Wednesday, December 20, 2017

A Christmas Charivari in Verse, and more

A verse to Christmas 
It’s great to have a holiday, to revel in good cheer,
And  a verse to Christmas is something to hold dear;
The hustle and the bustle, from shop to shop for days,
Cannot dispel the spirit, that the shopping overlays.

The science that we practice, in labs across the land,
Takes Nature from its setting, and puts it in our hand,
To look, to touch, to taste, to hear, its every angle seen,
Experience the place we’re in, to understand its mien.

The world is out there waiting, for all of us to scope,
To parse, and map, and sequence—but shun the facile trope:
It’s great to have a holy day, to show respect forsooth,
But always keeping holy, not promises, but truth!

The gifts we give, the bounty get, divert us for the day,
And let the world take forms we wish, our rev’ling minds a-play:
We wander through the fields of dreams, our cares for now on hold,
Though know we must, tis but a day when dreams we let be told.

If what we want is fantasy, and not the world we’re in,
Then reveling occasions can’t be excessive sin,
But then--back to reality our duty is to steer:
I'm not averse to Christmas, at least one day a year!

-------------- ***** ---------------

Intermission: Even a grump can have good cheer--at least once a year!
(From the mega-wonderful Pogo, by Walt Kelly, representative of Porky's visit every Christmas eve; color added)

Thoughtful good wishes are what count at this--or any--time of year

-------------- ***** ---------------

A turkey talks turkey about Christmas
You talk of peace, of love, and grace
And revel in the innocence
Of newborn mangered babe.
But then when dinner comes, you violent be,
And me de-feather, baste and roast,
And, carving, say a ‘grace’—to love!

I had a life, you know
With verve, and spirit free
We chased around the barnyard all
With no known cause to fear.

If love is truly in your hearts,
And peace, goodwill to all--
A wish to be that which you claim:
Eat Brussels sprouts today!

-------------- ***** ---------------

A sonnet for our times
When, in dispute with favored theory's eyes,
I all alone beweep my outcast state,
And trouble deaf journals with my skeptic's cries,
And look upon myself and curse my fate,
Wishing me like to one more rich in hype,
Featured like him, like him with grants possessed,
Desiring that man's genome-promise trope,
With what I most esteem acknowledged least;
Yet in these thoughts myself almost despising,
Haply I think on Truth, and then my state,
(Like to the lark at break of day arising
From sullen earth) sings hymns at heaven's gate;
      For thy sweet troth remembered such wealth brings
      That then I scorn to change my state with Collins.

[after W. Shakespeare, Sonnet 29]


Sunday, December 3, 2017

What do ravens do?

"As behavioral ecologists, we try to reveal rules of behavior as though we were discovering truths.  In reality, the word 'rule' as applied to animal behavior is a verbal shortcut.  A 'rule' means nothing more than  a consistency of response.  It is not adherence to dictum.  Animals adhere no more to rules than we do by showing up at the beach when its 110 degrees but not when it's 30 degrees.  Rules are the sum of decisions made by individuals that are then exhibited by crowds, not vice versa.  Rules are thus a result.  They are the average behavior that we and many animals are programmed with, learn, or make up as we go along."

This is a cogent quote from Bernd Heinrich's book Mind of the Raven (1999, Ecco books), which I was given as a birthday gift.  The idea was that I would like to read about the various capabilities of ravens, relative to our informal and even formal ideas about what 'mind' or 'consciousness' mean and how we might know, and whether these interesting birds might have it, whatever it is.

However, the quote I've given is more than just the author's views on what ravens' internal experiences might be.  It applies to much that we have to deal with in science--at least, in biological and behavioral sciences themselves.  I've used it because I think the observation also applies to something I've been writing about in recent posts--related to what may seem to be a very different topic, whether life is parametric or not.

The physical world seems to be parametric, that is, driven ultimately by some universally true processes, like gravity, that are in turn reflections of underlying, universal, fixed parameters, or numerical values.  Of course, 'numerical values' refers to human-derived mathematics and science, and might, from some wholly different point of view, be differently perceived or characterized.

But to us, phenomena like the speed of light, c, and various quantum phenomena etc., have fixed, universal values.  The value is the same everywhere, even if its manifestation may be modified by local circumstances.  For example, c is specified as in a vacuum.  Whether or not there exists any true total vacuum, the idea--and the belief in its universality--are clear and important bedrock aspects of physics, chemistry, and cosmology.  In some other substance, rather than a vacuum, the speed of light is altered in an orderly way.

But what about life?
We can ask whether, while life is a physical and molecular phenomenon, it is part and parcel of the same parametric cosmos, or if it has exceptions at the level at which we want answers to our basic questions.  That would be analogous to physics adhering to a dictum, in the raven quote.  But maybe life is not analogous to a vacuum.  This, at least, is what I mean by asking whether life is a parametric phenomenon, and expression doubts that it could be so.

An a priori reason, in my mind, is that life is a molecular process of regular molecular activity (genes, proteins, and so on), but it evolves because the specifics are different--they vary.  Without that, there would be no evolution, and organismal complexity, and the underlying genetic and proteinic complexity by which life, and its interacting ecosystems have come about, would not be here.  In that sense, I think it is appropriate to suggest that life is not a parametric phenomenon.

This, to me, is not the same as saying that life is a kind of self-organized complexity. It certainly is that, but the phrase misses what I think is the underlying fact, which is that life is not parametric.  Complexities like the mandelbrot set (figure below) are parametric: they repeat the same phenomenon in an evermore complex but always rigorously.  This is a form of 'complexity' but it is very rigorously regular.  Life is, if anything, rigorously irregular, among individuals, populations, species, and the structures within each of those.

Mandelbrot set.  From Wikipedia entry
Many people have written about life's complexity with analogies to things like the Mandelbrot set and many others of the sort.  But while that sounds as if it acknowledges the complexity of life, it really is an implicit hunger for just the opposite: for regularity, tractability, and 'parametricity'.   I think that is at best an ad hoc approximation but theoretically fundamentally wrong.

The consequences are obvious: we can describe existing data by various statistical and even mathematical data-fitting procedures.  But we cannot make predictions or projections with known 'precision' and indeed that is why I think that rhetoric like 'precision genomic medicine' is strictly an advertising slogan, scientifically misleading (and culpably so), and misunderstood by most people even those who use it, and perhaps even by the NIH that proffer it as a funding or marketing ploy for its budgets.  It is a false promise, as stated (saying instead that we want funds for research to make medicine more precise by including genomic information would be honest and appropriate).

Heinrich's description of ravens' behavior seemed an apt way to make my point, as I see things at any rate, clear by an easily digested analogy.  Some ravens did what they were seen to do, but that was the net result of what some observed ravens did on some occasions, not what 'ravens do' in the parametric sense.  The ravens are not all following a rule and even the 'consistency' of their responses is not like that (different ravens do different things, as Heinrich's book makes clear).

We want rules that explain 'truth' in genetics and evolution.  We ought to be able to see that that may be a misleading way to view the nature of the living world.  And, seeing that, to change what we promise to the public and, as important as what we promise to them, to change how we think.

Or, as quoth the raven: nevermore!

Thursday, November 30, 2017

Statistics controversy: missing the p-oint.

There is a valuable discussion in Nature about the problems that have arisen related to the (mis)use of statistics for decision-making.  To simplify the issue, it is the idea that a rather subjectively chosen cutoff, or p, value leads to dichotomizing our inferences, when the underlying phenomena may or may not be dichotomous.  For example, in a simplistic way to explain things,  if a study's results pass such a cutoff test, it means that the chance the observed result would arise if nothing is going on (as opposed to the hypothesized effect) is so small--less than p percent of the time--that we accept the data as showing that our suggested something is going on.  In other words, rare results (using our cutoff criterion for what 'rare' means) are considered to support our idea of what's afoot.  The chosen cutoff level is arbitrary and used by convention, and its use doesn't reflect the various aspects of uncertainty or alternative interpretations that may abound in the actual data.

The Nature commentaries address these issues in various ways, and suggestions are made.  These are helpful and thoughtful in themselves but they miss what I think is a very important, indeed often the critical point, when it comes to their application in many areas of biology and social science.

