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Some fortnights of links – 28 Sep 2013

It has been awhile since my last link round-up.  I few months ago I had gotten in the habit of book-marking items I came across online that I thought were interesting or relevant to the topics of this blog, and then posting them online every two weeks.

Jason Collins over at Evolving Economics posts a similar round-up of links weekly. A few months back, when I went to post my bi-weekly list, I discovered that he had already posted ~90% of them. So, as not to be redundant, I gave up for awhile and decided to finish my dissertation instead.

However, now that the dissertation is over, I am getting back to blogging. I also have not been reading as much on the internet lately, so this week’s list will be relatively short:

Florid or falsifiable? The use of metaphors in science. Cultured Primate’s discussion of the “ratchet effect.”

Steven Pinker embraces scientism. Bad move, I think. The internet seems to be well over Pinker’s seemingly humanities-dissing essay.  But I think Massimo Pigliucci’s response is worth a link.

Neville Chamberlain Was Right: The maligned British prime minister did what we would want any responsible leader to do.

Some friends may have moved to the Switzerland of Europe, but I have moved to East Tennessee, the Switzerland of America.

Journal article of the week (a new feature):

War, space, and the evolution of Old World complex societies by Peter Turchin, Tom Currie, Edward  Turner, and Sergey Gavrilets (disclosure: Gavrilets in my post-doc mentor) in PNAS.  The article is open access. It was covered in Wired and a lot of other outlets. Peter Turchin blogs about it here and here.

Entertaining in that internet sort-of-way:

Every Second on the Internet

My New Job: Post-doctoral Fellow at NIMBioS

Today I start as one of three new post-doctoral research fellow at the National Institute for Mathematical and Biological Synthesis (NIMBioS).

NIMBioS Logo

NIMBioS is an NSF-funded research center hosted at the University of Tennessee, Knoxville. Most people pronounce it “nimbus” (like the raincloud). An excerpt from the NIMBioS mission:

A major goal of mathematical models and analysis in biology is to provide insight into the complexities arising from the non-linearity and hierarchical nature of biological systems. Primary goals of NIMBioS [are] to foster the maturation of cross-disciplinary approaches in mathematical biology and foster the development of a cadre of researchers who are capable of conceiving and engaging in creative and collaborative connections across disciplines to address fundamental and applied biological questions.

Read as mathematically-inclined biologists and biologically-inclined applied mathematicians doing science!

One of the best things about this post-doc is that I have the freedom to focus on my own research interests. Another is that I have an awesome research mentor. Another is that I will get to work with a great group of people. Another is that I get to bring together researchers I admire from different fields by organizing two transdisciplinary working groups.  And I get to participate in workshops already underway.

In any case, watch this space for updates about my scientific adventures in Tennessee. (Apparently, there’s a chance I’ll finally become a college football partisan.)

Navigating Black Rock City: Geometrically-based Heurisitcs

I spent much of the past week in Black Rock City which at ~68,000 people is, for one week a year, the third largest city in Nevada.

Photo Source

Unlike most other cities, BRC is laid out in polar coordinates. Some roads radiate out from the center that are numbered on an hour-system (like a clock) with intervals every half-hour. Other roads follow the circumferences of the circles with the innermost road called the “Esplanade” and the rest given names following the alphabet from innermost to outermost (this year from A to L).  (See a diagram of the 2013 layout here and a huge aerial photo of the city here.)

While navigating a normal grid is pretty straight forward.  Navigating a polar grid is less intuitive for most of us. One thing that becomes clear rather quickly is that sometimes moving to an inner circle and then navigating back outward is shorter than staying on an outer circle.  Often the question arises “when is it more direct to travel inward to a smaller circle and when is it more direct to just travel around a given circumference.” This blog post is an attempt to develop a heuristic

(Note that some BRC participants may object to the very idea of trying to get somewhere efficiently.  The journey, they may argue, is often more interesting than the destination. I have some sympathy for ,this view.  However, you sometimes just want to be first in line for some cold pizza* or get the best seat for a geology lecture. Furthermore, folks who would like a higher journey to destination ratio, can simply follow the opposite heuristic from that developed in this post to extend their travel times.)

