Tag Archives: Dawkins


Today is the first day of the Coursera Cyrptography class taught by Stanford Professor, Dan Boneh. I follow courses like this every once in a while in order to learn a bit about topics that I would not otherwise get any exposure to. Boneh’s course is a little math-intense, but there is another more concept-driven course on the same topic being offered on Khan Academy. If you haven’t taken advantage of either of these two sites, you should look into them. Both are entirely free, and both are taught by excellent educators.

Here’s a video from the Khan Academy site introducing the Caesar Cipher, a simple cipher like those used on radio dramas of the past (get your secret decoder ring!).

If you want to crack a simple substitution cipher like this, you might want to start by using a frequency chart of letters used in the English language, like this one:

The Caesar cipher: Brit explains the Caesar cipher, the first popular substitution cipher, and shows how it was broken with “frequency analysis”





However, once you figure out the easiest letters (e,t,and a), things get a bit more difficult. At this point, you will probably have to start looking at letter pairings (Bigrams) to see if any useful patterns show up there. Here’s a listing of the most common Bigrams (again, in English).







It’s interesting that these kinds of codes might ever have been considered sophisticated enough to use in the real world. After all, it’s easy to find examples of these types of ciphers in daily newspapers around the world presented as cryptograms that people do for fun.




                                               -AVWQRAI IRCNVDJ

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Posted by on September 8, 2014 in Education


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Dawkins and Chopra

Unfortunately, I missed the live stream of a debate between Richard Dawkins and Deepak Chopra this weekend. I made the faulty assumption that I would be able to view / listen to it later, but for some reason that I don’t understand, youtube has blocked replay of this event in the United States. I’ve been assured that there was nothing particularly groundbreaking in this event…

Chopra says, “Blah blah, quantum, blah blah blah, consciousness, other way of knowing…”

Dawkins replies, ” What in God’s name are you talking about?”

A clip of a prior interaction between the two can be found at:

As my previous post hints, there is a problem in the communication of science to the public. It may be added that there is a deep valley between the way that scientists speak and the way that the public – or more importantly, the way some public personalities like Chopra- speaks.

Dawkins can be heard in the video clip above trying to make sense of Chopra’s language. Is he speaking in metaphor or does he mean to speak literally?

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Posted by on November 11, 2013 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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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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Unit II Genes, Heredity and Inheritance- reading recommendation

Just a quick note about an excellent book about genetics

I just added some links to books that I use in my classes – but WordPress doesn’t really like that kind of link, so I had to pass you over to my Recommended Reading List at the DHS official site. One of them is the book we are already reading in class, Your Inner Fish, by Neil Shubin. The other is the one I really wanted to highlight. It is a recommended book that does an excellent job discussing much of the work that we will go over in Unit II. It’s called The Cartoon Guide to Genetics, by Larry Gonick. It really is great – it covers all of the material I address in Unit II and is also very easy reading. After all it’s a comic book. If you’re interested in taking a look, follow…


And you’ll find a pointer to each of these books, as well as some others that I think provide an excellent foundation in biology.

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Posted by on November 5, 2012 in Uncategorized


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Another old essay – Morgan and Memes

This essay was originally published in the Osawatomie newspaper (The Graphic?) a year or two ago. It was prompted by an article in my local newspaper that showed how two ideas that have no logical connection can sometimes appear to be intimately ‘linked’ to one another.

Morgan and Memes                                                                                           

Thomas Hunt Morgan in the Fly Room

In the early 20th century, a scientist at Columbia University, named Thomas Hunt Morgan did work establishing the connection between the observations of Gregor Mendel and some lesser known scientists, Flemming, Sutton and Boveri. Mendel, an Austrian monk, was the first naturalist to see deep into the workings of nature and establish a clear, testable theory of how inheritance operates in organisms of all types. Trained in mathematics, Mendel saw that if each trait he observed was controlled by two ‘factors’ (one from each parent,) then inheritance followed a predictable pattern.

