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Guest Blogging Fun

The past few weeks turned out to be pretty busy for me online (at least compared to the past oh, 24 months), though from this site alone, it may be hard to tell. Since much of my posting has been at other places I thought a quick summary of the months posts (and links) would be helpful for those interested:

  • Sergeant Major (Abudefduf saxatilis) – A post at Larval Images about one of my favorite ecosystems and one of the great juvenile fish that are commonly found there.
  • Budget Hacking – A post here about the importance of NOAA for the myriad jobs they do, many of which are important for public safetly and economic security in addition to research. A post that I feel is a very important read, especially as the 2012 budget fight may still cut NOAA deeply, including the satellite’s needed to track and predict severe weather events as well as we do. Without NOAA’s work I think it is safe to say the Alabama death toll would have definitely  been significantly higher.
  • Gulf of Mexico Dolphin Mortality Event – Posted as Scientist in Residence at Deep Sea News – in which I use the data from NOAA to take a more slightly more detailed look at deaths of dolphins since the oil spill in the Gulf, and explain the box and whisker plot.
  • Dolphin Whiskers – now only Babies – published a few days later here, to address the concern that there is a higher that normal number of babies washing ashore, but the graph, as presented by NOAA and in the MSM, does not really support that claim. So again come out the box and whisker plots.
  • My ‘Seascape of Fear’ – A second posting as  Deep Sea News Scientist in Residence, I discuss my recent trip to Belize as a teaching assistant for a coral reef fish ecology class and the arrival in Belize of the highly invasive Lionfish.
  • How does a floating plastic duckie end up where it does? – A guest Blog post at Scientific American Part of a four post series on drifting junk in the oceans and how, sometimes, they can help us explore and learn more about the ocean currents. Other posts in the series include a review by Lindsey Hoshaw of the book Moby Duck (I’ll post my own review here later, I liked the book quite a bit more than Lindsey), an interview by David Manly with Moby Duck author Donovan Hohn, and a Matthew Garcia review of Dr. Curtis Ebbesmeyer’s bookFlotsametrics and the Floating World about tracing accidental drifters and the information they can give us.
  • Is It Time to Relax Fishing Regulations? – Another Scientist in Residence post at DSN, this was a response to fisheries biologist Ray Hilborn’s recent op-ed in the New York Times advocating a relaxation of the current fishing regulations. (Enric Sala, Peter Singer, Daniel Pauly and Mark Kurlansky all replied to the paper.)
  • Finally, Reflections, posted here, in which I examine where I have been, where I am and the options going forward.

Hopefully in the next few days we will have a guest posting or two here by Johann. Discussing some of his recent adventures and science from his point of view.

In addition to the postings there are several new YouTube videos I uploaded in the past weeks, mostly of the underwater variety.

Some R + Google magic

Nothing much to see, just me making sure I understand everything going in in the post over at R-Ecology to use Google Visualization API. Using this we can get excellent presentation of data like Hans Rosling’s brilliant TED Talk. Took the fish harvest data set and added a new column for trophic level (using fishbase for species I didn’t already have literature references for). First the basic modification to make sure I understood the subsetting etc.

Be sure and play with the axis and selecting species etc.




Data: trophdata2, Chart ID: MotionChart_2011-01-23-00-26-21

R version 2.12.1 (2010-12-16),

Google Terms of Use

Generated on Sun Jan 23 00:26:25 2011 with googleVis.
Powered by R.rsp v0.4.1.

This would be sweet to use on the Vinal Edwards data! I know i still have it around here somwhere… or the NEBO data?

Next add subsort by price per pound and trophic levels then….[edit] done!

Deadly Waters For Whom?

How was your opinion of sharks formed?

All my life I have struggled to overcome negative exposure to sharks. I think I have won, but it has been a long haul.

My earliest memory of sharks is from 1975. I was spending the night at a friend’s house. Across the street from his building was the base movie theater. All that Friday night we were scared witless by the constant screams we heard coming out of that theater during the three showings. We had seen the posters on the movie theater billboard and our imaginations filled in all the rest, which is not too hard for imaginative 7–year–olds. It would be years later before I actually saw the movie, which only reinforced my abject fear of sharks.

Fortunately, my folks exposed me to National Geographic and the Cousteau Society, so I was also exposed to sharks as amazing animals and important parts of the ecosystem. Yet, whenever we’d visit the coast and go swimming, in the back of my mind I would worry about the sharks. As an adult in the Caribbean, I was revisited by that fear when I began diving. I have to admit my greatest concern when I began diving was that I was entering their realm. I slowly got over that fear (mostly) as I got more dives under my belt, including several dives with reef and nurse sharks. Then came Somalia.

