Monthly Archives: December 2012



Counties Declared in Drought Emergency Summer 2012 (4)

It would be easy to forget that we are still in a fairly severe drought in the midwest. Over the summer of 2012 82 counties in Kansas were declared as federal drought emergencies in early July 2012. Just two weeks later governor Sam Brownback declared every county in the state to be in a drought emergency. Each declaration has different meanings as the first allows for federal aid for agriculture and related industries, while the second allowed water to be taken from lakes in state parks to aid the same industries(1,2). 


100% of Kansa counties in drought emergency August 2012

This summer the drought was hard to miss. Ponds were down to puddles, crops were failing and getting tilled back into the soil all around, trees were turning autumn colors and dying in July and lawns were dead with the ground dry and cracked.

Personally, I’ve never seen anything like it. Apparently, this was the worst drought in 25 years, if not more. Not long after, the East coast was getting hit by freakishly early winter storms and ‘superstore Sandy’. (I got regular updates from my family, who all live in the mid-Atlantic region).

Now, on the last days of December, the drought feels like a thing of the past, however, we are still in severe conditions here in the Midwest (I live in Kansas). I heard yesterday on NPR that Kansas is still 17″ below normal rainfall, and a quick look to the NOAA shows that the entire state is somewhere between ‘severe’ and ‘exceptional’ conditions (3). 

With luck, I will be shoveling endlessly this winter and we can recover somewhat by spring.


I want to apologize, I haven’t been posting much lately because my family has been away and I have spent most of every day outside working on the shop from first light until dark and then collapsed exhausted inside. 

I did have some time while waiting for my wife’s car in the shop yesterday to get a simple children’s book I wrote for/with my son put together as an iBook. It was submitted yesterday and will likely be available for free download sometime this coming week. I’ll post again when that’s available. (Don’t expect much though, the original was a hand-drawn mini book that I redrew using Fifty Three, Inc.’s ‘Paper’ App and an artist’s stylus… and I’m not that much of an artist)








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Posted by on December 30, 2012 in Uncategorized


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Brainstorming a new class

I’m not certain whether I can push this through or not where I teach, but I’m interested in designing and teaching a course on the nature of science and addressing some of the philosophical questions around science. I brought this up with my wife on the way to the airport yesterday to discuss it and we identified two central problems: What is the appropriate scope of a class like this? i.e. Should it address just a few central questions or cover more of the reach of science? Secondly, how much can I really expect students to read in a semester? Many of my students are part time and have full-time jobs and children they are managing around their academic schedules.

Let me be honest, I really want to do this course because I want to read or re-read a lot of these books and do a much better job when I have to discuss it in front of a class.

Here’s the rough draft outline of what I would love to teach in a perfect world. I’d love to get comments and suggestions about how to shape this course. More readings, key chapters of books to excerpt from the books I identified or others, etc. Also, if you’ve taught or taken a course like this, what was the reading load like?


The Nature of Biology: A Reading Course

A Proposal for a one credit course in biology focusing on reading, discussion and writing assignments.  Student grades come entirely from written and oral discussion – no tests

Format: Meet once or twice a week for one and a half  hours to discuss readings, organize schedules and discuss writing assignments

Assignments: Ongoing discussion groups online – every student must write at least one post with a significant contribution AND at least one reply to another student’s post for each book read.

Objective: To consider the physical and chemical laws of the universe and assess how these come together to ‘create’ biological life. Also, to discuss what we know of the origins of the universe, the earth and life itself. How does science teach us to think about these things? How do we know what is real and what is not?


Unit I: The Nature of Science

  1. What makes us think that we can believe what our senses tell us? What is reason and how can we make rational decisions in this world?
    1. Something on the nature and philosophy of science
    2. How can we tell the real from the make believe?
      1. Show the scene for 2001 when Dave Bowman is running around the inside of the Discovery.

i.     “What are we seeing?”

ii.     “How is it possible that he can run continuously and keep going around in circles?”

iii.     Why do we need an explanation at all. Can’t we just accept what we see?