In his laboratory in Germany, totally unaware of Mendel’s work, Walther Flemming watched and documented the precise orchestration of cell division under the microscope. What he saw, less well known than Mendel’s work, was how chromosomes seem to form as threads in the cell that group along the center line of a cell before splitting and separating into each of the daughter cells formed by division. Sutton and Boveri saw the connection between these sorting chromosomes and Mendel’s ‘factors,’ but could not finish connecting the dots. Hunt’s conclusion, which seems so obvious now, was that chromosomes carry genes. To prove this he tracked two special chromosomes, X and Y and found that they determined the sex of the organism. Like humans, when flies had two X chromosomes, they were female; one X and one Y and they were male. Chromosomes were controlling the sex of the organism. This conclusion changed the way genetics was studied for years to come.

One thought that beguiled him though, was that Mendel’s work predicted that all genes sorted independently, but there were only so many chromosomes, and many, many genes. This was troubling because Mendel’s work was otherwise very clear and stood up to rigorous testing, yet it was inconsistent with what he saw with chromosomes. Mendel said that all genes are randomly inherited – and here he was, working with fruit flies and finding that it just couldn’t be true with so many genes and so few chromosomes. To skip the details, Morgan, and his lab members eventually discovered that chromosomes are tricky – and sticky. The two sets of chromosomes you get from each of your parents pair up and swap bits promiscuously. This swapping, or ‘crossing over,’ imitated randomness in all genes except those that were very close together. And so, while most genes adhered to Mendel’s law of independent assortment, those genes that lie close together on the chromosomes travel together and can be seen as traits that go hand-in-hand down the generations.

In 1976, Richard Dawkins, wrote “The Selfish Gene” in which he buried a nifty little idea. He proposed that thoughts are like genes- he called them memes– that get passed along from one person to the next, taking on a life of their own in a sort of world-wide game of telephone. He has written often about this idea, which is an interesting analogy, but not altogether useful scientifically.

Nevertheless, I had the thought of memes in my head, and when I read an article about organic farming our local county paper, I suddenly realized that memes too travel together! In the article a farmer described her farm as organic and natural – all the things that I like to hear about. I was immediately excited and wanted to join her co-op to get food that was a little more a part of the earth and a little less a product of chemistry. But then I got to some ideas that just didn’t make sense to me – things that often travel with the less well informed members of the organic food crowd: She doesn’t vaccinate her animals – or her children. She went on to suggest that cancer and autism are causally linked to genetically modified organism (GMO) foods – a completely groundless hypothesis.

Two chains of Memes (Memosome?). Memes 1-3 are all linked in some way, Memes 4 and 5 are also linked to one another, but not to Memes 1-3.

Yet, I’ve seen these memes travelling together in the past without giving it as much thought, and here they are again: The natural food meme and science-makes-us-sick meme. On one hand I see the connection and agree, I don’t think GMO foods are natural and vaccines are a way of unnaturally generating immunity without being exposed to disease. But, GMO foods are not inherently unsafe. They simply put together traits that exist in nature, but in combinations that would take breeders eons to produce ‘naturally.’

I love to know that my food comes from a natural, organic farm. And I expect to pay more for food of that sort, mostly because it is not as abundant and does not take advantage of advances in science. Advances that make it possible to feed all the billions of people on this planet. Billions that could not all be fed without modern, scientific agriculture. But there is something wholesome about foods grown in this way: the great variety of fruits and vegetables with their subtly distinct flavors and colors. Like GMOs, vaccines are also something of an unnatural creation – unnatural creations that spare us from the all too natural world of smallpox, measles, poliomyelitis.

I don’t mean to impose my values on anyone, but I do think that it can be enlightening to consider what ‘natural’ means. There are many things from the past that we should not forget and good food is one of them, but we ought not to also forget the ravages of disease that once kept children from playing outside together in the summer months or made them deathly sick only to recover and lead a life blinded, paralyzed or otherwise retarded from exposure to all things natural in the world.

I don’t think that anyone leads an entirely consistent life, but we are intelligent creatures and we don’t have to accept anything without consideration. So take some time, examine what you believe in and see just what memes are in your head just catching a ride. Maybe there’s some cleaning out to do.

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Posted by on October 24, 2012 in Uncategorized


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