Mason Posner teaches anatomy and physiology, marine and vertebrate biology at Ashland University in Ohio. He does research on the evolution and function of the vertebrate eye lens and has interests in undergraduate research and teaching technology. He leads a science communication capstone courses that teaches Biology majors how to develop science blogs
I’ve been reading a number of reports from the recent ScienceOnline 09 science blogging conference in Raleigh, NC. The Southern Fried Scientist and Anne-Marie from pondering pikaia have some nice write-ups from the sessions they attended. What caught my attention most was a session titled Teaching College Science: Blogs and Beyond. I am teaching my department’s senior capstone biology seminar this semester for the first time, and am focusing on science writing as a central theme. I started this blog, my first, back in September and have become totally absorbed with the science blogging community. I also have a strong interest in playing with different teaching technologies. So for this capstone course I decided to merge the two. My students are starting their own science blogs in groups of three or four to develop skills in communicating science. I hope that this will also facilitate discussion of what a well-trained biologists should know – another central them of the course.
You can follow along with this experiment at our central course blog. My students will have their blogs up later this week, so check back to see our progress.
The Southern Fried Scientist is having his Marine Invertebrate Zoology students produce 2 minute videos on scientific journal articles. They are really fantastic, especially one on the effects of reduced predation risk on mollusk evolution. What a great way to engage students in the literature and get them thinking about how to communicate science. Enjoy:
When teaching marine biology I warn my students that if they are there to just learn about sharks and dolphins they will be sorely disappointed, because only microscopic plankton have the biomass to really affect the oceans. Being an ichthyologist this always hurt a bit. A recent paper in Science has restored my faith that all that microscopic stuff is just fish food – fish CAN change the world. Better yet, this story involves some animal comparative physiology.
First a little background on how we are killing our oceans. The same CO2 that is accumulating in the atmosphere from the combustion of fossil fuels and other sources, leading to global warming, is diffusing into the oceans and changing their pH. When CO2 reacts chemically with H2O, H+ ions are released making water more acidic. This declining pH is already adversely affecting marine organisms, which are often adapted to a narrow pH range. Calcium carbonate, however, can react with CO2 and limit the drop in pH. The production of calcium carbonate by microscopic organisms like coccolithophores is thought to be the major player in this regulation of ocean pH.
So where do the fish come in? Research on the toadfish, Opsanus beta, showed that this fish produces little calcium carbonate rocks in its digestive tract. Subsequent physiological research showed that the production of these “gut rocks” was involved in the absorption of water in the gut. Marine fish are less salty than the surrounding ocean. Water, therefore, diffuses out of the fish into their environment leaving them very thirsty. But when they drink they fill their guts with salty water, which would pull fluids from their bodies leaving them even thirstier. It is for a similar reason that you should not drink ocean water when stranded in a life raft (that’s when you drink your own urine instead). But the fish apparently have a trick. They accrete some of the salts in their urine as carbonate precipitates, lowering the salinity of the water in their gut and facilitating its absorption. And then the fish defecate the rocks.
Radiographic images of a live European flounder accumulating carbonate precipitates in its gut. The fish on top was living in freshwater and lacks "gut rocks". The same fish is shown below after only three hours in seawater. Note the opacities in the gut resulting from the accretion of carbonates (white arrows).
But would this calcium carbonate release affect the Ocean’s pH balance considering the relatively low biomass of fishes compared to plankters like the coccolithophores? In their paper Wilson et al. also calculate the total biomass of fishes in the Ocean and the amount of calcium carbonate they produce. While these types of calculations require a good number of assumptions, the authors claim that their conservative estimate is that fishes produce 3-15% of the Ocean’s calcium carbonate.
R. W. Wilson, F. J. Millero, J. R. Taylor, P. J. Walsh, V. Christensen, S. Jennings, M. Grosell (2009). Contribution of Fish to the Marine Inorganic Carbon Cycle Science, 323 (5912), 359-362 DOI: 10.1126/science.1157972
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.
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?
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 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.
Lottia digitalis – the ribbed limpet
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 3D structures of cold (left) and warm (right) adapted limpet cMDH proteins. The one amino acid difference between the two species is at position 291, shown on the right side of each molecule.
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
The long history of sociologists ignoring the role of genetics in human behavior is being challenged. The Chronicle asks:
If sociologists ignore genes, will other academics — and the wider world — ignore sociology?
Some in the discipline are telling their peers just that. With study after study finding that all sorts of personal characteristics are heritable — along with behaviors shaped by those characteristics — a see-no-gene perspective is obsolete.
this supplement should make some great reading (a few of the articles are open access if you do not have a subscription). Hopefully the integration of genetics and sociology will break through the academic barriers that have made nature/nurture debates unproductive.
With many of us going back to teaching in the next week or so I wanted to post about an application I have been using for the past three years to podcast some of my courses. Coursecasting, as this type of podcasting is called, is a great way to provide lecture material to students for review or for students who miss a class. You can also use this technique to record and share any talk or critique your own presentation skills. There is extensive online information on coursecasting, but in my own experience I have found that overall students like the ability to review course material on their own time. And I have not found that attendance drops when podcasts are made available – although I teach at a small University where attendance usually is not a problem. Your results may differ.