Instrumentation errors
In these (as other) sciences, various measurements and technologies are used to collect data.  These are mechanical, so to speak, and are always imperfect.  Sometimes it may be reasonable to assume that the errors are unrelated to what is being measured (for example, their distribution is unrelated to the value of a given instance) and don't affect what is being measured (as quantum measurements can do), then correcting for them in some reasonably systematic way, such as assuming normally distributed errors, clearly helps adjust findings for the inadvertent but causally unconnected errors.

Such corrections seem to apply quite validly to social and biological, including evolutionary and genetic, sciences.  We'll never have perfect instrumentation or measurement, and often don't know the nature of our imperfections.  Assuming errors uncorrelated with what is being sought seems reasonable even if approximate to some unknown degree. It's worked so well in the past that this sort of probabilistic treatment of results seems wholly appropriate.

But instrumentation errors are not the only possible errors in some sciences.

Conceptual errors: you can't 'correct' for them in inappropriate studies
Statistics is, properly, a branch of mathematics.  That means it is an axiomatic system, an if-then way to make deductions or inductions.  When and if the 'if' conditions are met, the 'then' consequences must follow.  Statistics rests on probabilism rather than determinism, in the sense that it relates to and is developed around, the idea that some phenomena only occur with a given probability, say p, and that such a value somehow exists in Nature.

It may have to do with the practicalities of sampling by us, or by some natural screening phenomenon (as in, say, mutation, Mendelian transmission, natural selection). But it basically always rests on some version or other of an assumption that the sampling is parametric, that is, that our 'p' value somehow exists 'out there' in Nature.  If we are, say, sampling 10% of a population (and the latter is actually well-defined!) then each draw has the same properties.  For example, if it is a 'random' sample, then no property of a potential samplee affects whether or not it is actually sampled.

But note there is a big 'if' here: Sampling or whatever process is treated as probabilistic needs to have a parameter value!  It is that which is used to compute significance measures and so on, from which we draw conclusions based on the results of our sample.

Is the universe parametric?  Is life?
In physics, for example, the universe is assumed to be parametric.  It is, universally, assumed to have some properties, like gravitational constant, Planck's constant, the speed of light, and so on.  We can estimate the parameters here on earth (as, for example, Newton himself suggested), but assume they're the same elsewhere.  If observation challenges that, we assume the cosmos is regular enough that there are at least some regularities, even if we've not figured them all out yet.

A key feature of a parametric universe is replicability.  When things are replicable, because they are parametric--have fixed universal properties, then statistical estimates and their standard deviations etc. make sense and should reflect the human-introduced (e.g., measurement) sources of variation, not Nature's.  Statistics is a field largely developed for this sort of context, or others in which sampling was reasonably assumed to represent the major source of error.

In my view it is more than incidental, but profound, that 'science' as we know it was an enterprise developed to study the 'laws' of Nature.  Maybe this was the product of the theological beliefs that had preceded the Enlightenment or, as I think at least Newton said, 'science' was trying to understand God's laws.

In this spirit, in his Principia Mathematica (his most famous book), Newton stated the idea that if you understand how Nature works in some local example, what you learned would apply to the entire cosmos.  This is how science, usually implicitly, works today.  Chemistry here is assumed to be the same as chemistry on any distant galaxy, even those we cannot see.  Consistency is the foundation upon which our idea of the cosmos and in that sense, classical science has been built.

Darwin was, in this sense, very clearly a Newtonian.  Natural selection was a 'force' he likened to gravity, and his idea of 'chance' was not the formal one we use today.  But what he did observe, though implicitly, was that evolution was about competing differences.  In this sense, evolution is inherently not parametric.

Not only does evolution rest heavily on probability--chance aspects of reproductive success, which Darwin only minimally acknowledged, but it rests on each individual's own reproductive success being unique.  Without variation, and that means variation in the traits that affect success, not just 'neutral' ones, there would be no evolution.

In this sense, the application of statistics and statistical inference in life sciences is legitimate relative to measurement and sampling issues, but is not relevant in terms of the underlying assumptions of its inferences.  Each study subject is not identical except for randomly distributed 'noise', whether in our measurement or in its fate.

Life has properties we can measure and assign average values to, like the average reproductive success of AA, Aa, and aa genotypes at a given gene. But that is a retrospective average, and it is contrary to what we know about evolution to assume that, say, all AA's have the same fitness parameter and their reproductive variation is only due to chance sampling from that parameter.

Thinking of life in parametric terms is a convenience, but is an approximation of unknown and often unknowable inaccuracy.  Evolution occurs over countless millennia, in which the non-parametric aspects can be dominating.  We can estimate, say, recombination or mutation or fitness values from retrospective data, but they are not parameters that we can rigorously apply to the future and they typically are averages among sampled individuals.

Genetic effects are unique to each background and environmental experience, and we should honor that uniqueness as such!  The statistical crisis that many are trying valiantly to explain away, so they can return to business as usual (even if not reporting p values) is a crisis of convenience, because it makes us think that a bit of different reportage (confidence limits rather than p values, for example) will cure all ills.  That is a band-aid that is a convenient port-in-a-storm, but an illusory fix. It does not recognize the important, or even central, degree to which life is not a parametric phenomenon.

Wednesday, November 29, 2017

There is no obstetrical dilemma

Josie Glausiusz wrote a very nice piece published at Undark today called,

Of Evolution, Culture, and the Obstetrical Dilemma: Anthropologists are revisiting long-held beliefs about human evolution and the difficulty of human childbirth

In it, I'm thrilled to get something I furiously worry about across to a wide audience with this part toward the end of the piece:

“I worry that this idea [of the obstetrical dilemma] is justifying status-quo high rates of C-sections and other childbirth interventions,” Dunsworth says. “People say, ‘it’s just evolution — there’s nothing we can do, and here’s how technology helps, and that’s fabulous. But I know we’re overdoing it. Everybody knows that.”
It's a complicated issue, the obstetrical dilemma (OD), so it's no surprise that there are missing pieces in this particular discussion. The most important, biggest flaw in OD thinking is its assumption that we're born early, an assumption that is featured at the start of the piece with Karp and Washburn. But it's not true. We are not born early and that didn't make it in there. When you stop believing we're born early, the whole thing starts to crumble.

And here's where I am now with some of this...

First of all, we need to change the story so that it's not, no matter how slightly, bolstering unnecessary childbirth interventions. Though my OB/GYN seemed unfamiliar with the obstetrical dilemma hypothesis when I explained it to her as she gave me a pap smear, I think the thinking is pervasive in medical schools. This hunch is getting support on Twitter as we speak. (For some context, I am the first that I know of, several decades after the 'obstetrical dilemma' was born, to tack on "hypothesis" to the name of the idea.)

And, second of all, here's where I get "crazy"(see the piece for crazy) but all over again... Okay. In 2012, in one of a series of blog posts about our then recent paper questioning the obstetrical dilemma hypothesis I wrote this:

Women aren't called broads for nothing. We have, on average, larger dimensions of the pelvis that comprise the birth canal (linked into broader hips) than men do and this is not just relatively but absolutely and this is not just in the U.S., this is species-wide (1). 
There is no better explanation for this than it's due to selection for successful childbirth.

I think I was wrong. I think I know a better explanation for why women have bigger "obstetric" dimensions in the pelvis than men and I THINK IT'S BECAUSE WE HAVE FEMALE-SPECIFIC ORGANS THAT GROW INSIDE AND OCCUPY THAT SPACE AND THEY DO NOT.

Stay tuned for more about vaginal, clitoral, and uterine growth and space-taking... yessssss.

Tuesday, November 28, 2017

Sherlock Holmes, the Galtonian!

In the late 1800s, in England, Darwinism and its intellectual cousin, genetic determinism, were the hot topics.  And Darwin's literal cousin, Francis Galton, was riding high, too.  He was read by the intelligentsia and his ideas both reflected, and seeped into, daily thinking about life.

The Sherlock Holmes story "The Adventures of the Reigate Squires", was published in 1893, and in it we see a reflection of those times, in the view of the role of inheritance that was then common (and still rides rampant for some today).  On a murder case, our sleuth was examining the paper shown here, which was a written note that was vital to solving the crime:

In his perceptive diagnosis of the writing on the note, Sherlock noticed that alternate words were written in different hands, that is, by two different people. The way the t's and e's were written gave that away.  In the story, this implicated two brothers, because the note was written to tie them together to their crime by each brother writing part of the note.