In Somalia there was a strict order not to swim in the beautiful waters around Mogadishu. I have to tell you it is VERY tempting to take a small dip in the water to escape the equatorial heat, especially when you’ve been riding convoys in full battle gear and are caked in sweat, dust, and dirt. A moment of wading in cool salt water to escape it all was very inviting. I wanted nothing more, but the order was there for a reason. In a little over a year 6 UNOSOM workers were bit by sharks in Mogadishu. Three died of their injuries. I knew Mogadishu was a unique place for the sharks. The area had become a rich hunting ground for them, thanks in part to a history of townspeople throwing carrion and refuse into the waters nearby. Eventually the UN installed a shark fence around the beaches at the airport. I wonder if it’s still there.

To the south in Kismayo, I did a couple dives with several sharks in the area. My job was to keep an eye out for sharks while the underwater specialists carried out their jobs. I was pretty scared, but I was young and dumb and diving with a bunch of seriously gung–ho types, so I wasn’t about to admit it. The funny thing is the sharks were there, but their behavior was very non-threatening, even the largest of them. They occasionally came into view, swam lazily at a distance, then receded back into the blue. They were not terribly interested in us or our activities.

I continue to dive, even in the “dive by touch” conditions that the locals call “high visibility” in Long Island Sound. I have studied sharks a bit more and the critical part that many sharks play as part of their ecosystem. Intellectually, I know that even as a diver and someone who works in the marine environment, I am less likely to be bitten by a shark than I am to be struck by lighting or electrocuted by my toaster. Yet, in the back of my mind, there is still a little kernel of concern. When I see the replica of the great white in the cafe on campus (caught just outside of Long Island Sound), or I hear of the juvenile great white found in the estuary near here, I find myself having to shake off that fear and refocus my thoughts.

I have been fortunate to see sharks up close in the wild and I realize that they are not the killing machines that the media often portrays them as. Even the Discovery Channel uses sensationalism and fear to sell their Shark Week. I haven’t watched Shark Week for several years, since I was disgusted by their inaccurate and sensationalistic portrayal of sharks the last time I did watch. Shark Week then was about 80% fear and sensationalism, 15% interesting factoids, and 5% conservation, proactive education, and recent science. The shame is that Shark Week could be a force for genuine education about shark conservation and the importance of sharks in the ecosystem.

I certainly hope that they have changed their portrayal of sharks, especially since the sharks are in desperate need of our help. Even Peter Benchley, the author of Jaws, expressed his deep regret over having written Jaws after the damage it caused.

“Knowing what I know now, I could never write that book today,” said Benchley, who also co-wrote the screenplay for “Jaws.” “Sharks don’t target human beings, and they certainly don’t hold grudges.”

Unfortunately, with shows such as “Deadly Waters” and “Sharkbite Summer” in the lineup, it doesn’t look likely. I could take a very optimistic view and hope that “Deadly Waters” is describing the terrible daily massacre of sharks for shark fin soup. Maybe “Sharkbite Summer” is about us putting the figurative bite on sharks. But as far as the Shark Week advertising and show titles go on the Discovery Channel website, the message is still all about fear.

I mean really, how far have we come in 34 years??

The 1975 film poster for Jaws

The 1975 film poster for Jaws

and 34 years later, the 'Web Poster' for Shark Week 2009

and 34 years later, the 'Web Poster' for Shark Week 2009


David (aka WhySharksMatter) at Southern Fried Science is a marine biologist studying sharks and working everyday on shark conservation and public education. He and other shark scientists and conservationists are taking the issue to Discovery Channel and challenging their portrayal. The best part is, you can help. Southern Fried Science will host an interview with Discovery Channel Senior Science Editor and Executive Producer Paul Gasek. Paul will give his side of the story, which David says he is eager to do, but David also wants to show him a range of questions from all over the community. Help us by visiting David’s call for questions and submitting any questions about sharks and the portrayal they get in the media. David will select 10 questions to use for the interview with Paul Gasek.

Rainy Day at the Museum

Torosaurus latus

Torosaurus latus bronze in front of the Yale Peabody Museum

Darwin, Domestication, and Dana

Johann studying and sketching part of the Darwin Exhibit on evolution while Tammy studies the exhibit on Dana.

"You see how the teeth..."

Johann and Tammy discussing Hesperonis crassipes

Lost in thought

Johann was fascinated by the Hesperonis crassipes skeleton.

Moeritherium

Another favorite, Moeritherium, a prehistoric mammal that Johann identifies almost as a friend.