  1. Dawkins, The Magic of Reality
  2. Massimo Pigliucci, Nonsense on Stilts

Unit II: Physical Origins

  1. What do we know about the universe?
  2. How did it begin and how will it end?
  3. We are all star-stuff: Basic Physical and Chemical Laws
    1. a.     ____________, Carl Sagan
    2. Origin of Earth
      1. a.     The Earth, the Moon and the Solar system – some video…. What if we had no moon?

Unit III: Biology

  1. What is Biology?
    1. What makes Biology Special, Ernst Mayr
    2. Life is United
      1. Something on Evolution??? Mayr again? –or- Why Evolution is True, Coyne
      2. Craig Venter on creating synthetic life in the lab

Posted by on December 27, 2012 in Uncategorized


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Christmas Eve

Staying up late on Christmas eve to wrap presents while watching ‘Sixteen Candles’ brings memories of years gone by. 

Merry Christmas to all!



Mac Classic

Here’s a blast from the past:

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Posted by on December 25, 2012 in Uncategorized


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The Hobbit: An (Un)expected Disappointment

images-2A prequel trilogy seems to be a director’s opportunity to push CGI beyond its usefulness and try with all
their vast wealth to demonstrate that more is better- in every case, all the time. Regardless, the films make money providing the only feedback that matters to Hollywood. So we, the audience, ensure our future dissatisfaction.
I wanted to like The Hobbit- I really, really wanted to like The Hobbit. Despite the problems one might expect after hearing that this book was to be divided into three films, I still wanted to like it. And there were parts that I did enjoy tremendously. But, assuming I had the ability to make the film myself, I wouldn’t be expecting a good performance review or raise based on this effort.
Now (spoiler alert), I want to talk about what did and didn’t work specifically.
Beginning with the good…
I though that the film was paced very well from the start giving ample time for character development and slow immersion into the world of middle earth. Of course,the characters that were best introduced were Bilbo and Gandalf, both of whom we already knew from The Lord of the Rings.
Getting to know the dwarves was mixed, but overall quite good. The story paralleled the book well taking ample time to convince Bilbo to come along on the adventure of a lifetime, but it’s difficult to get to know thirteen dwarves no matter how long we take. I’m giving Jackson a pass here and will say that he did a very good job or balancing the dwarves’ gravity and lightheartedness and included the song of the dwarves to set the mood.
Although my wife and I have different opinions about it, I was happy with the backstory of the orcs to provide an antagonist to root against, fear and revile. (However, I would have gone with goblins to keep consistent with the book and get to see a new race of people)
Lastly, the scene with Gollum was easily as good as any he starred in previously and saved the movie in no small  manner. Gollum represents CGI at its finest, a triumph of technology.
Now the bad…
My wife argued that there was too much effort made to stretch things out to make a trilogy out of what should be one long movie. I didn’t find this to be a major fault, but I certainly saw her point.
My problems started with the rock/ mountain giants. I know they were in the book, but I think they were an easy thing to skip and a hard thing to do well. Jackson took the hard road and got a rather pointless CGI heavy scene that didn’t add anything to the film.
This was followed by our introduction to the goblins… I’m sorry, orcs. In my mind, the caverns of the goblins were cold and dark and populated by a rather simpleminded, but malevolent race. Never did I imagine wide open spaces laced with miles of timber (where did this all come from?) it was consistent with the LOTRs orcs’ cave, but does it give us anything? Perhaps just lots of room for a big, silly chance scene that reminded me of another big budget loser, The Temple of Doom. What filmmaker wouldn’t want their work to be compared to that?
Again, I’m just giving my two bits, but the last fight scene in the trees is a great opportunity to cut a few minutes as well. Less is more, right? Then, as if an echo of the Fellowship of the Ring, I would fade to credits with the eagles in the air.
I get it though, we need the tree fight to develop the relationship between Bilbo and Thorin… And then we have a resolution on the high rock promontory, but forget it – that’s not character development I needed. Bilbo is only just supposed to be showing his worth here, not becoming bestees with the dwarf.
Overall, I think it was about a 6 out of 10. I just wonder if Peter Jackson has gotten so big and respectable that no one says, “hell no, that sucks!” to him anymore. CGI, chase scenes and cultivated emotion aren’t what’s needed to make this a good film. I agree, if there’s no giant eagles in the world, you would have to use Special effects to show someone getting off of one. Or you could cut away and trust the viewers imagination.
I appreciate that you’ve grown up since Dead Alive, Peter (which was awesome, by the way). You don’t have to try very hard to make Tolkien a good story just don’t get in the way and you’ll have a winner.