So what?  To Holmes, there was a profound reason he could connect the brothers, not just two different conspirators writing one note, to the crime.  As he said:
"There is a further point, however, which is subtler and of greater interest. There is something in common between these hands. They belong to men who are blood-relatives. It may be most obvious to you in the Greek e's, but to me there are many small points which indicate the same thing. I have no doubt at all that a family mannerism can be traced in these two specimens of writing. I am only, of course, giving you the leading results now of my examination of the paper. There were twenty-three other deductions which would be of more interest to experts than to you. They all tend to deepen the impression upon my mind that the Cunninghams, father and son, had written this letter.

In 1893, Mendel had not been rediscovered, so there were no genetics, and Darwin's nebulous 'gemmules' were basically quantitative determinants of traits.  But using such concepts at least implicitly, Francis Galton had been writing much about inheritance and family resemblance at that time, including behavioral traits such as intelligence, and one can presume that Conan Doyle, a physician by training, would have known about that work. At least, years later and in regard to fingerprints in a later Holmes story, the two were in at least some correspondence (see: ).  Galton coined the word eugenics in 1883, ten years before the above Holmes story, an idea he advanced, in the spirit of viewing human traits as inherent, and thus amenable to improvement: preferential breeding to proliferate the positive, and the opposite to remove the negative, traits from the human  population.

Art imitates life....

Tuesday, November 21, 2017

The Knowledge Factory Crisis: A different, anthropological way to view universities

Nothing we humans do lives up to its own mythology. We are fallible, social, competitive, acquisitive, our understanding is incomplete, and we have competing interests to address, in our lives and as a society.  I posted yesterday about universities as 'knowledge factories, reacting to a BBC radio program that discussed what is happening in universities, when research findings seem unrepeatable.

That program, and my discussion of what is going on at universities, took the generally expressed view of what universities are supposed to be, and examined how that is working.  The discussion concerned technical aspects that related to the nature of scientific information universities address or develop.  That is, in this context, their 'purpose' for being.  How well do they live up to what they are 'supposed' to be?

Many of my points in the post were about the nature of faculty jobs are these days, and the way in which pressures lead to the over-claiming of findings, and so on.  I made some suggestions that, in principle, could help science live up to its ideal.

Here in this post, however, I want to challenge what I have said about this.  Instead, I want to take a somewhat distanced viewpoint, looking at universities from the outside, in a standard kind of viewpoint that anthropologists take, rather than simply accepting universities' own assessments of what they are about.

Doing poorly by their ideal standard
My post noted ways in which universities have become not just a 'knowledge factory', but more crass business factories, as making money blatantly increasingly over-rides their legitimate--or at least, stated--role as idea and talent engines for society.  Here's a story from a few years ago about that, that is still cogent.  The fiscal pursuit discussed in this post is part of the phenomenon.  As universities are run more and more as businesses, which happens even in state universities, they become more exclusive, belying their original objective which (as in the land-grant public universities) was to make higher education available to everyone.  In addition to becoming money makers themselves, academia has become a boon for student-loan bankers, too.

But this is a criticism of university-based science, and expressed as it relates to how universities are structured.  That structure, even in science, leads to problems of science.  One might think that something so fundamentally wrong would be easy to see and to correct.  But perhaps not, because universities are not isolated from society--they are of society, and therein lies some deep truth.

Excelling hugely as viewed anthropologically
If you stop examining how universities compare to their ideals, or to what most people would tell you universities were for, and instead look at them as parts of society, a rather different picture emerges.

Universities are a huge economic engine of society.  They garner their very large incomes from various sources: visitors to their football and basketball stadiums, students whose borrowed money pays tuition, and agencies private and public that pour in money for research.  Whether or not they are living up to some ideal function or nature, they are a major and rather independent part of our economy.

Their employees, from their wildly paid presidents, down to the building custodians, span every segment of society.  The money universities garner pays their salaries, and buys all sorts of things on the open commercial economy, thereby keeping many other people gainfully employed.  Their activities (such as the major breakthrough discoveries they announce almost daily) generate material and hence income for the media industries, print and electronic, which in turn helps feed those industries and their relevant commercial influences (such as customers, television sales, and more).

Human society is a collective way for we human organisms to extract our living from Nature.  We compete as individuals in doing this, and that leads to hierarchies.  Overall, over time, societies have evolved such that these structures extract ever more resources and energy.  Via various cultural ideologies we are able to keep things going smoothly enough, at least internally, so as not to disrupt this extractive activity.

Religion, ownership hierarchies, imperialism, military, and other groups have self-justifications that make people feel they belong.  This contributes to building pyramids--whether they be literal, or figurative such as religions, universities, armies, political entities, social classes, or companies.  Often the justification is religious--nobility by divine right, conquest as manifest destiny, and so on.  That not one of these resulting societal structures lives up to its own ideology has long been noted.  Why should we expect universities to be any different?  These are the cultural ways people organize themselves to extract resources for themselves.

Universities are parasites on society, very hierarchical with obscenely overpaid nobles at the top?  They show no limits on the trephining they do on those who depend on them, such as graduating students with life-burdening debt?  They churn through those who come to them for whom they claim to 'provide' the good things in life?  Of course!  Like it or not, by promising membership and a better life, they are just like religions or political classes or corporations!

Institutions may be so caught up in their belief systems that they don't adapt to the times or competitors, or they may change their actions (if not always their self-description).  If they don't adapt they eventually crumble and are replaced by new entities with new justifications to gain popular appeal or acceptance.  However, fear not, because relative to their actual (as opposed to symbolic) role in societies, universities are doing very well: at present, they very clearly show their adaptability.

In this anthropological sense, universities are doing exceedingly well, far better than ever before, churning resources and money over far faster than ever before.  Grumps (like us) may point out the failings of lacking to live up to our own purported principles--but how is that different from any other engine of society?

In that anthropological sense, whether educating people 'properly' or not, whether claiming more discoveries that stand up to scrutiny, universities are doing very, very, very well.  And that, not the purported reason that an institution exists, is the measure of how and why societal institutions persist or expand.  Hypocrisy and self-justification, or even self-mythology, are always part of social organization. A long-standing anthropological technique for understanding distinguishes what are called emics, from etics: what people say they do, from what they actually do.

Yes, there will have to be some shrinkage with demographic changes, and fewer students attending college, but that doesn't change the fact that, by material measures, universities are incredibly successful parts of society.

What about the intended material aspect of the knowledge factory--knowledge?
But there is another important side to all of this, which takes us back to science itself, which I think is actually important, even if it is naive or pointless to crab at the hypocrisies of science that are explicable in deep societal terms.

This has to do with knowledge itself, and with science on its own terms and goals.  It relates to what could, at least in principle, advance the science itself (assuming such changes could happen without first threatening science's and scientists' and universities' assets).  That will be the subject of our next post.

Monday, November 20, 2017

The 'knowledge factory'

This post reflects much that is in the science news, in particular our current culture's romance with data (or, to be more market-savvy about it, Big Data).  I was led to write this after listening to a BBC Radio program, The Inquiry, an ongoing series of discussions of current topics.  This particular episode is titled Is The Knowledge Factory Broken?

Replicability: a problem and a symptom
The answer is pretty clearly yes.  One of the clearest bits of evidence is the now widespread recognition that too many scientific results, even those published in 'major' journals, are not replicable.  When even the same lab tries to reproduce previous results, they often fail.  The biggest recent noise on this has been in the social, psychological, and biomedical sciences, but The Inquiry suggests that chemistry and physics also have this problem.  If this is true, the bottom line is that we really do have a general problem!

But what is the nature of the problem?  If the world out there actually exists and is the result of physical properties of Nature, then properly done studies that aim to describe that world should mostly be replicable.  I say 'mostly' because measurement and other wholly innocent errors may lead to some false conclusion.  Surprise findings that are the luck of the draw, just innocent flukes, draw headlines and are selectively accepted by the top journals.  Properly applied, statistical methods are designed to account for these sorts of things.  Even then, in what is very well known as the 'winner's curse', there will always be flukes that survive the test, are touted by the major journals, but pass into history unrepeated (and often unrepentant).

This, however, is just the tip of the bad-luck iceberg.  Non-reproducibility is so much more widespread that what we face is more a symptom of underlying issues in the nature of the scientific enterprise itself today than an easily fixable problem.  The best fix is to own up to the underlying problem, and address it.