The key to sticking with coursecasting is making it simple. Your techie urges may keep you going for a while, but to continue semester after semester you want it to be easy. Quick setup and no post presentation editing. You may be fortunate to work at a school with IT support for coursecasting, but I don’t. The apps and services I’ll describe below require no help from your IT department.
OK – you’re excited. But what do you need?
The only thing you will have to buy is an application called Profcast. This is Mac only software at the moment, although the developers promise a Windows version soon (yet another reason to switch). The current cost is $60 ($30 academic pricing). If you are using Windows there are other software solutions. Either way, get your department to pay for it.
Presentation software – ProfCast supports either PowerPoint or Keynote.
A microphone that provides audio input to the computer playing your presentation- I use the internal mic on my Mac laptop and the sound is fine. The downside is that when you walk away from the laptop your voice level drops, but the laptop mic does pick up student voices when they comment or ask questions. You can use a wireless lapel mic, but then you cannot record students in the class.
With this simple setup you can record a podcast in any room that has a digital projector. Your studio moves with you. To record your lecture or talk you simply open profcast and drag your presentation into this window:
ProfCast will open your presentation and when you are ready to start you click the record button. The software will record your voice in synch with each slide. When have finished your talk, you click the share button and ProfCast turns the recording into a .m4a or .m4b enhanced podcast file – this means that chapter headings are inserted so that students can easily advance to any slide in your talk and listen to that specific part of the lecture/talk. Your talk will look like this when viewed in iTunes:
Podcast viewed in iTunes showing chapter selection – click to enlarge
Recording the presentation is that easy! The trickiest part is actually distributing your recordings to students. You can link each one to a webpage or distribute them using classroom support software like Blackboard or Angel. If your University has an iTunes U setup you can use that. I have played with a few solutions but am now using the following:
Upload your podcast episodes (the individual lectures) to an internet server. This can be on your University servers or using your own personal web host. I started using Bluehost (which also hosts this blog) because I could not access my University servers from off campus. ProfCast makes this process easy by providing a built in podcast publisher. This part of the software will add each new episode to your podcast and then upload them to your server space. ProfCast will also write the RSS file (the most technical part of this process). The RSS file tells podcatching applications, like iTunes, when you have published a new episode (lecture) so that it will be downloaded automatically. This brings us to the last part of the process. How do students subscribe to or download your podcast:
Set up a Feedburner feed for your course. You bloggers reading this may already know what that means. For the rest of you, Feedburner is a free service that makes it easy for others to subscribe to your podcast using programs like iTunes. This is the application that my students almost always use to get my podcasts. Once you sign up for a free Feedburner account and tell the website where your RSS file and podcast episodes live, you just need to give your students the feedburner URL for your podcast. For example, my anatomy and physiology course is found at http://feeds.feedburner.com/anatomy. When students go to that address they see:
The beauty of using Feedburner is that you do not need to maintain a website for your podcast, Feedburner does that for you. Students can then either subscribe to your podcast so that iTunes will download the episodes for them when they are posted, or they can download each individually. Feedburner will also keep stats on how many people subscribe or access your podcast.
On last bit of advice – start slow. I found that it took several weeks to get this system working smoothly. Pick one course and consider it an experiment. Let students know that you are trying this out for the first time and ask for feedback along the way. This way if things do not work students will not be relying too heavily on the podcast and will not get upset when they do not appear. I still have the occasional technical glitch that kills an episode (usually once a semester I forget to hit the record button at the beginning).
I receive very positive feedback from students about my podcasts during course evaluations and when talking to them about the course. I would highly recommend that you give this a try.
If you are already podcasting your courses please let me know in the comments section what software/techniques you use. I’d also like to know about any interesting teaching uses you have found for podcasting. I plan to post about that in the future.
Ed Yong over at Not Exactly Rocket Science beat me to the punch on this one. You should check out his summary of a new paper by a group of excellent fish eye people on the spookfish, Dolichopteryx longipes. Like many mesopelagic fishes that live in these low light conditions, the spookfish has tubular shaped eyes that look straight up to try and spot the shadows cast by soon to be prey items. This oddly shaped eye allows the fish to collect as much light as possible from above, but it does not allow the fish to see around or down. To do this some mesopelagic fishes have a secondary retina that looks laterally and ventrally, but this part of the eye does not use a lens to focus light. It was thought that the images produced by this secondary retina would be crude, but the new paper by Wagner et al. on the spookfish shows that instead of a lens, this species uses a reflective surface, yes a mirror, to focus light on its secondary retina. This is the first described example of a vertebrate eye that uses reflective optics to focus light, but may not be the last.
Next time you’re reeling in that fish, picture Whiskers or Fluffy hooked through the mouth on the end of your line. At least 
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