Tag Archives: tiktaalik

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 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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