Monthly Archives: January 2014

Agriculture, emigration, deforestation and Malaria

ImageWhen malaria first began to infect humans is something of a mystery. It was a mystery that I hadn’t thought about much before now because … well, I don’t know, it just never occurred to me.

However, recently a colleague mentioned that there was a connection between it and the beginnings of agriculture. Despite the fact that I should know better, I dismissed the idea out of hand. That’s too recent, I thought. There’s no way that could be the case.

The idea of a connection was originally suggested by Frank Livingstone, who “suggested that Plasmodium falciparum (which is by far the deadliest of the several parasites that cause human malaria) had jumped into Homo sapiens from chimpanzees. He speculated that the rise of agriculture had led to human encroachment on wild forests, giving the chimp version of the bug, P. reichenowi, the chance to find a new host.” 1 

Despite my dismissal, the idea did come back to me late last night and I started to look into what was published on the subject. The first thing I found was one of Scientific American’s 60 second science podcasts on the possible connection between recent deforestation in South America and a resurgence in Malaria.  “Researchers looked at stats for 2006 …[and] compared those cases to deforestation in the same health districts over the previous 10 years. They found that a loss of just four percent of forest cover was associated with nearly 50 percent more malaria cases.”2

As always, correlation isn’t causation, but something is happening, and because Malaria is more common in open areas than forests, causation isn’t much of a stretch. And, if malaria does increase when land is cleared of forest, the connection to the advent of agriculture may not be far fetched at all.

Humans started domesticating animals and farming the land about 10,000 years ago , so we do have a date to shoot for in our estimate. The question is, ‘was malaria widespread prior to ~8000 B.C.E.?”

One way to ask this question was to question whether Malaria was with us before we (humans) left Africa, or more recently. This moves the timeframe back to about 50,000 years ago (a reasonable landmark prior to agriculture). One way to ask this question is to look at diversity of the parasite’s genes. Just as the greatest diversity among humans occurs in Africa with less diverse groups coming out from this population, the same should be true of the microbe.

“The researchers found that genetic diversity did indeed decrease at greater distances from Africa. The correlation is very strong, says lead author Francois Balloux of the MRC Centre for Outbreak Analysis and Modelling in London, and the pattern matches human migration out of Africa, which scientists believe started some 50,000 to 60,000 years ago.”3 ( See here and here

For a visual representation of the genetic argument for the origin of malaria, see the map below:


                                         Genetic Variation of Malaria                                                     (grey dots represent possible sites of origin)

Whether Livingstone’s idea may be correct or not probably has no bearing on the idea that human disease originated in chimps and does nothing to undermine the possibility of a connection between recent outbreaks of disease and clearing land for farms.



1. “The source of malaria” The Economist. Aug 4th 2009.

 2. “Plasmodium falciparum Accompanied the Human Expansion out of Africa “Kazuyuki Tanabe  et al. Current Biology, Volume 20, Issue 14, 1283-1289, 17 June 2010

 3. “When Humans Left Africa, Malaria Came Along” MARTIN ENSERINK. Science Now. 18 June 2010.


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Posted by on January 30, 2014 in Uncategorized


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The Amazing Zoltar

Find your own fortune here:


Click Me



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Posted by on January 27, 2014 in Uncategorized


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A Correction

The problem with audio books is that it is easy to lose your place. A lapse of attention and a new chapter starts – or you wonder if one has. This is exactly what happened to me while listening to Why Evolution is True this weekend. I accidentally listened to two chapters (2 and 3) together thinking they were all part of the same.

ImageSo, for my class that is reading this book, the posts I made about Vitamin C and its genetics will be things we discuss when we get to chapter 3. For Tuesday, I’ll have to come up with another topic, probably the evolution of whales, which is a field with a number of new discoveries to discuss.


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Posted by on January 27, 2014 in Uncategorized


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Glucose – 6 Phosphate

For my Ecology class, consider the question below as you think over Why Evolution is True chapter 2. I will post this and several more questions later today on blackboard…

There a lot of talk about biochemical pathways in this chapter. Mostly, Coyne sticks to the one used to synthesize ascorbic acid (vitamin C), however this reaction involves the use of a compound called Glucose-6-Phosphate. This molecule is common to a number of important metabolic pathways. In addition to making vitamin C, see if you can find one anabolic and one catabolic pathway downstream of this molecule. 

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Posted by on January 26, 2014 in Uncategorized


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Arrr! Ye Scurvy Dog

‘I’m sorry, sir. But dogs don’t get scurvy.’Image

It may seem ironic that people get Scurvy, but dogs do not. Scurvy, of course is vitamin C deficiency, that we associate with pirates and other men of the sea because their seafood diets provide little, if any, vitamin C. As they stay longer and longer at sea, fresh fruits run out and eventually signs of scurvy present themselves.

The cause of this disease is discussed in chapter two of Jerry Coyne’s Why Evolution is True, which we will be discussing in Tuesday’s ‘Ecology’ class.