For those not interested in the mathematical details, here are the rules of thumb I derive below:

1) If your starting point is farther from the circles’ center than your destination, travel to the circumference road that corresponds to your destination (e.g. if you are starting on H and your destination is on C, travel to C).

2) If you would rather stick to the Esplanade than cut across the inner circle: If your destination is four or more hours away, take the Esplanade and then travel up the nearest radial road to your destination.  If your destination is fewer than four hours away, take the circumference road and then travel up the nearest radial road to your destination.

3) If you are willing to cut across the inner circle: Cut across the circle if your destination is 3.5 or more hours away. If you are on A or B road, cut across the inner circle if you are three or more hours away. Otherwise, stay on the circumference road and then travel up the nearest radial road to your destination.

Note that my analysis ignores the complicated business around six o’clock which is confusing enough to be avoided anyway.  And I ignore the open circle at the top.  If you are crossing it, the rule is just to take a straight line to your destination on the other side.

The Maths Part 1 (we need roads edition):

The logic behind step (1) above is pretty straight-forward.  It is shorter to travel around an inner circle than an outer circle, so if you are going to travel to a point on an inner circle, it makes sense to travel there first.  Similarly, if the point you are going to is on an outer circle from your starting point, it doesn’t make sense to move to the out circle until the end of the journey.

This insight effectively reduces the problem to one where your start and end point are on the same circle and the question becomes whether one should move to an even smaller circle that this starting point.

These two options are shown in this figure, where r is the distance from the center of the circles to the inner circle and d is the distance between the inner and outer circle:

Using the formula for the circumference of a circle (where h is the angular distance traveled around the circumference in hours) , the distance of the inner route is:

\frac{h}{12} 2 \pi r + 2d

The distance to the outer route is:

\frac{h}{12} 2 \pi (r + d)
When is the inner route shorter than the outer route:
\frac{h}{12} 2 \pi r + 2d < \frac{h}{12} 2 \pi (r + d)

Which reduces to:

h > \frac{12}{\pi} \approx 3.8

Notice that this answer is independent of both d and r.   Since the roads are at half-hour intervals, it is best to go to the Esplanade when one is four or more hours away (one third of the circumference of BRC) and it is best to stay on one’s circumference road when one is 3.5 or fewer hours away.

The Maths Part 2 (where we’re going we don’t need roads):

The above analysis assumes that one stays on the Esplanade, but it is always a shorter distance to cut across the inner circle (though the  road conditions are not as good).  Does this change the analysis?

Now the options look like this:

The length of the outer route is the same as above:

\frac{h}{12} 2 \pi (r + d)

However, the formula for the inner route uses the formula for the length of a chord:

2 r \sin \left(\frac{\theta}{2}\right) + 2d

The condition for cutting across the inner circle vs taking a circumference, where theta is in radians is:

2r\sin \left(\frac{\theta}{2}\right) + 2d < \theta (r + d)

Because of the sin function, solving this inequality is tricky.  So I just solved it numerically using the ratios of r to d from the official BRC layout — the distance from the Esplanade to A is 1/5 the distance from the center to the Esplanade, r, and the distance between each subsequent concentric circle is 1/10 of r.  Plugging these values in to the above inequality for various times from 0 to 6 hours gives the following conditions where it is shorter to cut across the inner circle:

Radians 0 0.26 0.52 0.79 1.05 1.31 1.57 1.83 2.09 2.36 2.62 2.88 3.14
Hours 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 5.5 6

Therefore, it is always shorter to cut across the inner circle when your destination is 3.5 of more hours away.  But if your starting or ending points are on A or B, it is also shorter to cross the inner circle when your destination is three or more hours away. Otherwise, it is shorter to stay on the outer circle.

* Especially when they run out of pizza by 11:55 – before their 12:00 start time.