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Posted by on December 23, 2012 in Movies, Personal Life


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Listening to House of Dreams

Today the midwest got hit by its first winter storm. At least it was the first storm to hit the Kansas City area. It even had a name, Draco – I didn’t know storms like this were named. Because of this storm, I had a lot of time in the car going to Home Depot and back to pick up some building materials to repair the workshop (which looks like it has been neglected for a decade or more).

All this time in the car means a lot of podcast listening. We heard the latest Radiolab, which contained a great lead-in story about Aleksander Gamme’s solo walk to the South Pole and back.

But, the podcast that really touched me on a personal level was from Freakonomics. It was about a family home and how it can feel like another member of the family, a living part of your memories. This podcast took a turn to talk about how the host, Steven Dubner’s, home had gone from a family centerpiece to a swingers’ retreat. But that’s not what intrigued me.

Instead, I got to thinking about memories and the feeling of ‘family.’

When I was a kid, I had some wonderful ‘golden years.’ I don’t know how else to describe them. Our family was close – both geographically and emotionally. We celebrated holidays together, had group birthday parties (because otherwise there would be too many) and vacationed together. These vacations were all coordinated by my grandparents, who rented a beach house in Rehoboth, DE every summer and had everyone down.

We spent the days on the beach and the nights playing cards together around the dinner table. Playing cards was my favorite part. We mostly played a version of solitaire, which oxymoronically, combined the games of innumerable players into one raucous mess. We also played Hearts a lot and would delight in not just winning, but pounding one poor victim mercilessly through the night (usually a younger, weak player).

Then, in 1994, my grandmother died and shockwaves went through our family. I think we all knew that she was the one who coordinated things, but none of us knew just how central she was. When she was gone, the family fractured and drifted apart.


Hermann Hesse

Years later, I think some things have improved, but we will never be the close unit we once were. Perhaps it was inevitable. As families grow, there are simply more people and the family unit refocuses. I’m reminded of the Hermann Hesse novel, The Journey to the East.

This novel has a story, but the story is not what is important. What is important is “The League’s” spiritual journey. From the Wiki page, “Although at first fun and enlightening, the Journey runs into a crisis in a deep mountain gorge called Morbio Inferiore when Leo, apparently a simple servant, disappears, causing the group to plummet into anxiety and argument.”

Leo, the servant was really the leader. Only no one knew this until he was gone.

I never thought of her as a servant, but I never knew how much a leader she was.


Posted by on December 21, 2012 in Personal Life


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How Old (Con’t)

From 1912 until about 1953, biologists interested in human evolution were being duped.

One hundred years ago, Charles Dawson presented his new find, a transitional fossil of an organism that plainly appeared part human and part ape, bearing a number of hallmarks of being a ‘missing link’ between modern man and early ancestors.. The fossil, found in Piltdown, England and was dubbed Eoanthropus dawsoni and was accepted as a welcome addition to the record of humanity’s existence.

It was just what was expected.


The Piltdown Gang

Expectations make fertile soil for a hoax.  Darwin’s work predicted such a find would be made. The question was merely, who would find it? What would it look like? And how famous would this make the man who discovered it?

“Sir Arthur Keith, famous British paleontologist, spent more than five years piecing together the fragments of what he called a ‘remarkable’ discovery. He said the brain case was ‘primitive in some respects but in all its characteristics distinctly human.'”1

Over time, When the skull fragments of E. dawsoni, commonly called Piltdown man, were examined, doubts were raised as to whether it represented a single organism or several, which just happened to become mixed together in the unearthing. But these doubts took decades to culminate into action.

The best way to address the question was to determine whether the several pieces of skull were at least contemporaries of one another. They could still be a jumble, but it was a start. To assess the age of the fragments, fluorine dating was done. This method is used to determine the amount of time that a sample has been buried underground. The principle is that groundwater contains fluorine and the longer a sample remains buried, the more fluorine will become absorbed into the sample. This testing confirmed that the samples could still have come from the same source, but that they were both considerably more recent that initially suggested.2

708px-Pildown_manFollowing this analysis, Carbon dating gave a more accurate age of the samples themselves indicating that they were both quite recent, but not from the same organism. Once this data came in, the house of cards fell and a number of other observations came to light confirming the hoax.