We’re not alone though. Many animals lack the ability to synthesize vitamin C due to the loss of a single enzyme, L-gulono-γ-lactone oxidase (GLO), responsible for converting L-gulono-γ-lactone into ascorbic acid, also known as vitamin C. Many primates lack this gene – or, rather, we have it, but it doesn’t work. This happens often when a gene that was necessary to our ancestor’s survival becomes unnecessary to our own. There are a number of examples of this in our genome, because we can still find the genes sitting like so many unused, derelict ships, we identify them as pseudo genes.

Pseudo genes may be considered nature’s unemptied trash can, filled with the remnants of old or abandoned projects. This occurs because natural selection keeps the pressure to maintain useful genes, but does not act as strongly – or at all- on those that provide little benefit.

In our own family tree some early primate started including enough fruit in its diet that making its own vitamin C was so inconsequential that when they had babies that couldn’t make it themselves, no one noticed. And, more importantly, that baby was just as healthy as any other.

 When that happens, mutations pile up over time that continue to degrade this gene at, what we assume is a uniform rate. The last part of that is difficult to demonstrate directly, but if true, it gives us a yardstick to measure how far back in time the initial mutation occurred. It is estimated that this mutation occurred about 61 million years ago in our ancestor.1

This was long enough ago that not only do humans lack this ability, but a number of other related primates lack it as well, including gorillas, gibbons and macaques.2 

 Another animal lacking the GLO gene is the guinea pig, which lost its ability to make vitamin C only recently (as evidenced by the animal’s close relatives – rats and mice – retaining functional copies of GLO. A comparison of the functional rat protein with that predicted from the remains of the gene in guinea pigs show only three small sections missing from the guinea pig protein, while no effective (>30% similarity) alignment with a human sequence occurs due to the degree of gene degradation.

The Rat:: Guinea Pig (cavia porcellus) alignment:


The best match of Rat: Human sequence:


The rat and canine alignment quite clearly shows that the whole functional gene remains in dogs:


However, if you want to insist that dogs can get scurvy, head to the Pirate Shop at Ye Scurvy Dog to load up on pirate merchandise.   

(alignments performed using the NCBI’s BLAST alignment tool.)


  1. Lachapelle MY, Drouin G. “Inactivation dates of the human and guinea pig vitamin C genes.” Genetica. 2011 Feb;139(2):199-207.


  1. Guy Drouin,* Jean-Rémi Godin, and Benoît Pagé “The Genetics of Vitamin C Loss in Vertebrates” Curr Genomics. 2011 August; 12(5): 371–378.



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Posted by on January 26, 2014 in Uncategorized


Creativity and Regression to the Norm


I was listening to Stuff to Blow Your Mind’s War on Creativity (a cute play on the War on Christmas, which I had to stop the podcast to explain to my son) today in the car.

This episode asks why it is that we say we value creativity and that businesses want to bring it in-house, but very few businesses actually act like this is something it wants. Creativity is disruptive, it requires risk-taking, and it often results in failure.  Yet, no one hits a homerun by playing it safe.

Regression to the Norm

This is the phenomenon where new, statistically significant observations tend to evaporate upon re-examination. The now defrocked Science writer at The New Yorker, Jonah Lehrer wrote about this back in 2010   in an article describing the diminishing effects of psychiatric medications over time – meaning that the experiments actually showed these medicines to have less potency every time they were tested – not that they are less effective for a particular person over time. Lehrer explains that a lot of this may be the way that we involuntarily allow confirmation bias  into even the best designed experiments, and over time, as investigators with less personal investment in the results repeat the same work, they lose the confirmation bias and subsequently see less convincing results.

I would argue that the same effect occurs in design. It’s something that I’ve always personally thought of as the Taurus Effect. I propose this to mean that there is the occasional breakthrough in unique, engaging design, but this gets co-opted by the more conservative elements of the business who (not to mince words) suck the life out of these designs bit by bit until there is nothing left. In this way even the most unique, exciting automobile design eventually gets eroded into the most boring of all cars, a 1999 Ford Taurus.


Consider the Camaro, one of America’s most iconic muscle cars. What starts as great design gets whittled away year after year into what I assume must be more and more aerodynamic designs that completely abandon any semblance of cool.

Another icon of American Design is the Chevy Malibu. This car started as a mean hunk of metal that demanded to be noticed. By the 1980s it way reduced to … well, not a Taurus, but something possibly worse.

malibuA lot of these cars have seen a renaissance with the introduction of new designs that can only have been inspired by real designers, not committees of businessmen and engineers hell bent on perfect aerodynamics.

Last week, however, I was at the Chevy dealership to get work done on my truck when I noticed the new 2014 Camaro. At first, I only saw it from behind and thought, ‘is that a Ford Taurus?’

Welcome back to the norm, Camaro.Image

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Posted by on January 21, 2014 in Uncategorized


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Holy Crap! This is spot-on

As a follow-on to This a recent replay of the Doppelgänger episode of This American Life, Ira had Fred Arminsen on to do his Ira Glass impression. On the radio Fred was good. On this video he’s perfect. The word is that this segment never actually aired on SNL, but lucky for us, we have the interwebs!

