Comparative Physiology: A Streamed Video Course (authored by Richard Vogt)

NOTE: The order of lectures listed here is different from the 2007 syllabus. Lectures for Fall 2007 should be viewed in order of:

I. Introduction
II. Digestion / Hormones
III. Kidneys / Muscles
IV. Circulation / Gas Exchange

• About This Course: Comparative Physiology
• Viewing the Lectures
• Making the Videos

Comparative Physiology: The Lectures

About Comparative Physiology, The Course: www.biol.sc.edu/courses/phys/sylb543-06.html

The lectures. Lectures were produced Autumn of 2000, concurrent with my presentation of formal lectures in class: Comparative Physiology (Bio 543). A course in Comparative Physiology can take two directions; it can present diverse solutions to a common problem or it can focus on basic principals learned from diverse model organisms. My version of this course takes the latter direction, and uses the text Animal Physiology, Mechanisms and Adaptations (5th Edition, 2002) by Burggren, French, Eckert and Randall (a revision of Roger Eckert's book). My goal is to broadly serve upper level undergraduates or early graduate students interested in ecology, physiology, cell biology, molecular biology or medicine. These lectures do not include a specific unit on the nervous system, and yet the nervous system pervades the course, just as it pervades nearly all aspects of physiology.

The class period. I am fortunate to teach in a classroom with 4 very large chalk boards, sufficient to accommodate 8 student groups. I created a series of questions, 8 for each class period that attempt to be broadly encompassing and range logically through the lecture associating with that class period. As students enter the room, I "randomly" hand out numbers associating with each questions. Students gather in their "random" groups and over the course of 30-40 minutes develop an answer to the questions; all 8 groups work simultaneously. The remainder of the class period is spent discussing the answers. The class is lively and serves 40-48 students. Students are strongly encouraged to visit/interact with other questions/groups once they have completed their own. I tell the students that exam questions will be drawn from the In Class Questions, which is largely true.

I took a different approach during the initial 2 years of the course: I assigned students to arbitrary groups and assigned specific questions to each group. Groups were to stand before the class and present and discuss answers with the class. In practice, I was able to ask the group specific questions and get decent answers. But typically only a few members of the group actually participated. The same was true with the class at large; several students were willing to ask and discuss, but most remained passive and inactive. My switch to the ransom assignments and simultaneous activities appears to engage more students in the process, though still many choose to remain non-participants.

Student performance. Whatever problems the students and I suffered during the early years, I would say the problems that persist relate to the seemingly unstructured nature of the course in an otherwise extraordinarily structured university environment. Students are too used to being passive recipients of knowledge. It takes some time for the students to take seriously the idea that they have to look at the lectures. Some students remain lost. But the course is highly reiterative in content; most of the principals tested in the first exam are presented in the second and third exam. By the end, students seem to be understanding the principals I am stressing. Their biggest problem is competition with other courses and overall sheer exhaustion / saturation by the end of the term.

Student access. I was concerned about student access to the material via the internet during the first offering, specifically over available bandwidth. This was a small issue during the fall of 2000, but has apparently not been an issue since. An increasing number of students are investing in Cable or DSL internet connections, or are finding appropriate access on campus. One concern I have is over sound availability. However, since starting the class sound boards are standard equipment on computers (surprisingly they were not always in class room computers as recently as 2000-2001). Headphones are a pretty standard personal accessory these days, providing students with sound access on almost any computer. Reaching students by streamed video is cheap, reliable, flexible and enormously user friendly. Since I started this process, recordable DVDs have become remarkably cheap (<50 cents per disc in 2005); the entire course lecture collection fits on one DVD and provides another venue for students with limited bandwidth access (i.e. dial up modems).

VIEWING THE LECTURES

VIDEO LECTURES REQUIRE REAL VIDEO PLAYER. The REAL PLAYER is FREE, and can be obtained by downloading the installation file from www.real.com. (The link to the FREE player is usually hidden at the bottom of their page; they also sell several upscale versions of the player, but the free version is all you need). Save the file on your computer, click on it to open and the player will self install.

VIDEOS ARE BEST VIEWED ON CAMPUS OR USING FAST INTERNET CONNECTION (Cable modem or DSL). They can be viewed on a phone modem (56kbs) but the quality is poor.

ADJUST THE BANDWIDTH OF YOUR REAL PLAYER: If the video is not smooth (audio is OK but video seems like a slide show), adjust your Real Player's bandwidth. Do this by opening the Real Player, under "View" choose "Preferences". In "Preferences" choose "Connection". For both "Normal Bandwidth" and "Maximum Bandwidth" choose the highest setting that will work for you (10Mbps>T1>512>384>256>112>56>33.6...).
My Suggestion: If you are on a fast connection (University, Cable Modem or DSL), choose 10Mbps for both "Maximum Bandwidth" and "Normal Bandwidth". If you are on a regular phone modem, choose 56K for both "Maximum Bandwidth" and "Normal Bandwidth". If the video is very jerky, try the next lower setting. Finish by clicking OK to save. This should give you the smoothest video you can expect.

