Monthly Archives: January 2013

A good post – I might object to only one thing: I believe that one of the things that makes Hayao Miyazaki’s films so wonderful is that they don’t have good and bad characters. Instead, like the real world, no one is completely one or the other, only shades of grey. Everyone should watch at least these four films and possibly Studio Ghibli’s others as well.

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Posted by on January 30, 2013 in Uncategorized


Why Sex is Fun, Chapter 2

Chapter 2 is lowering my expectations of this book. It remains somewhat interesting and well researched, but for a book titled ‘ Why Sex is Fun’, an extended discussion of why males of most species abandon their sex partners to raise their young alone is not exactly what I was hoping for.

I wasn’t expecting penthouse forum, but I guess I was expecting some discussion of why sex is fun.

Nevertheless, I will certainly continue reading and reporting on my progress here.

As I said above, chapter 2 parses the involvement of each parent in the rearing of offspring and finds (unsurprisingly) that this directly correlates with two things:

  1. Certainty of paternity
  2. Energy investment in making each offspring vs the ability of this offspring to survive in the absence of care.

Paternity Testing

Together, these considerations account for why males of many (but not all) species tend to be dead-beats. Given the low cost of sperm production and the ability to reproduce with a number of females concurrently, coupled with the lack of assurance that any given child is the male’s own, it pays to remain uninvolved in raising any one specific (potential) offspring.

Several exceptions to the rule are presented and a few good considerations that must be made to actually weigh against the low cost of sperm – just because it’s cheap to make one doesn’t mean one is enough. And sometimes women aren’t that eager to have sex with you just because you have sperm. – Amazing!


Male penguins incubating eggs while mom is away


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Posted by on January 29, 2013 in Uncategorized


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Your Inner Fish – Chapter 1

tiktaalik_reconstructionThis semester, like the preceding three or four semesters, my general biology class is reading ‘Your Inner Fish’ by Neil Shubin. Every week, we cover one chapter and my students write an essay with their thoughts before we discuss that chapter in class.

Last week was our first week with this book, so I’ve just completed reading several essays on chapter 1 from my students. Overall, I’d say that the book seems to be getting a good response and at least interests most people. I’ve had a wide variety of responses with respect to accepting the author’s interpretations of Tiktaalik, his find of a ~375 million year old fossil species that shows evidence of being a transition species for the first quadrupeds to come onto land.

This is always a fun group of essays for me to read because it challenges students to consider their perception of science as a way of viewing the world. Or, perhaps I should say, ‘science, as a way of understanding the world around us.’ A scientific view of the world is actually a fairly unnatural one. It is easy to see how it is even evolutionarily disadvantageous to have a scientific view of the world. If you have been a victim of a crime (you imagesget mugged walking down a city street) don’t you always expect that crime to happen again? It doesn’t matter that this happened only once out of thousands of times you walked the same route home, you now feel convinced that this is dangerous and are more alert and cautious. You may even find a new way home. And who would blame you? We’re programmed to look out for our own safety. This often means over-exaggerating  our fears and assuming the worst. It also means that we will now overestimate the real danger.

The other thing this discussion brings up is: what does science do for us?

The answer is supposed to be, ‘it enables us to learn from the past and have a better ability to predict the future.’  We can make predictions about things if we closely observe the world and learn its laws. The corollary to this is, if you can’t learn from the evidence you see about you, how can you ever know what to expect from the world?

All of these are interesting questions. All of them challenge how we look at the world, what we take for granted and what we can expect to get from our experiences. I’m really looking forward to reading more of my students’ reflections on this text and hope that you (anyone reading this) feel free to engage in a dialog about either this book, or the questions it brings up.

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Posted by on January 28, 2013 in Uncategorized


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Holy Crap!
(I know, I need to actually write more posts myself rather than just repeating what’s found elsewhere, but LOOK AT THIS THING!)

Why Evolution Is True

Update: Reader Dennis Hansen, a biologist who works on the Indian Ocean island of Aldabra in the Seychelles, which (like the Galapagos) has giant tortoises, sends three coconut crab photos and a note:

Here’s a few photos of coconut crabs from Aldabra, for your perusal. They leave the giant tortoises alone, it seems. At least until a tortoise dies, by which time the crabs tear it apart from the inside. When staying in one of the remote field camps on the atoll, they do what they can to rob us of our meagre field rations, though. Don’t leave food on the table, or it will disappear within a few minutes.

crab & nut

field camp crab

crab & tortoise


This photo and caption are from Professor Brian Cox’s Facebook page, and apparently appear in his new book, Wonders of Life with the caption:

“These animals are known locally as robber crabs on their native Christmas Island because…

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Posted by on January 28, 2013 in Uncategorized


In New Zealand, no one can hear you bleat.