What does this teach us?

1. Science is difficult business. When everyone is working honestly, it is difficult. When people are willfully trying to subvert the process, it can take years to remedy. (I immediately think of the damage done by Andrew Wakefield’s fraudulent 1998 Lancet paper and subsequent work that undermined the public’s trust in vaccines)

2. Science is self-correcting. Again, this can take time, but eventually, mistakes are worked out and our understanding of the world gradually improves.

3. People are people. With an obvious prize, people sometimes make their own luck.

4. No single experiment will always give accurate data. Extra-ordinary claims require extra-ordinary evidence.


1. “The Piltdown Man Discovery: Unveiling of a Monolith Memorial”Nature 142, 196-197 (30 July 1938) | doi:10.1038/142196a0

2. “Relative Dating of the Piltdown Skull” Kenneth P. Oakley, Advancement of Science 1950

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Posted by on December 20, 2012 in Uncategorized


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How Old?


In the beginning…

This is an interesting question in evolutionary biology. I come to it a lot considering how the things we know of the world tie together.

How old is the universe?

How old is our sun?

How old is the Earth?

How old is life on Earth?

How long has life included something more than just bacteria-like prokaryotes?

How long have people been around? (And what does this question even mean? Do I mean the hominid lineage? Do I mean modern humans? Perhaps humans with language? Civilization?)

I can’t go into all of these at once, but something recently came up that’s on topic with this and specific enough for a post…

In our discussions of Neil Shubbin’s book, my class talked about how old color vision is. How can we answer a question like this anyway? And what ‘purpose’ does color vision serve?

I have my students write essays on their thoughts about each chapter in the book and more than one spent a good deal of time discussing the evolution of color vision. I’m paraphrasing here because I turned back all the essays, ‘How would our eyes know to evolve color vision?’ —An excellent question. I wish we had several more weeks of classtime to discuss questions like this. This semester was difficult for me because we did not get nearly as far into the discussion of evolution and population genetics as I would have liked. It’s my favorite part of the semester, but we just couldn’t get through the material.

How do eyes know to evolve color vision?

For an eight word question, there is certainly a lot to unpack.

1. Language builds anthropomorphism right into itself. I did it right there with that sentence.

It’s the way we talk, and it’s difficult to pull ourselves out of the habit. I do it myself all the time, even though I know it’s misleading. To be honest, I think it’s foolish to break our language from it entirely anyway. Let’s just acknowledge that it’s not the way things work, but only the way we talk and move along. Eyes don’t know. Things don’t seek to evolve. Evolution is driven by chance: chance provides a diversity of forms, the ones that are most fit to survive do so. That’s it. No knowing. No direction. Just chance and selection.

2. What is color? What is it to perceive it? Who perceives it?


Sound as Vision

Not all animals see in color. Amongst those that do, not all of them see the same colors. This is something that I discussed earlier with respect to bees. As humans, we devote 30% of our total sensory genes to vision. We rely on it a lot and much of how we perceive the world around us is through this sense. But not all animals are the same in this way. Consider two things: 1) All that we see is just our brain’s interpretation of sensory input & 2) Bat’s fly using sonar almost exclusively. How do you think their brains perceive the world?

3. Do we get to choose how we evolve?

Lamarck thought so. He thought that day after day, the things we do and strive to do change our bodies (I’m OK with that) and that these ‘improvements’ get passed on to our descendants (I’m not OK with that). Darwin first realized how it actually worked, he reasoned that there are more organisms born than survive. Amongst all those that were born, there is a wealth of variety, and from this variety, the ‘best’ or ‘most fit’ organisms survive and pass on their genes. Richard Dawkins restates this elegantly as ‘The Non-Random survival of Random variants.’ We don’t choose to evolve in any direction or towards any end whatsoever. Evolution just happens, like gravity happens. And it doesn’t happen to individuals, it happens to species

4. So when did color vision arise?


This looks delicious

About 50 million years ago. Right about the same time that colorful fruit began appearing. The fruit didn’t know it was being seen. The eyes had no foreknowledge that fruit about to get colorful. They evolved together, not because they wanted to, but because they each helped the other become more successful. Animals with color vision could better see when fruit was ripe for eating; fruit-bearing plants get their seeds dispersed by animals that like their fruit. Everyone benefits. A peaceful co-evolution.