Is it rats, or scientists who are in the treadmill?
Scientists today are in a rat-race, self-developed and self-driven, out of insatiability for resources, ever-newer technology, faculty salaries, hungry universities....and this system can be arguably said to inhibit better ideas.  One can liken the problem to the famous skit in a candy factory, on the old TV show I Love Lucy.  That is how it feels to many of those in academic science today.

This Inquiry episode about the broken knowledge factory tells it like it is....almost.  Despite concluding that science is "sending careers down research dead-ends, wasting talent and massive resources, misleading all of us", in my view, this is not critical enough.  The program suggests what I think are plain-vanilla, clearly manipulable 'solutions.  They suggest researchers should post their actual data and computer program code in public view so their claims could be scrutinized, that researchers should have better statistical training, and that we should stop publishing just flashy findings.  In my view, this doesn't stress the root and branch reform of the research system that is really necessary.

Indeed, some of this is being done already.  But the deeper practical realities are that scientific reports are typically very densely detailed, investigators can make weaknesses hard to spot (this can be done inadvertently, or sometimes intentionally as authors try to make their findings dramatically worthy of a major journal--and here I'm not referring to the relatively rare actual fraud).

A deeper reality is that everyone is far too busy on what amounts to a research treadmill. The tsunami of papers and their online supporting documentation is far too overwhelming, and other investigators, including readers, reviewers and even co-authors are far too busy with their own research to give adequate scrutiny to work they review. The reality is that open-publishing of raw data and computer code etc. will not generally be very useful, given the extent of the problem.

Science, like any system, will always be imperfect because it's run by us fallible humans.  But things can be reformed, at least, by clearing the money and job-security incentives out of the system--really digging out what the problem is.  How we can support research better, to get better research, when it certainly requires resources, is not so simple, but is what should be addressed, and seriously.

We've made some of these points before, but with apology, they really do bear stressing and repeating.  Appropriate measures should include:

     (1) Stop paying faculty salaries on grants (have the universities who employ them, pay them);

     (2) Stop using manipulable score- or impact-factor counting of papers or other counting-based items to evaluate faculty performance, and try instead to evaluate work in terms of better measures of quality rather than quantity;

     (3) Stop evaluators considering grants secured when evaluating faculty members;

     (4) Place limits on money, numbers of projects, students or post-docs, and even a seniority cap, for any individual investigator;

     (5) Reduce university overhead costs, including the bevy of administrators, to reduce the incentive for securing grants by any means;

     (6) Hold researchers seriously accountable, in some way, for their published work in terms of its reproducibility or claims made for its 'transformative' nature.

     (7) Grants should be smaller in amount, but more numerous (helping more investigators) and for longer terms, so one doesn't have to start scrambling for the next grant just after having received the current one.

     (8) Every faculty position whose responsibilities include research should come with at least adequate baseline working funds, not limited to start-up funds.

     (9)  Faculty should be rewarded for doing good research that does not require external funding but does address an important problem.

     (10)  Reduce the number of graduate students, at least until the overpopulation ebbs as people retire, or, at least, remove such number-counts from faculty performance evaluation.

Well, these are snarky perhaps and repetitive bleats.  But real reform, beyond symbolic band-aids, is never easy, because so many people's lives depend on the system, one we've been building over more than a half-century to what it is today (some authors saw this coming decades ago and wrote with warnings). It can't be changed overnight, but it can be changed, and it can be done humanely.

The Inquiry program reflects things now more often being openly acknowledged. Collectively, we can work to form a more cooperative, substantial world of science.  I think we all know what the problems are.  The public deserves better.  We deserve better!

PS.  P.S.:  In a next post, I'll consider a more 'anthropological' way of viewing what is happening to our purported 'knowledge factory'.

Even deeper, in regard to the science itself, and underlying many of these issues are aspects of the modes of thought and the tools of inference in science.  These have to do with fundamental epistemological issues, and the very basic assumptions of scientific reasoning.  They involve ideas about whether the universe is actually universal, or is parametric, or its phenomena replicable.  We've discussed aspects of these many times, but will add some relevant thoughts in the near future.

Friday, November 10, 2017

33 Syllabi for Intro to BioAnth/ Intro to Human Origins and Evolution

Two years ago, many of you generously sent me your syllabi for your introductory biological anthropology courses when I put out a call here at The Mermaid's Tale. Thank you! Four teaching assistants who are also anthropology majors worked with me on a little study of these syllabi. My collaborators are Alexa Bracken, Katherine Burke, Nadine Kafeety, and Molly Jane Tartaglia and I am grateful for their work on this.

Here are our results...

  • n = 33 syllabi, from 2015 or before, gathered mostly from your helpful submissions and also collected from AAA and departmental websites, though not extensively. Institutions in 3 different nations and at least 17 U.S. states are represented
  • 29/33 require a textbook (as opposed to other readings/resources) 
  • 14/33 have separate labs/recitations
  • 18/33 teach natural selection before learning the genetic basis for variation [this 2017 study supports doing the opposite] 
  • 2/33 mention genetic drift and/or neutral evolution
  • 2/33 mention epigenetics
  • 3/33 mention evo-devo and/or development
  • 3/33 mention controversy/controversies
  • 0/33 mention creationism and/or creation
  • 4/33 mention 'racism' 
  • 1/33 mention 'sexism'

I've typed and deleted a lot of words here and can't seem to avoid sentences that read like I'm telling a bunch of my brilliant friends and colleagues that we're doing it wrong. I don't believe we are.

I understand that syllabi aren't perfect or even great representations of what we do in our courses.

But maybe we could be better at highlighting some of the more complicated and significant terrain we cover in class, in the syllabus. Syllabi are posted publicly; they're seen by countless faculty reviewers and administrators. I think that we biol/evol/physical anthropologists could do better at getting the word out that our courses are not simply the human equivalent of "Intro to walrus origins and evolution."

Anthropology is what makes human evolution different from walrus evolution. And now that we're freed, mostly, from having to teach that evolution is true, why don't we really go for it and teach that it's also okay that evolution is true? Why not face the cultural controversies, recognize the sordid (and worse) history of our discipline and evolutionary science, and that history's massive influence on our culture and society to this day? We are! I know. But let's put it on the syllabus to make it official.

Human evolution is fundamentally different from the rest of evolutionary biology and I believe it's dangerous to pretend it isn't, or to unintentionally give the impression that it isn't. I hope you agree.

Thursday, November 9, 2017

What we can learn from the birds and why there are birds

Evolution is a fact of life, but there are many different interpretations of how it works. There is the persistent classically Darwinian view, in which natural selection explains everything as a deterministic 'force'--clearly the kind of imagery Darwin himself had.  This is nowadays focused around genes as the metaphor for the competing deterministic causal factors that are responsible.  We know that even clearly adaptive traits we see today evolved through earlier stages of adaptation that may have had nothing to do with current functions.

We know now that this is a deeply important factor about the origins of the major functional traits of organisms, but also that life is complex and chance plays a major role in its dynamics.  In one sense this means selection cannot literally be force-like: it must have some 'probabilistic' aspects, even if there isn't a fixed probability, or probability process like coin-flipping, at work.  That aspect, due to competing selection and so on, is more like a series of one-off effects.  At the same time, the fast fox doesn't always catch the fleeing rabbit, so that even if selection is favoring 'fast' genes, there is an element of what would appear afterwards to have been probabilism in the change of fast-gene frequencies.

Every organism is subjected to functional challenges on all of its traits, all of the time, so that even if natural selection acted as a force (which it cannot really precisely be), which adaptive functions among this array of competing constraints win out will be affected by chance, because from trait A's viewpoint, the relative impact of selection on the other traits will always be changing.

We also know that there is complex genetic control of complex functions, and this involves gene duplication and multiple more or less equivalent pathways to similar outcomes.  So any given gene's effect on the trait will be affected by the other redundant genes it carries.

There is still a widespread, almost ritualistic view of evolution, informally at least, in terms of the genes 'for' some trait whose favorable variation was driven essentially in a deterministic, force-like way to replace other genetic alternatives in their species.  This can easily be seen even among biologists, who should know better, and especially in the biomedical community, in which at least some pratctitioners have actually been taught the premises of evolution at a serious level--beyond, for example, what is often purveyed in medical schools. 

