins)
·        Why should we care about species? – Hey (Nature Ed)
·        Speciation: The origin of new species – Safran (Nature Ed)
·        The maintenance of species diversity – Levine (Nature Ed)
·        Macroevolution: Examples from the Primate World – Clee & Gonder (Nature Ed)
·        Primate Speciation: A Case Study of African Apes – Mitchell & Gonder (Nature Ed)

2.10
Assigned Reading/viewing
·        Things Genes Can’t Do – Weiss and Buchanan (Aeon)
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)
·        The Molecular Clock and Estimating Species Divergence – Ho (Nature Ed)
·        Lice and Human Evolution (video; 11 mins) http://video.pbs.org/video/1790635347/
·        Planet without apes? – Stanford (Huffington Post)

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)
·        Dating Rocks and Fossils Using Geologic Methods – Peppe (Nature Ed)
·        Desktop Diaries: Tim White (video; 7 mi– Posted on Sakai)
·        Ancient Human Ancestors: Walking in the woods (video; 4 mins)
·        Overview of hominin evolution – Pontzer (Nature Ed)
·        The Earliest Hominins: Sahelanthropus, Orrorin, and Ardipithecus - Su (Nature Ed):

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)

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)

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)
·        Evidence for Meat-Eating by Early Humans – Pobiner (Nature Ed)
·        Archaeologists officially declare collective sigh over “Paleo Diet”

3.5
Reading/viewing
·        IUB, Chapter 9: On the nature of limbsRoberts
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)

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

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)
·        The Neanderthal Inside Us (video; 4 mins)
·        Anthropological genetics: Inferring the history of our species through the analysis of DNA – Hodgson & Disotell (Evolution: Education and Outreach)
·        Testing models of modern human origins with archaeology and anatomy – Tryon & Bailey (Nature Ed)
·        Human Evolutionary Tree – Adams (Nature Ed)
·        Paternity Testing: Blood Types and DNA – Adams (Nature Ed)

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)
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)

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)
·        A True and Faithful Account of Mr. Ota Benga the Pygmy, Written by M. Berman, Zookeeper – Mansbach
·        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)
·        Are humans hard-wired for racial prejudice?  - Sapolsky (LA Times)
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)
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.