(sorry, this video is not available to be embedded, but you can catch it through the link below.)

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Posted by on January 21, 2014 in Uncategorized


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Film Trivia

What film took place at the Miskatonic University Medical School?



So, West, what kind of medicine are you involved in?



Posted by on January 20, 2014 in Uncategorized


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What makes the life of man, solitary, poor, nasty, brutish and short?

ImageHuman Nature

Tiling a bathroom floor is a good time to catch up on the long list of podcasts clogging up  my switcher queue.

Unfortunately, they all seemed to take a dark turn yesterday.  I felt hit one time after another with tales of what vicious animals we can be. As I listened I was thinking of the Faustian comic my son and I found as an iPad app / book, Howard Numlek, that tells the tale of Howard, a meek, uncertain, jobless man who is taken into the employ of Red Suit, Inc., the front company of Satan himself. Poor Howard doesn’t want to work for the Prince of Darkness, but he’s unemployed, the pay is good and he doesn’t have to sell his soul just to work there. All he has to do is collect on the contracts.

I started to think… ‘Yes, I would probably sell myself into such an evil position pretty quickly given the chance.’

The first podcast was Ira Glass’, This American Life. It’s always been a favorite of mine since I first started listening almost twenty years ago. The most recent episode is about ‘Good Guys,’ and the men who think of themselves as such. There were several acts, but the one I thought was most amusing was trying to get the ‘Good Guy Discount.’ … “Hey, you’re a good guy, I’m a good guy, how about we take a little off this purchase to ease the pain a little?” Amazingly, this kind of approach actually seems to work with some people under some circumstances. But the question is, ‘What kind of guy goes around saying he’s a good guy and looking for a reward?’

The obvious answer is: not a very good guy.Image

Next up, also on This American Life, was the story of an Afgan War veteran and his memoirs that show how effective the US Infantry is at converting a mild mannered man into someone whose greatest hope is that he will have the opportunity to kill someone.

Is this something that his experiences did to him – or is it simply uncovering the deep, dark truth inside of us all?

Finally, Freakonomics with their story “Fear Thy Nature”.  As if I wasn’t already doing that!

This story brought up the 1971 Stanford Prison experiment in which students were separated into two arbitrary groups, one becoming prisoners and the other becoming guards. The experiment was supposed to last two weeks, but was stopped after six days due to the abuses of power exhibited by the guards.

There is some controversy about whether this experiment went the way it did because that’s the way human nature takes us – or if the study volunteers knew what was happening and made an effort to play to the camera.

While I was listening to this I was reminded of a diversity training video I had seen while employed at a plastics manufacturing plant in Delaware City during college. The video illustrated just how easy it was to invent a stereotype about a group from thin air and make it sting in just fifteen minutes of conditioning.

The most amazing thing about this exercise was that I remember the trainer at our company turning off the video and starting a conversation with the employees only to find that they had picked up on the stereotype and were just as vehement in aggressively applying it as any other brand of prejudice that they had ever felt. They had to be reminded more than once that this was only made up as a lesson.

Thanks to the wonders of the internet, I was able to find this video from the little I remembered about seeing it twenty years ago. It’s still available as Blue Eyed with Jane Elliot from ABC Training. Although I can’t post it here because it is still used, you can follow the link and watch the entire 30 minute video online – it’s astounding.  For a taste of the lesson, watch some footage of Ms. Elliot putting this lesson in action with her 3rd grade classroom in Iowa.

What does this have to do with the low opinion of humanity’s moral character? Watch the video, see how easy it is to sow division between people. It’s a great lesson about the arbitrary nature of bigotry, but it’s also a sad testament to the willingness of people to learn a new stereotype.


Posted by on January 18, 2014 in Uncategorized


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Pervasive, persistent, problematic “prokaryote”

It’s true that the term Prokaryote is going away. The problem is not that it is a bad word when contrasting Bacteria and Archae to Eukaryotes, but that it implies similarity between the two ‘Prokaryotic’ domains.
I see the rationale, but I need to read up a bit on this before I start changing my lectures. Thanks to Nucleoid for pushing this topic.


There are reasons to avoid using “prokaryote” in biology teaching.  So, why are so many biologists resistant to the idea?

Why not use “prokaryote”?  Norman Pace published a one-page piece in Nature, “Time for a change” that raised concern about use of “prokaryote” (in education), and the common biology textbook paradigm of splitting organisms up into prokaryotes vs. eukaryotes. Pace highlighted many of the differences between archaea and bacteria, discussed evolutionary relationships/history, and made a case for avoiding use of the term prokaryote with students.  (Check out the 2005 article by Jan Sapp discussing the history behind the prokaryote-eukaryote dichotomy, too.) Pace expanded on this with a lengthier educational piece in 2008.

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Posted by on January 17, 2014 in Uncategorized