Gentle Introductions to Evolution: A Crowd-sourced List

My labmate, Ryan Baldini, recently sent a request to the UC Davis ecology, population biology, human behavioral ecology, and cultural evolution list serves asking for suggestions for “an accessible, non-textbook introduction to evolution (how it works, what it implies, and evidence) to recommend to curious friends and family.”
He specifically asked for works that were more about evolution and less about contrasting evolution with creationism. After getting responses he then, helpfully, compiled a disseminated a list of books with some commentary. I asked him if I could post the list here for a (somewhat) wider audience.

Below are his results.  If you, dear readers, have any additional suggestions, please leave them in the comments.

I received so many helpful responses to my question that I decided to share the results with everyone. Below I've listed all books that received at least two mentions, along with their number of mentions. I gave a half point if someone wrote "this is a good book, but...".
The most-recommended intro to evolution books, for a non-scientist, are:
 Coyne - Why Evolution is True: 9.5
 Weiner - Beak of the Finch: 5
 Shubin - Your Inner Fish: 5
 Dawkins - The Blind Watchmaker: 3
 Zimmer - The Tangled Bank: 3
 Mayr - What Evolution Is: 2.5
 Dawkins - The Selfish Gene: 2.5
 Maynard Smith - The Theory of Evolution: 2
 Dennett - Darwin's Dangerous Idea: 2
Some comments:
 Many people accompanied their suggestions with helpful opinions, which I'll do my best to summarize.
-On Coyne: People clearly thought Coyne's book was strong, but opinion varied on how appealing it would be to skeptical readers. Many wrote that Coyne does not explicitly challenge religion, which makes his book more inviting than, say, anything by Dawkins. On the other hand, Coyne appears to be largely motivated by the Intelligent Design school curriculum debate, which may turn off some readers. His book is primarily aimed at showing why evolution, and not ID, should be taught in schools - which may interfere with the goal of simply teaching what evolution is. In short, Coyne is probably ideal for showing you "why evolution is true," but there may be better options if the reader simply wants to know what evolution is and how it works, without any politics.
-Some recommended Mayr's What Evolution Is and Maynard Smith's Theory of Evolution, but said that these are on the advanced end of the casual reading spectrum.
-Carl Zimmer's Tangled Bank is technically marketed as a textbook, but written for non-science students.
 A few honorable mentions:
-Some illustrated books were suggested, which are probably great for very casual or younger readers. These include:
 Miller and Van Loon - Darwin for Beginners
 Keller and Fuller - Origin of Species: A graphic adaptation
 Hosler, Cannon, and Cannon - Evolution: The Story of Life on Earth
-Jeffrey Firestone recommended a unique book that I thought I should list. It is:
 Cameron Smith - The Fact of Evolution
 Jeffrey wrote: "[This book] has a different approach then we've been used to seeing. It doesn't do Darwin and genes and recapitulate intro bio. It points out that microevolution is a mathematical necessity, and the way that evolution works is logical when you go step by step, even if it seems illogical when looked at in separate chunks without preparation.

Announcing "Evolutionary Approaches to Peace Science" workshop @ Peace Science Society 24 Oct

Joslyn Barnhart and I are organizing a workshop on “Evolutionary Approaches to Peace Science” in conjunction with this year’s Peace Science Society meeting at the University of Tennessee.  The workshop will be hosted at the National Institute for Mathematical and Biological Synthesis on 24 October. Information is below.

If you would like to participate, please email me sometime this week.  The workshop is conditional on a threshold number of participants, if there is enough interest we will send out an email with more information by the end of the month. Also, please pass along this announcement to anyone, especially graduate students or post-docs, that you think might like to attend.

This workshop will take a broad view of “evolutionary approaches.”  The unifying thread is  that of “selection” which requires consideration of variation in entities (e.g., norms, preferences, policies, institutions) and selective retention or transmission of these entities through time. 

Existing evolutionary approaches to peace science have focused, independently, on a wide range of evolutionary processes at a wide range of physical and temporal scales. However, it is likely that they happen simultaneously and have interesting interactions.