ImageA movie review: Black Sheep, 2006. 70% positive on Rotten Tomatoes.


Watching this film, I can’t help but be reminded of such classics such as ‘Dead Alive’ (a fun zombie story by a little known Kiwi director, Peter Jackson) or ‘The Re-animator’ (a great mid-eighties mad scientist film starring Jeffrey Combs). The story is: Genetically altered zombie sheep are released by animal rights activists. This is terribly unlucky for Henry, the younger of two brothers inheriting a massive New Zealand farm, who suffers from acute ovinaphobia (an irrational fear of sheep – but can there really be a rational fear of sheep?) from a traumatic childhood encounter. Black sheep has it all – familial struggles, money and greed, a love story, the claustrophobic terror of spelunking in an offal pit, oh, yeah, and Zombie Sheep.

I’ve heard of this movie, but it took me quite a long time to actually see it. Luckily I caught it on IFC a couple weeks ago and taped it, so now I can strike it from my Netflix list.

Like so many other films of this kind, there is a great deal of tongue-in-cheek demonizing science and specifically genetics, because everyone knows that biotechnology inevitably leads to a zombie apocalypse.

If you don’t like gratuitous blood and guts with gobs and gobs of gore, this might not be the movie for you. And if you still can’t watch the scenes with the abominable snowman from Rudolph the Red-Nosed Reindeer,  you might want to cover your eyes from time to time because this is about that scary.Image

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Posted by on January 26, 2013 in Uncategorized


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All but extinct: the Stresemann’s Bristlefront.
This article states that only about 15 of these birds remain alive. Consider why this might be considered too few animals to ever recover. To what number can a species be reduced and have a chance to recover? (this is not necessarily a question that can be reasonably answered, but on interesting thought experiment and a consideration that wildlife conservationists make regularly.) Given the unliklihood of this species’ recovery, should resources still be spent to try to maintain them? What is the value of a species (i.e. what is lost when they are gone)?

Why Evolution Is True

UPDATE: Where to donate to save this bird.

I’ve heard back from The American Bird Conservancy, and they’ve told us where we can give money to help out this rare bird:

Thank you very much for your inquiry about how individuals can donate to help protect the Stresemann’s Bristlefront. Here is a link to American Bird Conservancy’s donation page on our website.  If an individual then types “Stresemann’s” on the mailcode line, their gift will be earmarked for this imperiled species.

Save the highly threatened Stresemann’s Bristlefront by helping American Bird Conservancy and Fundação  Biodiversitas protect the Stresemann’s Bristlefront Reserve for conservation. This reserve, created by ABC and Biodiversitas in 2007, now totals more than 1,400 acres. However, the forest surrounding the reserve is under severe threat from agricultural expansion and deforestation, making diligent management of the land already under protection critical and urgent. Stresemann’s Bristlefront Reserve is a top…

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Posted by on January 26, 2013 in Uncategorized


Is Saudi Arabia following Turkey’s Lead?

MukfellasIt’s unclear what the rationale was, but The Economist has recently reported that the Saudi Arabian Committee for the Promotion of Virtue and Prevention of Vice (CPVPV) has come in and closed the Dinosaur World exhibit / playground. I’ve looked around a bit to see if there is any further information explaining this action (is it a reaction to the very idea that once dinosaurs roamed the earth?, perhaps some incidents of improper behavior had been reported?). In the absence of information, we can only guess.

I was alerted to this news via a blog that I follow by the evolutionary biologist, Jerry Coyne. Coyne’s interest comes from his concern about the suppression of science that is sometimes found amongst religious organizations. Because this action was carried out by the CPVPV, it is reasonable to assume that the exhibit was closed because it violated a tenet of the islamic faith. The CPVPV is the Saudi religious police who enforce Sharia Law by monitoring the population to ensure that people adhere to dress codes, separation of men and women, etc.

t rex exhibition riyadhHowever, it’s difficult to look at pictures of this exhibit and see what could be wrong. Although he does not say it explicitly, I have a feeling that Coyne is worried that Saudi Arabia is going the way of Turkey in suppressing science that contradicts religious interpretations of creation. This is an issue in many Christian-dominated cultures, but many people do not realize that fundamentalists of Islam are very similar in their views as fundamentalist Christians. Read more about recent actions prohibiting teaching of evolution in Turkey here.