A typical habit is to today's functions and traits, and the past's traits (only rarely the past's genes as well), and to extrapolate from then to now, using reasoning--typically informal reasoning--to connect the dots with steady lines, the way we treat objects falling to earth or planets orbiting stars.

However, much of this is because evolutionary change is highly subject to time-compression that both reflects and is caused by these assumptions.  The 'million' aspect of a million years is skipped over as if it were just a few days.  Yet, we are wholly aware of the immense timescales that apply to most evolutionary changes in complex functions, like, say, our brainpower or our upright posture.  One way to try, at least, to unhitch ourselves from these illusory lapses into physics-like determinism, is to look at things over a much more vast time scale, for which we actually have evidence.

An instructive case
It is probably impossible for us to really grasp the meaning of evolution's timescale.  That's the enormous value of mathematical modeling, if it is used properly.  Our 'ancient modern human' ancestors in the fossil record existed around 100,000 years ago, or arguably much less.  Our species has occupied the world since then, but even much of that well within the last 20,000 or so years (only around 12,000 in the Americas).

But we have some really good evidence of things on spans of times a thousand times as long--that is, on the order of 100,000,000 (a hundred million) years.  This example has to do with the evolution of flight.  A very fine discussion of feathered dinosaurs can be heard on the podcast of the BBC Radio 4 program "In Our Time", that can be downloaded as a podcast or listened to online; here is the link:

How did dinosaurs or their precursors develop the complexly rearranged bodies, and the feathered exteriors that were required for flight and the evolution of birds?  What adaptations occurred and when, and can we know why?  Major recent fossil finds, largely in China, have opened these questions for much closer examination than was possible when the first bird fossil, archaeopteryx, was found in Europe in around 1861, right after Darwin's Origin of Species (1859).

This BBC discussion, even expressed implicitly in a strong selectionistic viewpoint, shows the subtleties of the issues, when 100 million years is the span and large the number of specimens.  If you listen carefully, you can see the many nuances, small changes, rudimentary beginnings and so on that were involved--and the nature of speculation and attempts to guess at the nature of the reasons for the existence of these small steps that eventually led to feathered flight--but that, in themselves, were mainly unrelated to flight.  It is a sobering lesson in evolutionary interpretation, and even this discussion necessarily lapses into speculation.

Tuesday, October 24, 2017

My so-called view of life

It's no secret I love evolution.

But I usually feel like such an outsider when it comes both to how it's done professionally and in pop culture. I think it's my tendency to see proximate rather than ultimate causes and it's the ultimate causes that seduce and bedazzle. I've learned that if you question ultimate evolutionary narratives, you're a party pooper. I'm a party pooper.

Here I am
Typing to myself
I've got the outsider's blues

Let's start with some recent fish science. These guppies of the same species, born big and born little, have been very nicely shown to grow at the same pace. The big ones are born later and into a competitive food environment. Researchers offer that it's due to selection for context-dependent control over gestation length/birth timing.  But why? What about a proximate view? Surely the mother's context and its impact on her biology and on her eggs and babies is important. There may be no need to imagine a fancy adaptation that switches birth timing so that babies are badass food competitors ... Like there is no need to imagine a fancy adaptation that switches birth timing so that human babies escape the birth canal in time.

And, also today, there's news of a conference paper on human inbreeding. Most everyone believes inbreeding is bad, especially evolutionary scientists, many of whom rely on it being bad to make sense of animal behavior through their own culturally-tinted, taboo-tainted goggles. It's also foundational to how many evolutionary scientists explain cooperation with non-kin and our taboos against inbreeding. The news report linked above describes an enormous study of parents, all over the world, who are cousins who produce children. There's a list of biological trends for the outcomes of inbreeding that are assumed to be less than ideal (e.g. these kids are 1 cm shorter than average and less than 1 kg lighter at birth) and it's explained by genetics, of combining genomes of close relatives. Included in these traits of interest is age at first sex (delayed in offspring of inbreeding), age at first birth (same), number of opposite-sex partners (fewer in the inbred), number of offspring (fewer begat by the inbred). Sooo, I trend with the inbred. Am I inbred? No. To me, these trends don't scream bad genes from naughty parents. These outcomes look like they'd be influenced pretty heavily by complex cultural conditions and socioeconomic status, which may be intimately linked with conditions that pair-up cousins in the first place. Did these factors enter into the analysis? We'll have to wait and see when the paper's published.

And another news item today has me kicking a can out here. What if, rather than it being due to a fancy adaptation to seasonal fluctuation in resources, shrews' skulls shrink over winter as they experience the pressure and temperature of hard, cold dirt?

For some reason today--and maybe it's because my life writ-large lacks much opportunity to hold these discussions with people in real life, and my life writ-small has me pulled hard away from learning and doing evolution, period--I'm feeling nostalgic. The guppies, the inbreeding, and the shrew skulls awoke some ghosts of my past...

What if perpetual evolution due to mutation* causes speciation, rather than natural selection?

There's no way that everything that differs between males and females is explained by sexual selection. So what if body size and strength differences are a bigger story than that?

In that vein, what if women are smart BECAUSE HUMANS ARE SMART, and not to outfox rapists?

What if man's big penis is due to man's big vagina and not so much due to survival of the biggest?

What if the same mutation in multiple individuals can be induced by a virus? That kind of head start would seem to make it much easier for a mutation to go to fixation whether due to drift or selection.

I'm more similar, genetically, than 50% to my mom, to you, and to every single person on this planet. So what are we actually supposed to learn from all these fancy evolutionary equations that insist I'm only 50% similar to my parents, and less and less similar to everyone else, including you, in the tree?

And, I realize this may sound silly and obvious, but animals don't know where babies come from. Given the words we use, reading about the evolution of animal behavior is so confusing, in this light.

To those who get it
To evolution's outsiders
Do you wanna form a band?

* (and, in the myriad species who have it, the coin-flip of extinction or inheritance for each part of the genome, known as recombination and segregation during the halving of the genome during sperm and egg production)

Sunday, October 15, 2017

Understanding Obesity? Fat Chance!

Obesity is one of our more widespread and serious health-threatening traits.  Many large-scale mapping as well as extensive environmental/behavioral epidemiological studies of obesity have been done over recent decades.  But if anything, the obesity epidemic seems to be getting worse.

There's deep meaning in that last sentence: the prevalence of obesity is changing rapidly.  This is being documented globally, and happening rapidly before our eyes.  Perhaps the most obvious implication is that this serious problem is not due to genetics!  That is, it is not due to genotypes that in themselves make you obese.  Although everyone's genotype is different, the changes are happening during lifetimes, so we can't attribute it to the different details of each generation's genotypes or their evolution over time. Instead, the trend is clearly due to lifestyle changes during lifetimes.

Of course, if you see everything through gene-colored lenses, you might argue (as people have) that sure, it's lifestyles, but only some key nutrient-responding genes are responsible for the surge in obesity.  These are the 'druggable' targets that we ought to be finding, and it should be rather easy since the change is so rapid that the genes must be few, so that even if we can't rein in McD and KFC toxicity, or passive TV-addiction, we can at least medicate the result.  That was always, at best, wishful thinking, and at worst, rationalization for funding Big Data studies.  Such a simple explanation would be good for KFC, and an income flood for BigPharma, the GWAS industry, DNA sequencer makers, and more.....except not so good for  those paying the medical price, and those who are trying to think about the problem in a disinterested scientific way.  Unfortunately, even when it is entirely sincere, that convenient hope for a simple genetic cause is being shown to be false.

A serious parody?
Year by year, more factors are identified that, by statistical association at least and sometimes by experimental testing, contribute to obesity.  A very fine review of this subject has appeared in the mid-October 201 Nature Reviews Genetics, by Ghosh and Bouchard, which takes seriously not just genetics but all the plausible causes of obesity, including behavior and environment, and their relationships as best we know them, and outlines the current state of knowledge.

Ghosh and Bouchard provide a well-caveated assessment of these various threads of evidence now in hand, and though they do end up with the pro forma plea for yet more funding to identify yet more details, they provide a clear picture that a serious reader can take seriously on its own merits.  However, we think that the proper message is not the usual one.  It is that we need to rethink what we've been investing so heavily on.