Some examples of existing approaches:
1) Policy learning and diffusion of successful policies
2) Normative and ideational change through “cultural selection”
3) Competition and selection on economic and political institutions

4) Computational and mathematical models of international conflict/cooperation

This workshop is intended to further a discussion of how to integrate these approaches into a useful whole, with a focus on mathematical and computational modeling and empirical techniques.

The format of the workshop will depend on the number of participants and their specialties and topics of interest. If the group is smaller, we will have a few “big picture” talks followed by facilitated discussion.  If the group is larger, we will likely divide the work into sub-groups who will report back to the larger group at the end.

Please contact us or comment below if you have any questions or suggestions.  

Perils of Writing 800-word Critiques of Social Science in the NYTs

I just sent my last dissertation chapter to my committee for comments, so I am back to blogging after a long hiatus while they decide whether I can graduate.

Today’s post is inspired by a back-and-forth between Andrew Gelman and Nicholas Christakis over an op-ed that Christakis wrote in the NYTs.  Christakis’s thesis is that we should shake up the current (historically contingent) disciplinary structure of the social sciences.  As an evolutionary social scientist who is frustrated by the seemingly arbitrary distinctions between different fields, I agree with much of what is in Christakis’s op-ed. (Though, for the record, Harvard and Princeton are maybe the last places I would look for collaborative interdisciplinary research – more like Arizona State.) I also agree with Gelman’s critique which is essentially about one paragraph.  But these are topics for another post.

This post is about the utility of publishing 800-word critiques of the social science for a general audience.  In his response to Gelman, Christakis wrote:

 As to your original complaint, let me say this: my main point (within a constrained 800-word format, for which the editors write the title, not the authors) is that we can learn something from the natural sciences about institutional forms and about ways of doing science (just as they surely can learn from us).

This is not without precedent.  Last year Kevin Clarke and David Primo also published an 800-word critique of the social sciences in the NYTs.  While I greatly admired their book, when condensed to a 800-word version for a general audience the argument lost a lot of its punch. 

In some sense this is to be expected. Scientific arguments and controversies are hard to distill in a short discussion for general readers without doing the science major harm. Even more difficult, may be making these arguments and controversies that seem so important to the scientists involved, interesting to general readers.  Some, like journalist Carl Zimmer, are masters of writing entertaining, understandable prose for general consumption without misrepresenting the state of the science.  But being Carl Zimmer is not so easy (as my relatives who persevere in reading this blog often remind me – I’ll keep practicing!)

One of the problems with critiquing all of social science is that there are literally tons* of social scientists with very diverse views, methodology, areas of study, and philosophies of science. It is very difficult to paint all of social science with one 800-word brush.  For example, my sense is that Clarke and Primo’s critiques apply much more acutely to their home discipline of political science than to any other social science discipline – which is something they make more clear in their book than the NYT article. Expanding their critique to all of social science might give readers a mistaken impression of the state of other fields.

My other sense is that making these types of distinctions does not help many readers of the NYT absorb the main point of the article – that social scientists should not emulate what they think are natural scientists methodologies (Clarke and Primo) or that social scientists should emulate the way natural scientists structure their disciplines (Christakis).  There may be a trade-off between accessibility and rigor that we non-Carl-Zimmers need to strike when making a general point to a general audience. 

The problem with this is that NYT articles written by distinguished scientists attracts audiences that are not entirely general.  For example, I am much more likely to read an op-ed written by Clarke, Primo or Christakis than I am to read one written by, say, Thomas Friedman or Maureen Dowd (even though the base-rate Friedman and Dowd op-ed writing is much higher). We specialist audiences have much more invested in these discussions, have stronger opinions, and make greater distinctions than the average reader of the NYTs.

This is one of the advantages of the blog format.  As I strive to become more Zimmer-like (maybe I should just drop my name’s last syllable), I have the luxury to err on the side of verbosity and distinction-making.  And I have the luxury of a self-selected audience who come into this with eyes wide open (or are my close relatives).  This gives me a safe, if public, space to develop my voice and ideas and gradually widen the circle to a wider audience.

* – Though, to be fair, this only requires about 27 social scientists assuming (conservatively) a mean weight of 150 pounds (at sea-level).