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Posted by on January 22, 2013 in Uncategorized


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Don’t you forget about us

an extra credit hint for microbio:



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Posted by on January 22, 2013 in Uncategorized


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Start of the New Semester

I’ve had a bit of a problem getting back into the flow of writing about science this semester. We started up again last week ending the frustrating period between semesters when all I have is time, but I can never seem to focus my attention on anything long enough to get much accomplished. Classes had a rocky start – in part because I was sick the weekend before our first meeting, but mostly because I’m fairly complacent about the first days of the semester – it’s a time of working through logistics and clarifying the syllabus and not there are always students who ‘add’ after the first days, so I don’t want to get moving too fast.

But that time is passed now and I’m looking to work through the last of the intro material quickly and get into the meat of the courses. Nevertheless, I looked back and found the link to this essay I wrote several years ago and recently published here a month or more ago. It’s on the nature of science and how scientists look at the world. I thought I would make a link to that for any students interested in thinking about science as philosophy or just anyone who was interested in thinking about how science shapes our understanding. Find that article here.


The Central Dogma

Next week I am hoping to finish our discussion of chemistry and biomolecules in General Bio and start in on cell structure and organization. In this class I will cover prokaryotes, but our main focus is on eukaryotic cells, specifically animal cells.I make the flow of information in biology (DNA->RNA->Protein) a central theme of this class and this is the first chapter where we actually begin to flesh it out as more than words on the board.

Microbiology will begin a survey of various forms of life, with emphasis on those organisms most important to human health / pathology. Again, we we start with prokaryotes, but stick mostly with bacteria, as archebacteria are primarily extremophiles and therefore don’t impact humans very often. Most importantly, we will focus on the difference between gram positive and negative organisms and how the proteoglycan cell wall is structured. This is vital because later in the semester we’ll discover that a large number of anti-bacterials target this structure specifically.

And one last thing, I wrote to Paul Offit this weekend, and he is very happy that we will be using his book, Vaccinated in class this semester. I’ll touch base with him again at the end of the term to let him know how it worked out and what the reception of his book was like.51vRtIGijUL._BO2,204,203,200_PIsitb-sticker-arrow-click,TopRight,35,-76_AA300_SH20_OU01_


Posted by on January 20, 2013 in Uncategorized


C++ coding in XCode

For some reason it took me forever to figure out how to use XCode as a C++ compiler. Recently, I figured it out and have worked on several projects without incident. 

I needed a compiler to use on my mac because I am currently taking a class on C++ algorithms that uses Microsoft Visual run on Windows. Not surprisingly, Visual doesn’t run on OSX (and it’s frankly too much effort and processing power to install windows on my mac and then run Visual through that. – possible, but unwieldy.) 

Frankly, once I started using Xcode for C++. I realized that it’s both simpler and better than Visual anyway. Especially for a new user: I’d rather spend my time and energy working in C++ than trying to figure out a complex compiler. So, without further ado…


1. Install XCode on your machine (it’s huge, so plan accordingly)

2. Open XCode and select File > New Project.

3. Select ‘Command Line Tool’ from OSX > Application


4. Give your New Project a name


5. Click Next and select a location to save your file (desktop / developer folder/ etc.)


6.Your New Project will open and you just need to select main.cpp to get the familiar ‘hello world’ skeleton program.


7. I erase the skeleton and replace it with a simple :

int main(){

return 0;


and start from there. 

8. In order to to compile and run your program, select Program > Build, correct any errors and Build again if necessary. Then hit the play button in the upper left corner of your window to run the program (intuitive is nice, isn’t it?)

Your program will run, giving you an output window at the bottom of the main window. You may need to click on that window in order to provide input if your program requires it.

I hope this helps you speed along to programming quicker and with less hunting than I had to do. I don’t know why I even tried to find something outside of XCode to start with.  

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Posted by on January 19, 2013 in Uncategorized


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