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:
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.
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.
As I begin the home stretch for my MSc in oceanography I have been looking very hard at the job markets and the world of research science out there. It is not pretty right now, but then, with the help of a loving and supportive family we’ve weathered this type of climate before. I know we’ll find our way through this and come out the other side, happy. Because that is just what we do Tammy and Johann and me. We cling tight to what matters most – each other and our closest family and friends.
One of the things I have to keep coming back to is “What do I want to be when I grow up”
But that has never been a simple question. When I was young I wanted to be a scientist and an explorer. I was excited and my imagination ignited by archeology, marine biology and the space program. I devoured national geographic magazines, Wild Kingdom and Jaques Cousteau’s specials. I remember reading and re-reading the articles by Dr. Eugenie Scott on the amazing fish of the Red Sea and sharks in general. I remember reading about Dr. Sylvia Earle’s descent to 1250m in a hard suit and her Tektite mission. I know it may sound crazy, but one of the highlights of my brief science career so far was to dive on the Aquarius site as a science diver… the descendant of Tektite, it was, part way to an old dream come true – to live and work in an underwater habitat studying the seas for hours and hours at a time. One day I still hope to make that dream come true.
Science diver approaching the NOAA/UNCW Aquarius Habitat off Key Largo, Florida
But my path took a strange turn and instead of going to Woods Hole or Scripts or Harbor Branch, I ended up in the Army working as an advanced communications specialist using, trouble shooting and fixing just about every type of communication technology in the Army, but specializing in satellite systems. It could be a challenging job, especially in remote combat deployments, but it really didn’t make me stretch. I spent my spare time reading and improving my animation skills as a form of entertainment. In Central America I learned to scuba dive and spent as much time on Roatan Island as I could, doing 3-4 dives a day. The more I dove, the more I needed to learn about the fish and invertebrates I was seeing. I subscribed to several diving magazines and bought every marine biology book my scuba instructor could get from the States. I invited my future wife to meet me in Roatan, unfortunately she declined.
Sunset on the Meso-American Reef. Copyright E. Heupel
After the army I worked in the computer industry in engineering and eventually web development until the bubble burst. When that happened I returned to school, studying computer systems and graphic design. Unfortunately returning to school also revealed that I had a memory issue. Tammy knew before, but I denied it of course. Unfortunately the tricks I had learned to use on the job, didn’t translate well to the academic environment. I struggled to find a new way of learning and studying, while my grades sank, eventually forcing me to admit defeat temporarily as I withdrew from school.
Fast forward to five years ago when I took advantage of an opportunity to again return to school. This time in Oceanography. I had since learned to deal with my memory issues with new strategies. I started slow, with only two classes, but soon took on a full course load completing the four year degree in three and a half years with a job, a family and still managed a 3.5 GPA. My old skills in electronics, optics, video production and web design all served me well working in labs and earning me opportunities to work with Remotely Operated Vehicles. At the end of undergraduate I knew I needed to take this further, I needed to revisit my old dream of being a scientist working in, on and under the ocean.
The motley crew of the SHRMP 2010 habitat monitoring program mission. Copyright E. Heupel
I was accepted to the graduate program and began learning more about sustainable fisheries and GIS than I thought was possible to learn (and yet I have still only learned a spall portion) . It has been a good run, but now it is almost over. I want to go on further, but I know I need a change in direction. My interests lay more with larval and juvenile marine organisms and their ecosystem roles (besides the stock answer I get from many: “as food” – too damn easy), or in the ecology of deep sea and mangroves and with invasive species in connection to any of the previous. I have at least a hundred questions banging around in my head, and I am loathe to even try to pick only one and say -> This is it.
One of my favorite fish of the mangroves is the juvenile sergeant major. Very cute, shy and nervous - darting constantly around the patch of mangrove they call home. Copyright E. Heupel
More than that there is the question of what good is a PhD, and is the cost too high to justify. I have put my family through a lot already. It has been financially very hard, and we have done without a lot. I have been fortunate that this program knows me, and knows the type of contribution I can make, and also understands that my family is the most important thing in my life. I will never be one of those scientists (or PhD students) so driven by the research that I sacrifice my family (which I have seem too much of in the past 5 years). Driven yes. If I had a spare $10,000 right now I would be on a plane to Belize to chase down one of my burning questions on invasive species and My Seascape of Fear (actually budgeted with no salary it a hair over 10,000). But I’m not going to throw my family under the bus to get there.
