Tag Archives: shubin

Science on Screen

You know, I’m pretty happy with the present state of science on the small screen. This week, we had the opportunity to choose between three excellent shows with real scientists explaining fundamental principles to a wide audience. These shows are:

Cosmos with Neil Tyson

Your Inner Fish with Neil Shubin

Wonders of Life with Brian Cox


ImageOf the three, I think Brian Cox is probably the best spokesperson for science – meaning he has a very casual and unassuming presence and speaks in a slow, measured pace that draws the listener in, eager to hear what’s coming. The camerawork in the Wonders of Life series is also good. It’s more artsy than you would expect from a science show, often putting the Sun behind Dr. Cox’ head to create moments of strong flares that’s muted post-production (I suspect). This technique works wonders when properly utilized. It creates drama and a bit of mystique because it flies in the face of one cardinal rule of photography. In many ways it reminds me of the cooking show Nigella Bites. Besides its production value, the science is solid, well presented and clearly explained. Here Dr. Cox explains the apparent retrograde motion of the planets (wanderers).



Cosmos works well because it is a reprise of a previously well-received series by the much-beloved Carl Sagan. How could it miss? So much is done well. I especially like the simple animations that bring history alive for us. People are hardwired for storytelling, so I firmly believe that science is learned best when it is part of a well-crafted story – and the stories told in Cosmos are right on. And one last word: wow. This is on Fox! Frankly, I’m amazed. Maybe Neil can teach O’Reilly why the tide goes in and out.


ImageYour Inner Fish was initially a book that I use every semester I teach General Biology. As a book it functions well, the story is clear and filled with examples – although we do get lost in the details from time to time. Overall, I like it and think it’s a great introduction to scientific thinking. As a series, the same story is told, but with a greater clarity and excellent use of digital effects to complement the story without getting in the way.


All three are excellent – and more than anything, I just enjoy knowing that popular television, reaching a wide audience, is seeing a surplus of high quality, entertaining, educational material that is not soft on science.

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Posted by on April 23, 2014 in Uncategorized


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Your Inner Fish Crawls off the Page

ImageI’ve been assigning Neil Shubin’s Your Inner Fish as a reading and discussion assignment in my General Biology classes for several years now. I believe that it’s a good introduction to understanding how the process of science works in the real world, it does a good job communicating the methods and findings of a number of complex experiments, and it also walks through the history of ideas and how new information changed these ideas over time.

If I can get students to think about all these things and perhaps do a little extra digging (into the research), then I’ve down my job.

Episode I of the adaptation of this book  just aired this week and I was very impressed by the way the material was put together- refining the story from the book a little- and coming up with a standard documentary supported by computer graphics that really add to the story rather than looking tacky of fake. In fact, I think the graphics really transform the material into a living experience.

The story is told in two converging arcs. In one, we follow Shubin’s field work, where he decided that he was interested in finding the remains of one of the earliest organisms to crawl out of the water and establish terrestrial life. Prior work suggested that the earliest tetrapod ancestor on land emerged from the Devonian Seas about 370 Million Years Ago. Shubin and colleagues identified an ancient river delta of about this age in the Canadian Arctic and set out to locate some fossils.

ImageThe other story walks us through the idea of relationship with other life on Earth. What suggests this relationship? What evidence is there for it? How long does it go back?

As I said above, I have liked this adaptation very much so far and I am already planning to bring at least parts of this video into my classroom to supplement our discussions.

More on this later…


Posted by on April 10, 2014 in Uncategorized


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Your Inner Fish on PBS



The HHMI’s Tangled Bank Studios will be airing a three part PBS documentary based on Your Inner Fish by Neil Shubin. The documentary, like the book of the same name, asserts that, “It took more than 350 million years for the human body to take shape.” And asks, “How did it become the complicated, quirky, and amazing machine it is today?” Broadcast is scheduled for Spring of 2014.

Perhaps this will be the last semester that we read the book in my General Biology class in favor of watching the film version and adding a new read to accompany the class. There are a lot of books I would like to go with, but here’s the opportunity for you to send your suggestions.


The Earth during the Devonian

While you’re at it, I am also starting to teach an Ecology / Genetics class next semester (offered for the first time at our campus) and would be interested to have your suggestions for a book to read with that class as well. So, please send your ideas for a fun reads (I would love to read The Selfish Gene, but have nixed it for failing in the ‘fun’ department) that you think students of General Biology and Ecology / Genetics should read.

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Posted by on September 2, 2013 in Uncategorized


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Your Inner Fish Chapter 3: Handy Genes

The basic thesis of Your Inner Fish is that we can learn something about ourselves by studying other organisms and observing the similarities between us. Chapter 2 examines the anatomy of the limbs of a number of different organisms. That chapter began with the observations of Sir Richard Owens who saw how many diverse organisms shared a common body plan, as exemplified by the structure of the limbs.

Darwin explained these similarities by proposing that the source of this commonality was that there exists a real relationship between even apparently diverse species. If this hypothesis is correct, we can expect that more similarities can be found and that these comparisons go well beyond skin deep.


Chapter 3 expands on this theme, retaining the focus on limb / hand construction and moving from simple anatomical comparisons to the underlying genetics that control the development of these structures.