Alas Poor Yorick, I knew him well.

Alas Poor Erectus…

Normally cold, rainy days are so dreary, but not when you get to go to the Yale Peabody Museum of Natural History! We desperately needed a family science immersion day to rejuvenate! Eric took the day off. I had hoped to get some yard work done, but that wasn’t going to happen with the rain. So we decided to buy membership to the Yale Peabody Museum and go. They have a reciprocity agreement with a lot of other science museums and centers. We have plans to go to all the ones we are interested in while we are still on the East Coast, especially the Museum of Science in Boston, so we now have two years to take advantage of the membership benefits.

At the Yale Peabody Museum there are three floors, but we only managed to cover the first floor, the Discovery Room for children on the second floor, and the gift shop in the four hours we were there. We will go back to see the third floor and view the Darwin exhibit again before it comes down August 23. Johann didn’t want to validate the parking ticket so that we couldn’t get the car out of the parking lot. He figured if that happened, we would have to stay at the museum overnight, maybe even indefinitely!

The exhibit “Darwin: 150 Years of Evolutionary Thinking” was very well done. There was information on Dana and Marsh as well, and it was very interesting to see the similarities between Darwin and Dana, who has been referred to as the American Darwin. Some of the correspondence between the two scientists was on display, as well as a map of the sea voyages each man went on as part of their path of scientific discovery.

The Hall of Dinosaurs and the Hall of Mammalian Evolution were amazing. Eric and I enjoyed seeing the wonder in Johann’s eyes and watching him soak it all in. We all kept thinking about the movie Night at the Museum while we were looking at the dinosaurs. Johann loved to see real examples of the animals he’s studied in his books.

Johann was also very excited to see everything in the “Fossil Fragments: The Riddle of Human Origins” exhibit. He recognized the discoveries that were written about and the specimens on display from the documentary shows he’s seen on the Leaky family’s work. He took time to draw sketches and make notes. The Age of Reptiles mural and the Age of Mammals mural were incredible. Since Eric was permitted to take pictures without a flash, we are going over the pictures of the fossils and can even read some of the information about them again.

The Yale Peabody Museum has a good interactive exhibit about energy conservation right now. We also enjoyed the smaller sections where the Hall of Pacific Cultures, Hall of Native American Cultures, and the scale model of Machu Picchu are. The Discovery Room has a leaf cutter ant colony, a black rat snake, and poison dart frogs. There were drawers full of fossils, rocks and minerals, and various preserved spiders and insects that each had a magnifying glass and a please touch policy. They had a variety of stuffed birds and preserved butterflies for kids to see. There were lots of books out for kids to read and a display comparing eggs from different birds. Johann particularly liked holding the cast of the T.rex tooth and the coprolite.

There was so much to see and learn in every room we went into, that even though we spent four hours there, we still feel like we missed some of it. Where some of the homeschooling families use their vacation time to go to the Creationist Museum, we prefer to revel in places like the Yale Peabody Museum. Now that we’ve gone, we might just have to make a weekly pilgrimage there!


The Next Phase

What a difference two weeks makes! I had an opportunity at UCONN for my M.Sc., but with no financial support and working a project that is not related at all to what I want to study. When I turned that one down, which was in itself a scary – some might say stupid – move, I thought that would be the end of the road for grad school at UCONN. But then a surprise opportunity presented itself for graduate studies with another professor at UCONN. When I was applying I considered him, but he didn’t have funding available to support a new graduate student at that time. With the economic cutbacks no new department assistantships are available, so support is entirely up to the professors. The department is also requiring that advisors can provide proof of substantial support for any new grad students this year. Fortunately, Prof. A. was able to rearrange some of his funding so that he could provide a research assistantship. To say the least, I’m ecstatic about the opportunity: GIS, conservation, a smattering of policy and lots of fish (my focus being larval stages and recruits), and fish habitat.

The Johnson Sea Link II being deployed from the R/V Seward Johnson.

The Johnson Sea Link II being deployed from the R/V Seward Johnson for Life on the Edge 2005