To their great credit, the authors melded behavioral, environmental, and genetic causation in their analysis. This is shown in this figure, from their summary; it is probably the best current causal map of obesity based on the studies the authors included in their analysis:

If this diagram were being discussed by John Cleese on Monty Python, we'd roar with laughter at what was an obvious parody of science.  But nobody's laughing and this isn't a parody!   And it is by no means of unusual shape and complexity.  Diagrams like this (but with little if any environmental component) have been produced by analyzing gene expression patterns even just of the early development of the simple sea urchin.  But we seem not to be laughing, which is understandable because they're serious diagrams.  On the other hand, we don't seem to be reacting other than by saying we need more of the same.  I think that is rather weird, for scientists, whose job it is to understand, not just list, the nature of Nature.

We said at the outset of this post that 'the obesity epidemic seems to be getting worse'.  There's a deep message there, but one essentially missing even from this careful obesity paper: it is that many of the causal factors, including genetic variants, are changing before our eyes. The frequency of genetic variants changes from population to population and generation to generation, so that all samples will look different.  And, mutations happen in every meiosis, adding new variants to a population every time a baby is born.   The results of many studies, as reflected in the current summary by Ghosh and Bouchard, show the many gene regions that contribute to obesity, their total net contribution is still minor.  It is possible, though perhaps very difficult to demonstrate, that an individual site might account more than minimally for some individual carriers in ways GWAS results can't really identify.  And the authors do cite published opinions that claim a higher efficacy of GWAS relative to obesity than we think is seriously defensible; but even if we're wrong, causation is very complex as the figure shows.

The individual genomic variants will vary in their presence or absence or frequency or average effect among studies, not to mention populations.  In addition, most contributing genetic variants are too rare or weak to be detected by the methods used in mapping studies, because of the constraints on statistical significance criteria, which is why so much of the trait's heritability in GWAS is typically unaccounted for by mapping.  These aspects and their details will differ greatly among samples and studies.

Relevant risk factors will come or go or change in exposure levels in the future--but these cannot be predicted, not even in principle.  Their interactions and contributions are also manifestly context-specific, as secular trends clearly show.  Even with the set of known genetic variants and other contributing factors, there are essentially an unmanageable number of possible combinations, so that each person is genetically and environmentally unique, and the complex combinations of future individuals are not predictable.

Risk assessment is essentially based on replicability, which in a sense is why statistical testing can be used (on which these sorts of results heavily rely).  However, because these risk factor combinations are each unique they're not replicable.  At best, as some advocate, the individual effects are additive so that if we just measure each in some individual add up each factor's effect, and predict the person's obesity (if the effects are not additive, this won't work).  We can probably predict, if perhaps not control, at least some of the major risk factors (people will still down pizzas or fried chicken while sitting in front of a TV). But even the known genetic factors in total only account for a small percentage of the trait's variance (the authors' Table 2), though the paper cites more optimistic authors.

The result of these indisputable facts is that as long as our eyes are focused, for research strategic reasons or lack of better ideas, on the litter of countless minor factors, even those we can identify, we have a fat chance of really addressing the problem this way.

If you pick any of the arrows (links) in this diagram, you can ask how strong or necessary that link is, how much it may vary among samples or depend on the European nature of the data used here, or to what extent even its identification could be a sampling or statistical artifact.  Links like 'smoking' or 'medication', not to mention specific genes, even if they're wholly correct, surely have quantitative effects that vary among people even within the sample, and the effect sizes probably often have very large variance. Many exposures are notoriously inaccurately reported or measured, or change in unmeasured ways.   Some are quite vague, like 'lifestyle', 'eating behavior', and many others--both hard to define and hard to assess with knowable precision, much less predictability.  Whether their various many effects are additive or have more complex interaction is another issue, and the connectivity diagram may be tentative in many places.  Maybe--probably?--in such traits simple behavioral changes would over-ride most of these behavioral factors, leaving those persons for whom obesity really is due to their genotype, which would then be amenable to gene-focused approaches.

If this is a friable diagram, that is, if the items, strengths, connections and so on are highly changeable, even if through no fault of the authors whatever, we can ask when and where and how this complex map is actually useful, no matter how carefully it was assembled.  Indeed, even if this is a rigidly accurate diagram for the samples used, how applicable is it to other samples or to the future?Or how useful is it in predicting not just group patterns, but individual risk?

Our personal view is that the rather ritual plea for more and more and bigger and bigger statistical association studies is misplaced, and, in truth, a way of maintaining funding and the status quo, something we've written much about--the sociopolitical economics of science today.  With obesity rising at a continuing rate and about a third of the US population recently reported as obese, we know that the future health care costs for the consequences will dwarf even the mega-scale genome mapping on which so much is currently being spent, if not largely wasted.  We know how to prevent much or most obesity in behavioral terms, and we think it is entirely fair to ask why we still pour resources into genetic mapping of this particular problem.

There are many papers on other complex traits that might seem to be simple like stature and blood pressure, not to mention more mysterious ones like schizophrenia or intelligence, in which hundreds of genomewide sites are implicated, strewn across the genome.  Different studies find different sites, and in most cases most of the heritability is not accounted for, meaning that many more sites are at work (and this doesn't include environmental effects).  In many instances, even the trait's definition itself may be comparably vague, or may change over time.  This is a landscape 'shape' in which every detail is different, within and between traits, but is found in common with complex traits.  That in itself is a tipoff that there is something consistent about these landscapes but we've not yet really awakened to it or learned how to approach it.

Rather than being skeptical about these Ghosh and Bouchard's' careful analysis or their underlying findings, I think we should accept their general nature, even if the details in any given study or analysis may not individually be so rigid and replicable, and ask: OK, this is the landscape--what do we do now?

Is there a different way to think about biological causation?  If not, what is the use or point of this kind of complexity enumeration, in which every person is different and the risks for the future may not be those estimated from past data to produce figures like the one above?  The rapid change in prevalence shows how unreliable these factors must be, at prediction--they are retrospective of the particular patterns of the study subjects.  Since we cannot predict the strengths or even presence of these or other new factors, what should we do?  How can we rethink the problem?

These are the harder question, much harder than analyzing the data; but they are in our view the real scientific questions that need to be asked.

Tuesday, October 10, 2017

An article in Issues in Science and Technology

Regular MT readers will know that some of us here have a very skeptical view of the obsession with genomewide association mapping (GWAS) for every trait under the sun.  We think that mapping served a purpose once upon a time, to show that complex apparently polygenic traits really were complex and polygenic.  Identifying many contributing genome regions showed that, and that each individual has a unique genotype and that many or most relevant variants were too rare or their effects too weak to be detected (most heritability wasn't accounted for by the mapping).  When tens, hundreds, or even thousands (yes!) of genome sites were claimed to contribute, it has seemed we're lost in never-never land when it comes to sensible explanations of causation.

But the funding keeps flowing for this mostly useless sort of Big Data (sorry, we can't salivate over that phrase the way so many do, because we're no longer out hunting for Big Grants).  Our view, expressed many times and in many ways here, is that we need better ideas about the relationships between genes and health, and between genes and our traits and their evolution.

We've written about this in the past, but rather than do that again, I've written some of these issues in a somewhat different way in a new paper.  That paper, in the new, Fall 2017, Issues in Science and Technology, "Is precision medicine possible?", lays out some thoughts about genetic causal complexity vis-à-vis 'precision' genomic medicine, and the challenges we face.

Rather than rehashing here what you can see in that article, if you're interested, just go to the article. It's in a journal related to policy, but the odds that any policymaker will read it carefully much less do anything constructive in response are between slim and none.  Still, blogs are for stating a point of view!

The people whose truly genetic disorders are not being alleviated because we're dumping so much resource into stale ideas are being shortchanged.  However, until we've made the alternative investment, in attack rather than 'mapping' disease, we'll not know how preventable or treatable they may be.

Friday, August 18, 2017

This year's (2017) textbook-free Introduction to Human Origins and Evolution

This is a tradition now. You can search the archives for previous years' and for my philosophy behind this course. It's always evolving. 

As usual there is no textbook. Students only need to get the much-loved book by Alice Roberts, The Incredible Unlikeliness of Being ("IUB"), and read it all along with many other articles as you'll see below.

This year I was happy to see a study supporting my own practice which I take to be common sense--that we should teach genetics before evolutionary theory for explaining how it works (e.g. its mechanisms):

I haven't looked in a while, but teaching genetics before the mechanisms of evolution is not the approach of a single one of the textbooks for this course and that's one of the many reasons I stopped using them!