If you study genetics for long you will see patterns in the way that genes work together. There often exists a number of genes responsible for some specific structure that are all controlled by a more limited number of regulator genes, these too are controlled by some master regulator. The master regulator often acts as a toggle switch that turns on or off certain other genes in a system leading to a cascade of effects. Possibly even more interesting is that these same master regulator genes may be found again and again initiating different outcomes in different locations.


In the case of the ZPA, it was found that this patch of tissue secretes a substance that provides a gradient across the developing limb leading to differential developmental patterning in digits according to the dose of hormone cells receive.  This effect was most clearly demonstrated by inserting a second ZPA in a fashion that creates a mirror image gradient, leading to a corresponding mirror image limb structure  (see below.)


Shubin describes one of these regulatory pathways as being controlled by a patch of tissue called the zone of polarizing activity (ZPA). This patch controls the development of limbs by providing chemical cues to cells in the area. Later, the chemical entity that is secreted from the ZPA and controls this behavior was identified and named Hedgehog / Sonic Hedgehog.  Further experiments have been performed using variable quantities of Sonic Hedgehog or modified hormone resulting in similar malformations of limbs.


One trick that Shubin highlights several times throughout Your Inner Fish is how genes or proteins from one animal may be swapped into another animal and work perfectly normally. The reason he likes to point out the success of these experiments is that that provide excellent support for his hypothesis that all life is related.

An alignment of Sonic Hedgehog proteins is presented below to illustrate the similarities across a number of species. Each organisms’ primary amino acid sequence is presented stacked upon other organisms’ sequences. Identical amino acids are highlighted in yellow.


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Posted by on February 6, 2013 in Uncategorized


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An article discussing early tetrapods in last week’s Science Magazine

I was reading through last week’s issue of Science magazine this evening and discovered an interesting summary of some work done by Philip Anderson at UMass, Amherst. He has been studying how early tetrapods (like Tiktaalik) may have struggled with eating while on land because they still had heads and jaws specialized for feeding in the water. “With fishlike mouths, early tetrapods would have faced a difficult task eating on land.” 1Image

He and others have wondered what these animals ate, where they hunted (land or sea) and how they even managed to get food into their mouths. Sam Van Wassenbergh has studied more modern animals that live at the land/water interface to see how they accomplish the same task and found some interesting strategies. One such example is the “eel catfish, Channallabes apus, catches unsuspecting victims by arching upwards and descending upon prey, trapping an insect against the ground before sucking it up.”2 Van Wassenbergh suggests that this may have been amongst the strategies of early tetrapods as they were adapting to life on land. Van Wassesbergh made a film of this behavior:


1. Pennisi, “Eating Was Tough For Early Tetrapods” Science 25 January 2013: Vol. 339 no. 6118 pp. 390-391

2. Hopkin, “The Fish that hunts on land” Nature, 12 April 2006 

3. Van Wassenbergh S., et alNature440. 881 (2006).

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Posted by on February 6, 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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For My Class

ImageFor those of you in my General Biology Class (especially those who missed Thursday), we will be having a quiz on Tuesday about DNA replication, transcription and translation. We will also be going over chapter 11 of Your Inner Fish (the last chapter!!!) and there is a homework exercise due. You can find it on Blackboard… ironically enough, it’s called ‘Genetics In-Class’. This exercise will be good practice for the sort of questions you can expect to see on Tuesday’s quiz.


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Posted by on December 1, 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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Your Inner Fish-Adventures in Body Building and Science Magazine Podcast

Today in class we discussed chapter 7 of Neil Shubin’s book, Your Inner Fish. This chapter explored how life on Earth went from being unicellular to multicellular. Later in the day, as I was driving my son to Karate, I was listening to the Science Magazine’s weekly podcast and was interested to hear an interview with Stuart Newman about a new article on this subject. 

A copy of the transcript can be found at:

The podcast can be found on iTunes or at science magazine at:


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Posted by on October 11, 2012 in Uncategorized


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Bio – Chapter 3


Einstein and Bohr

We’ll be continuing with Chemistry in tomorrow’s class (I’d like to get through most, if not all of what I want to cover in that day). But why is chemistry even important in a biology class?

Like I said in my previous post:

Physics –> Chemistry –> Life

It’s important to understand that chemistry is the basis of biology because it is setting the parameters within which life can function. I don’t go much further than explaining the basics of how and why the periodic table is depicted the way it is, the Bohr model of the atom, the octet rule and the three basic bonds atoms enter into.

The Bohr model is fantastic for students. So, it doesn’t depict the actual atoms as they exist in nature… not much actually does. The closer we look at their behavior, the stranger they are. So the Bohr model is just that: a model.

What it does provide is a very nice way of explaining how protons, electrons and neutrons interact. It also plants a seed of electron energy, that we will revisit when we get to photosynthesis (photons strike pigment molecules and raise an electron to a higher energy state). 

Ultimately, we lay just enough groundwork so that once we start talking about DNA and other biomolecules, these structures make some sense and students will know why the backbone of DNA sticks together, but the Hydrogen bonds between the strands are less stable and can be pulled apart and come back together in a reasonable way.

I’ll finish out the chapter on chemistry discussing these four basic biomolecules (nucleic acids, lipids, proteins and carbohydrates) as we drift into studying material that is more recognizably biology.

This week we also start our extra reading, ‘Your Inner Fish’ by Neil Shubin. I’ve been using this book for several semesters now and think it makes a good addition to the class. I’ll talk more about that later when we discuss chapter 1 on Thursday.



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Posted by on August 27, 2012 in Uncategorized


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