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Posted by on December 18, 2012 in Uncategorized


It’s Christmastime – Spend a little money on someone you love, it’ll make you HAPPY.


Can’t Buy Me Love

Can money buy you love?

Maybe, maybe not. But it turns out that it can buy happiness if you are spending it on someone else. This kind of spending, termed pro-social spending, has the capacity to make you feel better and feel happier than spending it on yourself. But don’t take my word for it. In a Science paper that couldn’t be more about the Christmas spirit, Dunn and Aknin of the University of British Columbia and Norton of the Harvard School of Business show that, “experimental results provide direct support for our causal argument that spending money on others promotes happiness more than spending money on oneself.”1

In the 2008 paper, “Spending Money on Others Promotes Happiness”, the authors suggest that the problem people have with money is that they expect the wrong things from it and don’t know how to spend it best to make themselves happy. Whereas spending money on yourself does not increase happiness, “higher prosocial spending was associated with significantly greater happiness (β =0.11, P < 0.01).” 

So, if you want to give yourself a treat this Christmas, go ahead and shop. Just shop for someone else, not yourself.


1. Science 21 March 2008: Vol. 319 no. 5870 pp. 1687-1688

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Posted by on December 14, 2012 in Uncategorized


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Neurotic sleight of hand

I can’t add anything to this.

Why Evolution Is True

Some lovely magic to end the day, from the International Magic Convention in Beijing.  The YouTube caption says this:

FISM award winner and French magic champion Yann Frisch is one of magic’s freshest talents. Yann has been creating a sensation wherever he goes with his unique take on classic magic, an absurdist take on the cups and balls. Cool, clever, stylish and oh so artful. We are proud to have one of France’s top performers at EMC.

Be sure to watch to the end; it’s only 4.5 minutes.

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Posted by on December 13, 2012 in Uncategorized


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Be Good – The evolving thoughts of Professor Wilson

Chapter 6 of Richard Dawkins’ opus, The Selfish Gene, is titled ‘Genesmanship.’ This chapter discussed the array of strategies that genes appear to take in order to guarantee their immortality.

-Immediately, I must say that Dawkins has already assured us that any altruistic speech about the intent of genes is given merely to provide suitable language for the discussion rather than to actually attribute any actual wants or needs of the genes in question. Further, the term ‘strategy’ is used in precisely the same way; if genes had brains, their actions could be described as strategy, but in the absence of this consciousness, their action merely resembles a strategy.

In this chapter Dawkins faces one of the most difficult conundrums for evolutionary biology: altruistic behavior. If genes truly do act in a selfish manner, how can acts of altruism be explained. This is not a new problem. Other biologists (including J.B.S. Haldane and W.D. Hamilton) had previously addressed this problem providing responses that approach an answer, but aren’t sufficiently quantifiable to satisfy Dawkins – and they shouldn’t be to you either.Screen Shot 2012-12-14 at 8.56.13 AM

The solution Hamilton et al approached was to recognize something called kin selection. This is putting a title of the idea that it is worthwhile to accept some risk to your own hide in order to keep your kin alive. The reason for this is plain, if genes are in the business of perpetuating themselves, then any body that contains them is as good as any other. By adding the notion of genetic distance, there is a quantifiable way to account for the extent to which another person in your kin group also carries your genes.

How does this become quantifiable? Simply, by using a value for relatedness to compare against the risk of ‘sticking your neck out’ for your kin. For example, you are related to yourself 100%. You carry 50% of your mother’s genes (and vice versa) and 50% of your father’s genes (and vice versa). An identical twin sibling would bear 100% of your genes as well, while a non-twin would bear only 25% of your genes. Given this, you are most likely to rescue your twin, then your parent (or offspring, who bear the same relatedness) and then your other sibling.

Hamilton described the following equation to model altruistic behavior:


where B is the benefit gained by the individual who is helped, times a relatedness factor r – as discussed above, and C is the cost to the individual who is acting altruistically.