So, minus the in-class handouts and worksheets, here are the daily portfolio assignments for the newest incarnation of my big introductory, general education course on human evolution. As usual, I apologize for the formatting issues caused by pasting from a Word Document into this blog.  It's all yours if you want it....

 Fall 2017
APG 201: Human Origins and Evolution
3 credits
Dr. Holly Dunsworth

1. Observe and Explain - This view of life. Our place in nature

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

1.1 - Introduction to course
Assigned Reading/viewing
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)  
The ape in the trees – Dunsworth (The Mermaid’s Tale)
How Do We Know When Our Ancestors Lost Their Tails? (video; 4 min)

Prompt:  This is an in-class prompt that you will be given in class.


1.2 - Do animals know where babies come from?
Assigned Reading/viewing
“Do animals know where babies come from?” by H. Dunsworth (Scientific American)- Located on Sakai, and linked here:

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.


1.3 - Scientific process 
Assigned Reading/viewing
IUB, Chapter 1: Beginnings - Roberts
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

Prompt 1: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t. What do you expect to learn from the rest of the book?

Prompt 2:  This has two parts, A and B. First, choose one of the following well-known and established observations. Indicate your choice by highlighting it.
  1. Children from low income homes show evidence of malnutrition.
  2. In most humans, the right humerus (upper arm bone) is larger than the left one.
  3. Pregnant mothers who smoke tend to have smaller babies than mothers who do not smoke.
  4. Chimpanzees living in zoos tend to be overweight compared to their relatives living in the wild.

A.    Without using anything but your own mind, come up with two different hypotheses to explain that one observation.

B.    Briefly describe how you would test these hypotheses you have offered. Include discussion of the methods and variables for obtaining evidence and the kinds of evidence that you would need to find to both refute and to support each hypothesis. 

1.4 - Linnaeus and the Order Primates
Assigned Reading/viewing
Characteristics of Crown Primates – Kirk (Nature Education)

Prompt: Answer the following questions (complete sentences are not necessary) by sticking to the reading above and these excellent resources:
Encyclopedia of Life:

1.    My primate is a(n)  [will be assigned to you in class]
2.    What is the species?
3.    Here is a link to a video of this species:
4.    Where does it live on Earth?
5.    What is the range of its habitat? Describe the nature of the habitat.
6.    Is your primate nocturnal, diurnal, or crepuscular?
7.    What does it eat?
8.    How does it move about? 
9.    How does it socialize? (i.e. solitary? groups?...)
10.  How does it raise offspring? (i.e. solitary? groups?...)
11.  Body size (both kg/g and lb/oz)? Are male and female different?
12.  Coloration?
13.  What are its predators?
14.  Is it protected or endangered?
15.  Anything else fascinating about it?
16.  At what point in the past (millions of years ago) did it share a most recent (aka “last”) common ancestor with humans? (go to to find out)

1.5  - Overview of Primate taxonomy
Assigned Reading/viewing
Many primate video clips –Posted on Sakai
Additional resources
Old World monkeys – Lawrence and Cords (Nature Education)

Prompt: In 200 words 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.

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

1.6 - Primate diet and locomotion; ecology and anatomy
Assigned Reading/viewing
IUB, Chapter 2: Heads and brains – Roberts
Additional resources
Primate locomotion – Gebo (Nature Education)
Our Fishy Brain (video; 2.5 mins)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

[Prompt for practice: Label all the bones that you can on the human skeleton. No need to demonstrate it here. Print out an  image and draw on it, but no need to scan into your portfolio (let’s keep this low tech, I trust you!). If you cannot name them all using only your memory, use a quality on-line resource (like to help you. (Do not concern yourself with the location of the individual carpals and tarsals but point out where the carpals and tarsals are.) ]
[Prompt for practice: Go to and based on what you see, draw the os coxa (half of the pelvis) of a chimpanzee and a human. (Same as before, do on your own, no need to include here… let’s keep it low tech.)]
Prompt: Describe the similarities and differences in anatomy between chimp and human pelves/pelvises (do not worry about applying technical jargon). What kinds of behavioral differences might correlate with the anatomical differences in the pelvis and why?
[Prompt for practice: Go to and based on what you see, draw the skull  (including teeth) of a chimpanzee and a human(Same as before, do on your own, no need to include here… let’s keep it low tech.).]
Prompt: Describe the similarities and differences in anatomy between chimp and human skulls and teeth (do not worry about applying technical jargon. What kinds of behavioral differences might correlate with the anatomical differences in skulls and teeth and why?
1.7 - continued 
Assigned Reading/viewing
IUB, Chapter 3: Skulls and senses – Roberts
Additional resources
Finding the Origins of Human Color Vision (video; 5 mins)
We Hear with the Bones that Reptiles Eat With (video; 4 mins)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

1.8 - Primate encephalization, tool use and communication
Assigned Reading/viewing
IUB, Chapter 4: Speech and gills - Roberts
Additional resources
Primate Communication – Zuberbuhler (Nature Ed)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

1.9 - Primate sociality
Assigned Reading/viewing
The Human Spark 2: So Human So Chimp – PBS, hosted by Alan Alda (video; 55 mins IF LINK IS BROKEN JUST SEARCH FOR IT)
Additional resources

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)

Prompt: In 200 words or more, react to The Human Spark 2, highlighting something you already knew and also something you learned that was brand new to you. What is the human spark?

1.10 - Evolution (shared ancestry over deep time) and Darwin's evidence for it
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)
Additional resources
Amazing Places, Amazing Fossils: Tiktaalik (video; 5 mins)
The Ancient History of the Human Hand (video; 4 mins)

Prompt: In 200 words or more, according to your impression of Darwin’s writings, reflect on the circumstances or experiences that influenced Darwin's thinking.

1.11 - Phylogeny
Assigned Reading/viewing
Reading a phylogenetic tree – Baum (Nature Ed)
Trait Evolution on a Phylogenetic Tree – Baum (Nature Ed)

Prompt: How could someone falsify the accepted fact of evolution? Remember, for something to exist within the realm of that which is knowable via science, there must be a hypothetical way to falsify it.


2. Explain and Predict - Explaining the similarities and differences. How evolution works.

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

2.1 - How eggs and sperm get made and how they make you
Assigned  Reading/viewing
IUB, Chapter 5: Spine and segments – Roberts
Additional resources
Gregor Mendel and the Principles of Inheritance – Miko (Nature Ed)
Mendelian Genetics: Patterns of Inheritance and Single-Gene Disorders – Chial (Nature Ed)
Developing the Chromosome Theory – O’Connor (Nature Ed)
Genetic Recombination – Clancy (Nature Ed)
What is a Gene? Colinearity and Transcription Units – Pray (Nature Ed)
RNA functions – Clancy (Nature Ed)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

2.2 - continued
Assigned Reading/viewing
Things Genes Can’t Do – Weiss and Buchanan (Aeon)
Additional resources
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)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t. Why is it important to consider what genes can and cannot do?

2.3 - Inheritance, gene expression, Mendel's simplicity and reality’s complexity
IUB, Chapter 6: Ribs, lungs and hearts– Roberts
Additional resources
Hox Genes in Development: The Hox Code – Myers (Nature Ed)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

2.4 - Mutation and gene flow
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)
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)
Mutation not natural selection drives evolution –  Tarlach (about Nei; Discover Magazine)

Prompt: Reflect back on your answer to “what is evolution” from Day 1.1 of class. What did you get right? What did you get wrong? What did you omit? How do the three assigned readings shape your view of evolution? What are you still left wondering about evolution?

2.5 - Natural selection
Assigned Reading/viewing
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)

Prompt: Write an answer for each of the questions below. In other words, come up with a hypothesis to explain the evolution of each of the four phenomena. These are evolutionary scenarios that you are writing.  This is brainstorming, so have no fear, but you should still write with clarity.
1.    How did the mandrill get that colorful face? What about the rear?
2.    How did the colobus monkey get a long, specialized gut?
3.    How did silverback gorillas become twice as big as females?
4.    How did humans become “naked”? (i.e. how did we cease to be as furry as the other primates)?