Prof. A. is also with the National Underwater Research Center for the North Atlantic & Great Lakes at UCONN (NURC-NA&GL or just NURC for short). Working for NURC, I have had the opportunity to work with some amazing video footage from dives they have done with many different platforms, including Alvin out of Woods Hole Oceanographic Institute (WHOI) and both the Johnson Sea Link I and Johnson Sea Link 2 (collectively “the JSLs”) manned research subs out of Harbor Branch Oceanographic Institute (HBOI). Unfortunately HBOI and Florida Atlantic University (FAU) have decided to retire the the Sea Link I and II and sell off their surface support vehicle, the R/V Seward Johnson. With depth ratings of 1000m these are two of the deeper diving vehicles in the U.S. science fleet. While the Alvin and Pisces V (out of Hawaii) both go far deeper, the JSLs are unique human operated vehicles (HOVs) for deep sea exploration with their distinctive full transparent acrylic sphere for the pilot and scientist. The sad thing is these are still highly productive vehicles (two of the youngest in the fleet) and there are no similar subs out there, in fact there are only about 16 manned research subs currently in operation world wide. It would especially be a shame if two of the research subs most suited to intermediate continental margin and continental shelf exploration were retired by the very same institution that was just selected as the lead institute for the Harbor Branch Consortium, which will be NOAA’s new cooperative institute. Two of their new primary missions will be “exploration and research of frontier regions of the eastern continental shelf and beyond, and improved understanding of deep and shallow coral ecosystems.” I would think this would be an excellent fit for the Sea Links. On a personal note, Alvin and the JSLs were inspirational to me when I was younger. I remember the National Geographic spreads from JSLs especially. To this day when someone says manned sub, my mind’s eye sees the Johnson Sea Link II* (Sorry Alvin!). Kevin also has a more powerful connection to the JSLs since he’s been down in them before (Check out the pic of Kevin in the bubble! Very Cool!). He also has a top ten list of JSL accomplishments, including over 1000 publications reliant on JSL.

Some people question the real need for manned submersibles, arguing that ROV‘s like Hercules, Jason and Kraken II can do anything a manned vehicle can do, only better and safer. It’s a valid question, and one that needs to be repeatedly asked, especially as more advanced ROV’s designed from the ground up for science come on line. But my answer today is that there is a need for both of them still. ROVs can not go everywhere an HOV can, and their mobility and responsiveness are limited, compared to HOVs, by the ever-present tether to the mother ship. An ROV also lacks the ability to provide 3D visual-spatial analysis and true in-situ contextual observations which only a scientist and pilot on the spot can provide, at least with todays technology. ROV’s while extremely capable are still a telepresence technology, and many of those that have used both HOVs and ROVs, such as Dr. Craig McClain at Deep Sea News, attest that something significant is lost in that translation.

These experiences combined to give me a first hand knowledge of an environment, that previously I had only studied remotely. I studied the deep sea for three years before my first deep dive and my understanding, although incomplete, of this environment has radically changed since those dives in the JSL.

Perhaps more important, these manned submersibles stir the imaginations of young minds, leading them, like me, to dream abut exploring the sea, maybe one day sitting in awe within a submersible 1 kilometer below the surface, surrounded by organisms we are still only beginning to comprehend fully.

Please help us let those in control of the JSLs fate aware of the JSLs importance to science and to our ability to understand the seas and stir the imaginations of the young explorers in our midst. Young explorers like Johann. Please GO SIGN A PETITION TO STOP THEIR LOSS.

So, a bit more on the new NOAA Cooperative Institute, since that also directly affects my future. NURC-NA&GL, along with all the other NURC centers, are NOAA supported, non-federal organizations under NOAA’s National Undersea Research Program (NURP). NURC-NA&GL’s mission is as a center for excellence in research related to the North Atlantic and Great Lakes region. They work with NOAA scientists on long term research goals including developing oceanographic research technologies (such as the Kraken II), fisheries and conservation research, historical site identification and documentation along with major outreach efforts. They are also tasked with Postdoc and graduate student training to provide the next generation of oceanographers. Unfortunately NURC-NA&GL may lose all NOAA funding with the establishment of the new center at HBOI, as it will replace the four existing East Coast NURC centers, including the one at UCONN. Personally I think cutting support for the existing centers is a mistake, even though the new Cooperative Institute sounds wonderful.

So my summer and the next two years are set, sort of. There are still some questions (second year funding, nailing down the thesis topic, now that we have health insurance, do we have another baby, etc., etc.), but at least the path forward is clear enough to begin charging down it! The summer will be hectic, split between two projects for NURC (video and GIS outreach products for high school teachers and students to use and possibly video highlights from a recent deep sea cruise), two projects for Prof. A. (both habitat related), a cruise for Prof. A, and then the remainder of my time will be dedicated to finishing up an outreach book and cards for grades K-12+ on molluscs. Whew!

4473*Johann pointed out that even Playmobil recognizes the JSLs and their full sphere compartments as the iconic submersible.

What is your iconic research submersible? Is it Human operated or remote?

Whatever it is, please do Sign the petition to keep the JSLs operating.

Check out the Deep Sea News collection of JSL videos.


Stop SOPA

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