Atop this, one might assume that a younger person is worth more than an older person to you because they are more likely to add copies of your genes to the gene pool in the future. So, If your father and your son have both fallen into the sea during a violent storm, you would put your son’s rescue ahead of your father’s.

Although this may explain a lot about how kin groups will work together to defend a family/tribe from outsiders, it involves a lot of calculating (how many cousins would I have to save to be worth one sibling?) that is unlikely to be happening in the real world. One person who noticed this and started doubting whether kinship calculations were realistic explanations for altruism was EO Wilson.

And this is odd. Odd, because it was Wilson who was a keen supporter of Hamilton’s work early on. But, like any good scientist, Wilson was ready to throw any or all of his ideas in the trash if a better explanation presented itself. (Am I being fair? Not really – scientists are humans and all humans cling to their ideas and identify with them, but scientists at least acknowledge that this is wrong and will come around to sensible thinking.)

Wilson was interested in the question of altruism for good reason. His passion is the insect world – and not just any part of the insect world, but the world of ants. Who isn’t interested in ants? You might think you don’t care, but spend a moment watching them work and you’re spellbound. How do these tiny creatures carry out such amazing actions? They build, they problem-solve, they farm – livestock and horticulture and they’re social.

It’s the social behavior that holds Wilson’s interest. It bears repeating what social means in this context. We, in our human lives think of social in a lot of ways: saying hello to people you work with, tipping your barber and pizza delivery guy, dating and  – recently – even computers (the definition of antisocial for decades) claim to be social. Twitter, tumblr, facebook, myspace(?), etc. But none of this fits the definition of social that ants engage in. Ants, like a number of their hymenoptera kin, are social to the extreme. Sure, they organize and divide labor amongst their numbers. Some are specialized so much that a glance will tell you who is the soldier and who is the worker.


These animals divide duties so rigorously, that even reproduction is done only by specialized individuals. If you think about evolution a lot, and subscribe to Dawkin’s selfish gene idea, then this arrangement needs explanation. Why do all these sister ants work so hard if they don’t get to pass on their genes?

But they do. Just like all the cells of your body that work together for the good of the organism. The cells of your arm – or your heart – or your brain – don’t get to reproduce. Only your sex cells do. But your arm and heart and brain all benefit from that because they are genetically identical. When your sex cells make a baby, all the genes of the organism get passed on, not just those of the sex cell – again, because they are all identical. Dawkins describes your body as one big survival machine built to pass on genes. I would be willing to bet that Wilson would describe ants using much the same language. The only difference being that ants have made a leap from specialization at the cellular level, to specialization at the organismal level.

So ants are social (and so too are bees and many wasps, etc). Does this have anything to do with altruism? Dawkins says yes. At the level of the social organism, we have pure altruism. Every being is tied to the survival of the group as intimately as every cell in your body is tied to the survival of your body as a whole. It’s tempting to say that identical twins should feel the same way. The survival of each individual is worth less than the survival of at least one of them, so twins should show the same degree of altruistic behavior between one another as our ants do.

But there is a difference. Social insects have mastered altruism to such an extent that they build it into their makeup from the start. Soldier and worker ants simply do not mate in most species (approximately 100 species of 12,000+ known do have workers that mate, but that appears to be the exception)1,2. Because the workers are not reproductive and are not even built for reproduction and identical twins do – so it’s not a fair comparison. Altruism is not truly altruistic if acting selfishly does not benefit you more than being pro-social.

And this is essentially where Wilson comes in, he extends this idea to species that are not genetically tied arguing that altruism doesn’t count when it’s selfish. And here he meets Dawkins, because Dawkins does believe that altruistic behavior is selfish, and that all altruistic behavior can be calculated (or at least approximated) based on relatedness. It is from this highly related group that benefits from pro-social behavior that society emerges. Wilson says this calculation is too unwieldy to represent what is done in real life and that behavior that appears altruistic can always be explained by straight up selfishness. In fact, he thinks that it is society that gets the ball rolling by promoting pro-social behavior among previously selfish individuals.

So, what do you think?

  1. Peeters, C. “The occurance of sexual reproduction among ant workers” Biological Journal of the Linnean Society (1991), 44: 141-152.
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Posted by on December 13, 2012 in Uncategorized


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