Which brings it once again back to what I want to do with the degree. I would like to be able to design and conduct my own research, which I would need a PhD for. I enjoy teaching small to medium size classes, as long as there is at least one or two kids turned on to learning. At a University or college a PhD is generally the ticket for admission to that. At community colleges, a PhD can be required, or a hinderance.
As for the most singlehandedly enjoyable thing I have done in the past 5 years – it would be the outreach efforts at Aquarius. Doing the science, putting on a live show, broadcasting it to kids in their classrooms and online – both doing science and helping to communicate it to a larger audience. That was for me a real rush. Many of the people involved in that team effort did not have PhD’s, but then again many did. I enjoyed the fact that we were communicating conservation, physics and biology directly and passionately to an audience eager to learn.
The marvelous crew of the Aquarius 2010 If Reefs Could Talk mission. Copyright E. Heupel
If I stopped right now, my ideal job, would be either as a freelance science communicator specializing in video and online production or it would be with one of the NURC centers or a similar scientific research organization or NGO where I can put my myriad skills to work – oceanography, diver, science outreach, video, animation, web, database, photography (normal and U/W) and ROV pilot (in training right now). But… likely I would not be able to do my own research, which is important to me.
If I were 23 and single, the answer for me would be easy – go for the PhD and study larval and juvenile ecology issues, especially in the mangroves and deep sea. But I’m not 23, or single. And I wouldn’t trade my family for anything, but it does mean I need to figure the 4-6 years of making (if I’m lucky) $30,000/yr while working very long hours into the equation.
Para-sight recently wrote a post at DSN urging caution in assigning blame to the BP oilspill as the cause of recent cetacean deaths along the Gulf Coast. To try and address one of the issues he raised, I wrote a guest post there using the raw data from NOAA to quickly try and get an idea of how bad the dolphin situation in the gulf really is when examined in the light of the historical data available. Unfortunately the graphs NOAA created comparing 2010 and 2011 to historic data made it hard to truly evaluate as they used the average value for each month for the historic data. Based solely on their presentation of the data all that can really be determined with any confidence is, as Para-sight noted:
…dolphin deaths are not that rare to start with and that this is the time of year for it (i.e. it’s not actually “unusual”, it’s “seasonally-appropriate”). Secondly, it means that it’s not much worse in magnitude than last year, albeit peaking a little earlier.
and
But in these cases, the devil IS so often in the details. I am not saying oil wasn’t involved; I’m just saying we can’t infer causality from correlation without a closer examination of the data.
Running the raw data through excel (to subtotal & clean) and R and I could see more of the information Para-sight warned was needed to get a better feel for the situation. And sure enough I was able to add to his observations that:
the pattern of the event does strongly suggest that the oil spill is related, but looking at the prior events, it is not outside the realm of possibility that this is not directly related to the oil spill. The best evidence to determine the involvement (or lack thereof) of the oil spill is going to be found in necropsy and toxicology reports of the stranded animals.
In the meantime however several people commenting on the original post pointed out that the biggest issue was with the a specific age class of dolphins. As “Dr. Ed Cake” commented:
…In the meantime, this year’s neonates continue to wash ashore dead in the BP spill zone and all potential mortality factors can be dismissed except the impacts of BP’s oil and Nalso’s Corexit dispersants.
and “Don” stated:
NOAA provides data specifically for “baby dolphins.” It shows a five-fold increase in mortalities in 2011 compared to 2010.
So that last bit especially really made me wonder. The more detailed data showed there was an unusual mortality event (UME) happening with cetaceans in general, though it is not clearly linked to the spill. But a five fold increase for one key age class??
