The course blog

I have [...]]]> Over the past couple of years I have played around with using blogs and wiki pages in my courses.  This past semester I incorporated both into my Marine Biology course and feel good about the results.  My reasons for using each type of web technology differed, so I will hit them separately:

The course blog

I have been assigning readings from science blogs over the past few years to reinforce material covered in class and engage students with outside, related content.  This past semester I used a blog in my Anatomy and Physiology course to answer student questions that stumped me in class, or that I needed to research more fully.  After class I would post an answer to the course blog with links to additional reading.  But in my Marine Biology course almost all of the content was student generated.  After adding a few of my own posts as examples, I told my students to add a post of their own once every other week.  With ten students in the course this meant almost a post each day (although they often came in droves).  The only guideline I gave them was that the information had to have some connection to marine science.  You can read the results yourself, but I was impressed with the range of information that students added, and happy to see students commenting on each other’s posts.  A Zoomerang survey given at the end of the semester showed that 8 of 10 students agreed or strongly agreed that the blog was a helpful part of the course (the other 2 were neutral).  The one thing I would change next time is to urge students to use more diverse sources for their posts.  Almost every post was a summary of a news story from Science Daily.

The course wiki

A few years back our University started running MediaWiki software on our internal servers so that we could host our own wiki pages.  When I taught Marine Biology two years ago I had my students write information guides for species they saw during our end-of-semester field trip to the Outer Banks of North Carolina.  I then used this content to write wiki pages on each species.  This year I assigned each of my ten students to write guides for two species each, and to add these to the wiki themselves.  Their entries needed to include some personal comment about their interaction with the species.  After some editing for style and format we now have the start of an online guide to Outer Banks coastal species that I plan to add to each year I teach the course.  And many of the students used their own pictures of the species they encountered, adding some new online content for others to use.

Both the blog and wiki seemed to engage students in material beyond the official meeting times of the class.  Students accepted both techniques quickly, and 80% found the blog valuable.  I will be curious to see how these tools work in two years when I teach the course again, as students will be building on an already rich set of content.

When your name can also [...]]]> Next time you’re reeling in that fish, picture Whiskers or Fluffy hooked through the mouth on the end of your line.  At least that is what PETA would like you to do.  In a new PR campaign the animal rights group is attempting to rebrand “fish” as “sea kitten”.  The rationale:

When your name can also be used as a verb that means driving a hook through your head, it’s time for a serious image makeover. And who could possibly want to put a hook through a sea kitten?

Point well taken.  But I am not sure how I feel about my subject of study (I am an ichthyologist that does research on the fish eye) being renamed.  PETA argues that:

People don’t seem to like fish. They’re slithery and slimy, and they have eyes on either side of their pointy little heads—which is weird, to say the least.

But I love fish, and I know legions of other ichthyologists that love fish too.  And yes, I occasionally meet people, tell them I am an ichthyologist, then explain what that means, find out that they think that is cool, but am then asked:  then you don’t eat fish, do you?  But I also love eating fish, as do most ichthyologists I know.  Is it weird to like eating the group that you study.  I have a mycologist friend (studies fungi) who doesn’t like to eat mushrooms.  But I think that’s an exception.  And yes, many of you study organisms that you probably don’t want to eat.  I am talking to you, entomologists and parasitologists.  But I bet you malacologists out there love your oysters and scallops.  Admit it, you ornithologists eat chicken.

While our love for eating fish, and the need for this important source of protein in the diets of many humans, is leading to the collapse of fisheries and marine ecosystems, making fish seem cute is not the solution.  Ironically, the economic importance of fish and other marine organisms as food will play an important role in turning back the decay of our oceans, if that is possible.  Whether it is restoration of the Chesapeake Bay to bring back the oysters and crabs, research in the Gulf of Mexico to maintain red snapper populations (check out that mahi my ichthyologist friend Will caught) or limits on trawling in the North Atlantic.

But I did have fun making my custom “sea kitten” (see the top of this post).  Although it was labeled a flounder, but clearly has only one eye on the side of its head.  What’s up with that?

The NPR story on the new PETA campaign attracted a money comment:

This story evokes a wonderful memory of a recent trip I had back to my mountain cabin. I had a nice hike and spotted a wonderful Sky Origami (falcon) crushing a Stuart Little (mouse) in its razor sharp talons. When I got back to the cabin I made sure the House Bunny (dog) was in so it wouldn’t get mauled by a Forest Angel (bear) that night.