MAKING THE LECTURES (written in 2001 - approach would be the same today, with appropriate hardware modifications - costs on many items would be much different today - either much lower, or hardware more powerful for same $$)

For initial lectures (Introduction, Digestion, Hormones, Circulation), tapes were transferred to my laptop (Gateway Solo, purchased May 1999, 366MHz, 160MB RAM, 6GB drive) via "Video Out" through a Dazzle Digital Video Creator. This means that the digital tapes were sent to the computer as an analog video signal, and converted back to digital using the Dazzle capture device and accompanying software. Compression was "on the fly" and in MPEG-1 format. Ten minute clips were taken (most my system could manage), and these edited into segments and fused together using the Dazzle software. This means that I was marking points on the MPEG file, and making a copy between these marks, and finally merging these files into a finished lecture. One hour of video created approximately a 1 GB MPEG-1 file. This file was then converted to Real Streamed format using the conversion program built into the Dazzle software. The Surestream option was available, but my ignorance had me use this option but constrained to only a single bandwidth, suitable for either broadband (Cable Modem - 1 Mbs) or phone modem (56 kbs).

For later lectures (Gas Exchange, Kidneys, Muscles), tapes were digitally transferred by Firewire to an Apple Cube (G4, 500MB RAM, 30GB Internal Drive, 70GB external Firewire drive, both drives 7200RPM) using Final Cut Pro (FCP) software. Lectures were edited using FCP, and finally saved as an FCP movie. This movie was compressed to Real Surestream format using Media Cleaner 5 software (Terran). The downside of this was audio clicks that were recorded on the computer during transfer. The upside was ease of editing, and, in spite of the clicks, a much superior audio quality in the finished lectures. I used a multi-bandwidth Surestream format, which required the most current Real Player upgrades for all users.

Editing in FCP (or Adobe Premier) involves creating a virtual movie that is simply time code marks that reference the initial digital "raw footage". This can be edited in a variety of ways (contrast enhancements, fades, etc), and then the entire "finished" movie "rendered", which means the adjustments are made and a lot of small files made. Then, after all that is done, a digital movie is made from the rendered instructions. This movie requires essentially as much hard drive space as the initial "raw footage". This movie is then processed through a separate compression program, in my case Media Cleaner (excellent and painless to use).

Times Requirements. Copying the file to the computer requires only the time of playing the tape. Editing using Dazzle requires time as the clips are digital copies, and require the time of copying large files, but the MPEG format is quite compressed so the files are reasonably small. The final fusion of files into a single "video" took up to one hour on my laptop, for a 30 minute video. Editing using FCP is very fast and easy. Rendering took about one hour if restricted to video, and up to 8 hours for a one hour lecture if rendering both video and audio. Making a FCP movie of the rendered file required about one hour for a one hour video. Conversion of this to Real required 5-8 hours for a one hour video.

Typical Schedule for Video to Real via Cube, FCP and Media Cleaner (times would of course be faster on current processors):
Scripting 3 lectures: 2-4 days (significant contemplation)
Recording 3 lectures: 6-8 hours (one day)
Transferring one lecture: 1 hour (length of video tape)
Initial Edit, per lecture: 1-2 hours (marking segments, add effects (sound level, titles, fades, brightness/contrast, etc).
Rendering: 2-8 hrs depending on whether sound was altered
Making Movie: 2 hrs for 45 min video
Compressing Movie to Real format: additional editing (20 min) plus 5-8 hrs for actual compression of a 45 min video

Rendering essentially incorporates the edits into the video. Rendering, Making and Compressing Movies are computer time, except for the actual starting and saving. Rendering and Compressing can take sufficiently long to require as much as 2 days to get one lecture onto the server.

Archiving. Not clear here. A 50 minute FCP movie is around 12GB, divided into several 1.99GB Quicktime files (largest the QT format can take). So, if archiving these uncompressed movies, the only option seems to be tape. Presumably one can record these files back to the video tape on the digital camera, but I did not for this series. So far, I am holding onto the original tapes, but I do not know how permanent those are. My big concern is that, while I have several copies of each Real file, who can say how long software will be able to read these. So a lot of effort with no assurance that these will be viewable in a few years. Hopefully Real will maintain backwards compatibility for a long time to come...

Server. We are using the Real Server configured for 60 simultaneous streams, purchased as an educational package. The computer is a Dell, 700 MHz basic desk top computer with 700MB RAM and a 20GB hard drive. Operating System is Linux (Red Hat) which is also running VMWare Windows 95, which was given 200MB RAM and 2 GB Hard drive space. The monitor (21") is shared by the Editing computer (Apple Cube, described above). Our building network is 100Mbs.

Costs:
Server Computer: $3000 (2003 - perhaps $1500)
Server Software: $2000 (incl. 1 year upgrade, educational discount)

Choice #1 (cheap) Dazzle Editing:
Laptop: $3000 (Gateway)
Dazzle converter / software: $250

Choice #2 (less cheap) Apple Editing (2003 - G5 or fast Pentium - max RAM and hard drive):
Apple Cube: $3000 (no monitor - using server monitor)
External Hard Drive: $450 (70GB firewire - 7200 RPM to match 30 GB drive in Cube)
Editing Software: $500 with computer (Final Cut Pro)
Compression Software: $450 (Media Cleaner 5, Terran)

I maintain multiple computer platforms in my lab. Because my department is primarily MS Windows based, this platform and its associating programs predominate. As such, my Cube is pretty much dedicated, which is keeping it extremely clean for my video projects.

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