2.6 - Genetic drift
Assigned Reading/viewing
The Evolution of Your Teeth (video; 3 mins)
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)

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

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

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

2.7 - Malaria resistance and lactase persistence
Assigned Reading/viewing
Additional resources
Natural Selection: Uncovering Mechanisms of Evolutionary Adaptation to Infectious Disease – Sabeti (Nature Ed)

Prompt: Answer the following questions:

A.    What are the components of natural selection scenarios?
B.    What are the potential benefits to losing grasping abilities in our feet? In what environmental context?
C.    Write an evolutionary scenario, using natural selection, to explain how humans lost grasping ability in our feet.
D.    Write an evolutionary scenario, without using any form of selection, to explain how humans lost grasping ability in our feet.
E.     Give a plausible explanation, in Darwinian terms (i.e. using the components of natural selection, or if you want, sexual selection), for how humans lost our body fur and are now what’s often called ‘the naked ape.’ There are many ways to answer this for full credit as long as you incorporate all the components of selection properly
F.     Explain body fur loss without selection, using drift:

2.8 - Building evolutionary scenarios
Assigned Reading/viewing
Prompt: Look back at 2.5, for each of your evolutionary scenarios (i.e. your answers to the four questions), describe which evolutionary mechanisms (discussed in class) that you hypothesized were at work.
1.    “How did the mandrill get that colorful face? What about the rear?” Mechanisms you used (even if you didn’t use the official terms):
2.    “How did the colobus monkey get a long, specialized gut?” Mechanisms you used (even if you didn’t use the official terms):
3.    “How did silverback gorillas become twice as big as females?”Mechanisms you used (even if you didn’t use the official terms):
4.    “How did humans become ‘naked’?” (i.e. how did we cease to be as furry as the other primates)? Mechanisms you used (even if you didn’t use the official terms):

Prompt: Rewrite each of the four explanations you wrote for 2.5 to make them more scientifically accurate, using only the four main mechanisms of evolution that we discussed in class and those terms: mutation, gene flow, genetic drift, and natural selection. You may need to just change a few words or you may need to completely revise the entire answer, it depends on what you originally wrote.  Important! Banned words for your scenarios include: Need(s/ed/ing), want(s/ed/ing), try(s/ed/ing), best, most, and of course fittest.

1.    How did the mandrill get that colorful face? What about the rear?
2.    How did the colobus monkey get a long, specialized gut?
3.    How did silverback gorillas become twice as big as females?
4.    How did humans become “naked”? (i.e. how did we cease to be as furry as the other primates)?
2.9 – Species and speciation
Assigned Reading/viewing
Planet without apes? – Stanford (Huffington Post)
Additional resources
Primate Speciation: A Case Study of African Apes – Mitchell & Gonder (Nature Ed)
Why should we care about species? – Hey (Nature Ed)
Speciation: The origin of new species – Safran (Nature Ed)
The maintenance of species diversity – Levine (Nature Ed)
Macroevolution: Examples from the Primate World – Clee & Gonder (Nature Ed)

Prompt: In 200 words or more, reflect on the reading assignment and explain why apes are in danger of extinction (thoughtful guesses are welcome).

2.10  - Genomics, molecular clocks, and the LCA
Assigned Reading/viewing
Lice and Human Evolution (video; 11 mins)
Additional resources
The Onion Test – Gregory (Genomicron)
The Molecular Clock and Estimating Species Divergence – Ho (Nature Ed)

Prompt: What are molecular clocks for and how do they work? What do the molecular clocks of lice tell us about human evolution?


3. Test and Observe - Evolving humans, past and present. Ancient evidence for our extinct relatives. Human variation.

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

3.1 - The earliest hominins
Assigned Reading/viewing
IUB, Chapter 7: Guts and yolk sacs – Roberts
Desktop Diaries: Tim White (video; 7 mins)
Ancient Human Ancestors: Walking in the woods (video; 4 mins)
Additional resources
How to Become a Primate Fossil – Dunsworth (Nature Ed)
Dating Rocks and Fossils Using Geologic Methods – Peppe (Nature Ed)
Overview of hominin evolution – Pontzer (Nature Ed)
The Earliest Hominins: Sahelanthropus, Orrorin, and Ardipithecus - Su (Nature Ed):

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

3.2 - Australopithecus and Paranthropus
Assigned Reading/viewing
Ardi-Ardipithecus ramidus and human evolution ((video; 3:33 mins)
Trowelblazers (blog):  
An Unsuitable Job for a Woman (blog):
Additional resources
Lucy: A marvelous specimen – Schrein (Nature Ed)
The "Robust" Australopiths – Constantino (Nature Ed)

Prompt: Find a woman from the ‘Trowelblazers’ blog and briefly (in less than 100 words) describe why she is there. Do the same for ‘An Unsuitable Job for a Woman’.

3.3 - Technological and ecological hypotheses for encephalization
Assigned Reading/viewing
IUB, Chapter 8: Gonads, genitals and gestation – Roberts
Ancient Hands, Ancient Tools (video; 5 mins)
Additional resources
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”

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

3.4 - Homo erectus
IUB, Chapter 9: On the nature of limbsRoberts
Additional resources
Homo erectus - A Bigger, Smarter, Faster Hominin Lineage – Van Arsdale (Nature Ed)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

3.5 - Neanderthals
IUB, Chapter 10: Hip to ToeRoberts
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)

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

3.6 - Homo sapiens
Assigned reading/viewing
What happened to the Neanderthals? – Harvati (Nature Ed)
The Neanderthal Inside Us (video; 4 mins)
Additional resources
The Transition to Modern Behavior – Wurz (Nature Ed)
Neanderthal Behavior – Monnier (Nature Ed)

Prompt: In 200 words or more, offer an explanation for what happened to the Neanderthals. Where did they go and why?

3.7 - Social hypothesis for encephalization
Assigned reading/viewing
IUB, Chapter 11: Shoulders and ThumbsRoberts

Prompt: In 200 words or more, react to the assigned reading. Include one thing you knew and one thing you didn’t.

IMPORTANT: For the remaining days, students will also be completing the workbook for the skin color lesson provided by the Smithsonian’s Human Origins team.  ( ) We’ll be accomplishing it bit-by-bit in class and with assignments to carry on outside of class. The complete workbook is due on the last day of class, in class. I find that having something due then increases attendance for evaluations and  increases the audience for my final, profound thoughts.

3.8 - The evolution of Homo sapiens diversity; Evolution, race, racism, sex, and sexism
Assigned reading/viewing
Testing models of modern human origins with archaeology and anatomy – Tryon & Bailey (Nature Ed)
Additional resources
Anthropological genetics: Inferring the history of our species through the analysis of DNA – Hodgson & Disotell (Evolution: Education and Outreach)
Human Evolutionary Tree – Adams (Nature Ed)
Paternity Testing: Blood Types and DNA – Adams (Nature Ed)

Prompt: In 200 words or more, react to the assigned reading. Include a description of one question that is important and how these authors are going about helping to answer it here.

3.9 - continued
Assigned reading/viewing
Additional Resources

Prompt: Peruse the whole site ‘Understanding Race’ then take the Human Variation Quiz, there, and record all of the correct answers here. (No, you’re not being asked to share how you did on the quiz because many will feel embarrassed.)

3.10 - continued
Assigned reading/viewing
There's no such thing as a 'pure' European—or anyone else – Gibbons (Science)
A lot of Southern whites are a little bit black – Ingraham (Washington Post)

Prompt:  In 200 words or more, react to the assigned readings. Be sure to include your take on whether Gibbons is being literal or rhetorical when she writes “untainted by mixing with immigrants.”

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

Prompt:  In 200 words or more, react to the assigned readings. What’s the link between racism and evolutionary theory? Is Ota Benga’s treatment justified by evolution? Is equality and peace possible, given our evolutionary history?

3.12 - continued
Assigned Reading/viewing
How Donald Trump Got Human Evolution Wrong – Dunsworth (Washington Post) 
Peace Among Primates – Sapolsky (The Greater Good)

Prompt:  In 200 words or more, react to the assigned readings. From your point of view, how prevalent is Trump’s take on human evolution in pop culture?  Do you believe it’s harmful? Why or why not?

3.13- continued
Assigned reading/viewing
Humans never stopped evolving – Hawks (The Scientist)
We are not the boss of natural selection – Dunsworth (io9)

Prompt:  In 200 words or more, argue whether or not we’re still evolving. Why is this a question?

3.14 - Conclusions
Assigned reading/viewing
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)

Prompt:  In 200 words 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.