This shark video is only creepy if you were in the submarine, and the sharks actually posed a threat.  Which they probably didn’t.  But it is still worth checking out.

Changing climates have the potential to wreck havoc on living things, which are often adapted to very specific local temperatures.  These changes can alter the structure and, therefore, the function of the tens of thousands of proteins that keep cells and their owners alive.  Yet, the presence of living things in extreme environments [...]]]>

Changing climates have the potential to wreck havoc on living things, which are often adapted to very specific local temperatures.  These changes can alter the structure and, therefore, the function of the tens of thousands of proteins that keep cells and their owners alive.  Yet, the presence of living things in extreme environments ranging from the freezing waters of Antarctica to the boiling hot springs of Yellowstone attest to the evolutionary adaptability of proteins.  An interesting place to study this adaptive process, and the possible effects of climate change, is the complex intertidal zone along marine coasts.

George Somero of Stanford University has used many types of intertidal organisms as model systems for examining how protein structure and function adapt to environmental temperature.  In his latest paper, just published in the Journal of Experimental Biology, he has compared the enzyme cytosolic malate dehydrogenase (cMDH) in six species of limpets (the genus Lottia) along the coast of California.  These mollusk species (a group of marine snails) live at different latitudes and different zones of the intertidal, meaning that they are covered by water and baked by the sun for different amounts of time each day.  Limpets living in the upper intertidal in lower latitudes would get the most sun – so they experience the warmest body temperatures.

Somero already knew that cMDH adapted to thermal conditions from work he had done in other species.  The ability of this enzyme to run its chemical reactions changed in tune with the body temperature of these species.  Because the three-dimensional structure of cMDH was well known it was also possible to map the location of amino acid variations between species and get an idea of how they produced altered protein function.  Somero hypothesized that the six closely related limpet species differing in physiological temperature would contain variations in cMDH amino acid sequence that would provide insights into how cMDH, and proteins in general, adapt to changing environmental temperature.  He was not dissapointed.

By grinding up the muscular foot from the six species Somero and his co-author Yunwei Dong were able to collect a crude cellular extract that contained cMDH.  They found that the enzymatic activity and thermal stability of cMDH was adapted to the environmental temperature of each species, confirming their hypothesis.  When they cloned and sequenced the cMDH genes from all six species and determined their amino acid sequences, they found 24 variable residues.  What is really interesting is that the amount of variation between any two amino acid sequences did not correlate with differences in protein function or thermal stability.  The amount of structural variation did not predict how different the proteins would behave.

Two species in this study are of particular interest.  The northern and cold adapted L. digitalis and more southerly warm adapted L. austrodigitalis are so closely related that they are often difficult to tell apart from their physical appearance.  But their respective cMDH proteins are the most divergent in function and thermal stability of the six in the study, matching their divergent latitudes.  And here is the kicker – they only differ by one amino acid.  When you map that one residue onto a computer generated 3D structure for cMDH it falls in an important substrate binding site.  

The amino acid variation in the warm adapted L. austrodigitalis provides greater hydrogen bonding and reduced flexibility – this means that this version of the protein can more stably stick to the molecules that it acts on.  A neat trick when it needs to grab another molecule at elevated temperatures.

How does this research relate to global warming?   Between the 1970′s and 1990′s the range of the southerly L. austrodigitalis expanded northward into Monterey Bay at the same time that waters in the Bay increased in temperature.  The southern range of L. digitalis moved northward during this same period.  These species are shifting northward as waters warm since their proteins (cMDH and presumably others) are finely tuned to a relatively narrow range of temperature extremes.  But this paper also suggests that proteins have the potential to adapt to warming environments.  In this case only one amino acid substitution is needed to dramatically change the ability of this protein to function at higher temperatures.

Will the powerful adaptive ability of proteins allow life on Earth to adapt to our warming planet?  Unfortunately that grand experiment is underway.  Perhaps bittersweet for the comparative physiologist.

Y. Dong, G. N. Somero (2009). Temperature adaptation of cytosolic malate dehydrogenases of limpets (genus Lottia): differences in stability and function due to minor changes in sequence correlate with biogeographic and vertical distributions Journal of Experimental Biology, 212 (2), 169-177 DOI: 10.1242/jeb.024505