So tonight I journeyed forth again to the NOAA website, and found on scanning down to the bottom of the page, there is a table of “baby dolphin” deaths as Don phrased it. It is more accurately “premature, stillborn, or neonatal dolphins”. NOAA used the cutoff of 115cm total length to split out these deaths and presented them as both a table and graph:
neonatal, stillborn and premature dolphin deaths
Graph of all neonatal, stillborn and premature bottlenose dolphins
As both commenters pointed out there seems to be a major issue going on here! Just look at February! a 36x increase from 2010 (pre spill) and an almost 18x increase in deaths over historic averages. And March is better, but still a 2x increase over last year and 3x increase over historic levels.
However, here again we are given historic numbers solely as the average. As Para-sight warned, and we saw with the complete cetacean data set, that is a dangerous way to look at data like this.
But what about the “baby dolphin” data?
From the truncated graph NOAA presented it appears there may be a seasonal pattern (not unexpected) but it is hard to tell with out the complete year graphed. It is also not possible (again) to tell what the range of values is for each month. The numbers 100 and 2 average out to the exact same value as 52 and 50 do, but the range of values, and the story it tells, is quite different! Back to the data set, with definition in hand I extracted all bottlenose dolphin records with lengths of 115cm or less and duplicated the analysis I did on the full set over at DSN. The resulting table:
Gulf Coast Strandings of Bottlenose Dolphin <115cm
First thing to notice comparing the two tables is that yes February deaths were an order of magnitude higher than the historic range.
The second thing to note is — they don’t match. Not just that I included the entire year in the table, but the numbers for the averages in each month they did include don’t match. They only averaged 2002-2007 for their historic baseline. So I redid the table using only 2002-2007, still the numbers were slightly off. Using their dataset and the definition for premature / neonatal / stillborn they gave, I get different numbers than they do. Aggravating. I am comparing historic data to the 2011 data, I double checked all the subtotals are correct and redid the summary table creation three times each time with the same result. I have verified that the data in the table is true to the definition given by NOAA and the raw data NOAA has provided. I really don’t like omitting data without good reason (which was not provided by NOAA) so I finished the evaluation keeping the 2008-2009 data in:
Box and Whisker plot of Stranded Bottlenose Dolphins less than 115cm. 2011 data blue diamonds, 2002-2010 data boxplots with outliers as open circles.
So what does this one tell us? And is it different from the conclusions inferred from the NOAA graph?
Based on the NOAA graph and table one would assume that all months except April were UME months, and April, one could easily argue, is on it’s way to being a UME month as well, after all, that is only 10 days of April data. However, looking at the box plots only January and February really stand out as a UME(s). February is clearly an outlier, in fact the most deaths and the most radical outlier of the entire data set. January is an outlier but is it a UME? I guess that depends on the definition, but it is two standard deviations above the mean January number of deaths, so I would say it is a UME. While March is high, it is still within the range of expected numbers from the historical data. Granted March is right at the upper edge of that range, but it is within that range nonetheless. If we were using Para-sight’s suggestion of using values greater than two standard deviation above the mean as the definition of a UME then only January and February would be as well. However when taken with the previous two months I would suggest that March is a continuation of the same UME.
As for April, with only 10 days of data for the analysis, it is right at the edge of the expected range of values from the historic April data. One could argue, I suppose, that it will climb much higher, but without the actual numbers any discussion of that is pure speculation. I expect that it will climb as well, but we’ll just have to wait for the rest of the data to come in to really say anything about it conclusively.
What is more interesting to me though than the month by month numbers is the pattern, both historic and for this year. Historically, just as with the larger population, bottlenose dolphins < 115cm have a clear pattern of strandings. The late winter and spring (January through May) is the period of strandings, with most strandings clustered in the February through April period with the sharp peak in March. The rest of the year have much lower numbers. The box plot and the full table also reveal that each year it would be unexpected to find no strandings under 115cm but in the summer through early winter (June through December) it is actually an unusual event to find a stranding, let alone more than one.