A Fortnight of Links – 13 May 2013

Charlemagne’s DNA and Our Universal Royalty. Carl Zimmer on why, if you are of European descent, you are descended from Charlemagne.  This 2004 paper explains why everyone who was alive 3000 years ago who has living descendents, are the ancestors of everyone living today. Coalescence! I really like that they present results from a series of models along the realism/tractability continuum – from a simple analytic treatment to a very complicated world-wide simulation. This is pretty mind-blowing stuff.

Fact of Fiction? The Legend of the QWERTY Keyboard. The QWERTY keyboard is often used as an example of an inefficient technology persisting through institutional inertia. The popular legend is that the QWERTY Keyboard was designed slow down typists so they would not jam mechanical typewriters. It looks like its design was really influenced to help those transcribing Morse code from telegraph machines.  Note that this still leaves the institutional inertia story intact.

The Groundbreaking Isaac Newton Invention You’ve Never Heard Of. Did Newton really invent the idea of averaging data to reduce variance?  That would be pretty neat, but it seems like someone would have come up with that earlier.

A Congressman’s Own Peer Review. Rep. Eddie Bernice Johnson may be my new favorite lawmaker.

What China and Russia Don’t Get About Soft Power. An interesting discussion of the pitfalls of soft power.

Science Communication Round-Up:

Why do kidneys need cells? “One person’s jargon is another person’s technical vocabulary”

Defensive Scholarly Writing and Science Communication. Kate Clancy on why scientists often write the way they do.

Over this past fortnight, members of the UC Davis Human Behavioral Ecology Lab group have been emailing around their favorite references on good writing: Politics and the English Language, George Orwell;  Fenimore Cooper’s Literary Offences, Mark Twain;  Economical Writing, Deirdre McCloskey; The Elements of Style, Strunk and White

Bonus Links (entertaining in an internet sort-of-way):

Is Your State’s Highest-Paid Employee A Coach? (Probably)

How long is the average dissertation?

A Curriculum in Quantitative Evolutionary Social Science

Peter Turchin’s recent post, How to become a Cliodynamicist, reminded me that a couple of years ago, for fun, I tried to put together an undergraduate curriculum for a hypothetical undergraduate majoring in quantitative evolutionary social science.  Something like the program I would have liked to have had, in retrospect, as an undergraduate. (I majored in engineering, but took a lot of biology courses.)

The idea was to put together a curriculum close to the quantitative rigor of an undergraduate engineering degree, but with an emphasis on social systems, human behavior, and evolution.

The self-imposed rules were that I (1) had to use only UC Davis undergraduate (not graduate) courses, (2) could not exceed the unit requirements of an UCD engineering degree (198 units), (3) could not ignore course prerequisites, (4) could ignore complicated university requirements on breadth/depth and whatnot.  Below is what I came up with.

I focused on applied quantitative analysis and modeling. It was really hard to leave out most of the physical sciences – especially intro physics, chemistry and thermodynamics. Also, I wish there were a introductory course in political science instead of a separate courses for each of the sub-fields.

Lower Division Units
ANT 1. Human Evolutionary Biology 4
ANT 23. Introduction to World Prehistory 4
ANT 50. Evolution and Human Nature 4
BIS 2A  Introduction to Biology: Essentials of Life on Earth 3
BIS 2B. Introduction to Biology: Principles of Ecology and Evolution 2
BIS 2C. Introduction to Biology: Biodiversity and the Tree of Life 4
BIS 20Q. Modeling in Biology 5
ECN 1A. Principles of Microeconomics 4
ECN 1B. Principles of Macroeconomics 4
ECS 30. Introduction to Programming and Problem Solving 4
MAT 21A Calculus 4
MAT 21B Calculus 4
MAT 21C Calculus 4
MAT 22A Linear Algebra 3
MAT 22AL Linear Algebra Computer Lab 1
PHIL 30. Introduction to the Philosophy of Science 4
POL 51. Scientific Study of Politics 4
PSC 1. General Psychology 4
PSC 41. Research Methods in Psychology 4
SOC 1. Introduction to Sociology 5
SOC 46A. Introduction to Social Research 4
SOC 46B. Introduction to Social Research 4
STA 32. Basic Statistical Analysis Through Computers 3
Two freshman writing courses 8
Upper Division
ANT 105. Evolution of Societies and Cultures 4
BIS 132. Introduction to Dynamic Models in Modern Biology 4
BIS 133. Collaborative Studies in Mathematical Biology 5
EVE 100. Introduction to Evolution 4
EVE 101. Introduction to Ecology 4
EVE 101Q. Introduction to Computer Models in Ecology 1
EVE 102. Population and Quantitative Genetics 4
EVE 131. Human Genetic Variation and Evolution 3
EVE 175. Computational Genetics 3
ECN 100. Intermediate Micro Theory 4
ECN 110A. World Economic History Before the Industrial Revolution 4
ECN 110B. World Economic History Since the Industrial Revolution 4
ECN 122. Theory of Games and Strategic Behavior 4
ESP 121. Population Ecology 4
MAT 124 Mathematical Biology 4
MAT 167 Applied Linear Algebra 4
NPB 102 Animal Behavior 3
NPB 102Q Quantitative Topics in Animal Behavior 1
POL 110. The Strategy of Politics 4
PSC 100. Introduction to Cognitive Psychology 4
PSC 101. Introduction to Psychobiology 4
PSC 120. Agent-Based Modeling 4
PSC 151. Social Psychology 4
STA 131A. Introduction to Probability Theory 4
STA 131B. Introduction to Mathematical Statistics 4
STA 131C. Introduction to Mathematical Statistics 4
STA 141. Statistical Computing 4
STA 145. Bayesian Statistical Inference 4

A Fortnight of Links – 29 April 2013

E. O. Wilson is Wrong Again —  About Collaboration – Jon Wilkins on E.O. Wilson’s WSJ op-ed I briefly mentioned a fortnight ago.

Why I Let My Students Cheat On Their Exam – This article has really been making the rounds! I have seen many positive responses. Negative responses have generally been fixated on all the free-riders. I think the main difference in attitude stems from whether one thinks the primary goal of undergraduate education is “separating the wheat from the chaff” or “maximizing student learning.”

Evolutionary psychology: You’re doing it wrong (but you could do it better!) – In my experience, evolutionary psychologists tend to think of themselves as the antidote to “standard” social scientists who deny or ignore the power of evolutionary thinking. Problematic for this self-conception is that evolutionary psychology research often rubs standard evolutionary biologists the wrong way as well.

James D. Fearon: Anarchy is a Choice – A video of political scientist James Fearon discussing “anarchy” in international relations.  This is roughly the observation/idea that altruistic cooperation between countries is difficult to achieve because there is no law-giving-and-enforcing body (leviathan) that is above and constrains the actions of countries.  The actions of countries must be constrained by other things.

The (sigh) Psychopath Brain – This post gets to one of my pet peeves of science reporting – assuming that because something shows up on a brain scan it is somehow “innate” or “genetic.” I plan a blog post on this soon (read: after dissertation.)

On Copycat Whales, Conformist Monkeys and Animal Cultures – A great discussion about culture in non-human animals. I would have liked something about cumulative vs simple cultural evolution – but that is really nit-picking.

Why are your friends more popular than you? – Spoiler Alert: Because people with more friends are, on average,  more likely to be friends with you

Replicated typo: Numerical vs. analytical modelling – A focus on linguistics, but a good discussion on the tractability/realism trade-off for different styles of modelling.

Cyberwar in the Underworld: Anonymous versus Los Zetas in Mexico – Cyberwarefare between non-state actors.

Are the Digits of Pi Random? – Well, what do you mean by random?

Numberphile: Why are there Infinite Primes?

Fun (most fun things are apparently space-related):

Kepler’s Tally of Planets – NYT visualization of all extrasolar planets discovered so far.

How Far Away is the Moon?

Wringing out Water on the International Space Station – for Science! 

Make XKCD-style Plots in Matlab