This is a direct clue to the reproductive biology pattern of the Bottlenose Dolphins in the Gulf of Mexico. I have very little knowledge of dolphins so had to turn to some local experts for help (contrary to popular belief all ocean scientists DO NOT work on dolphins). Turns out that Bottlenose Dolphins generally mate from late March to May and have ~11-12 month gestation period. At birth a bottlenose dolphin is anywhere from 85-110 cm long (the reason for the 115cm cutoff). Looking at the length records the smallest animal found was a January 2006 stranding at 40cm. Fully 83% of the strandings were of individuals between 85 and 110cm which combined with the seasonal pattern would corresponds essentially to very late term neonatal or newborn aged individuals. Examining the length vs. month of death did not provide any real patterns except that March had the widest range of sizes in the strandings, which is not too surprising as March had significantly more deaths than any other month in the aggregated data.
This year however the peak is clearly in February. Why? Unfortunately I did not see any length data for this year, just summary numbers. Were these individuals mostly less than 85cm? That would infer prematurely born babies or late term miscarriage. If they were mostly in the 85-110cm range? That would suggest they were from the early mating season, likely conceived before the oilspill, and at full term.
So, yes, there is a major unexplained mortality event that is causing a significantly higher number of neonatal, stillborn and premature Bottlenose Dolphin strandings. February’s mortality is the worst event for individuals under 115cm on record, by a fair margin. I expect the number for April will go higher, quite possibly being an outlier. From the timing, the oil spill is certainly a suspect for being a cause. That does not however mean it IS responsible. There is still no way to know the oilspill’s relation to these deaths without detailed necropsy and toxicity study results.
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.
One of the major concerns with climate change relates to habitat changes for the plants and animals. Will aspen survive anywhere in the United States? What trees will be able to survive in Connecticut in 2050? 2100? Where will elk be able to survive in 2100?
Of course these aren’t easy predictions to make since each species has distinct environmental requirements. Even more troubling though is that many have complex relationships with other organisms, both beneficial and detrimental. Then there are the often complex food webs that each species is a member. some webs are resilient to loss of several species but others collapse with the loss of only one.
While sea temperatures are generally more stable than air temps in terrestrial systems, many of the marine animals have even tighter requirements for temperature. Even a change in just a few °C can prevent reproduction, reduce lifespans, or even cause death. That is the case with the Icelandic Scallop. In some recent experiments it was found that the scallops had a significantly higher mortality in temperatures above 12°C. Average summer sea surface temperatures off Iceland’s southern coast have been in excess of 10°C in recent years and have been rising. A +2°C change over the previous decades has brought the average summer sea surface temperature very near the scallop’s maximum threshold. While the scallops are still able to survive, there has been a marked increase in adult mortality.
Icelandic Scallop - Image from http://www.osl.gc.ca/guide_sp/en/invert/sp/c-islandica.html
Increasing temperature may not directly be the primary cause of the recent increases in mortality of the scallops, though it has been strongly implicated. In recent years, a protozoan parasite has affected much of the stock of C. islandica around Iceland. As with the scallop itself, many protozoan parasites have been found to have temperature thresholds and ideal temperature ranges. For instance Perkinsus atlanticus populations under controlled experiments did not grow, in temperatures of 5°C, grew slowly at 16°C, and grew quickly at 20°C and 26°C. It also failed to grow and died out after 4 days at an experimental temperature of 37°C. Similarly, two other protozoan parasites of interest on the Atlantic Coast are also temperature controlled: Parkinsus marinus, the cause of the disease dermo in oysters, requires temperatures above 25°C to thrive, Haplosporidium nelsoni, which causes MSX in oysters (although it can survive and multiply at temperatures of 5°C-25°C) requires temperatures above 20°C to infect a new oyster. Temperature is likely also a controlling factor in the spread of the protozoan infecting C. islandica.
While the Iceland Scallop is what instigated this post, the topic of climate change and its effect on marine animals, particularly fish, is one I have been thinking of a lot lately. In much the same way that the scallops are temperature limited, fish have ideal and survivable temperature ranges, and temperature can play a significant role on growth and reproductive success. Complicating the issue is that many of the fish have very specific habitat preferences or needs as well.
Atlantic Wolffish - Photo copyright Peter Auster from http://www.nurc.uconn.edu/bigmouthfishes/photos/SBNMS/content/neg7_large.html
Take for instance the Atlantic Wolffish (Anarhichas lupus) a species of increasing concern in the Gulf of Maine, if fact they are likely to be soon added to the Endangered Species Act. They are a wonderful (dare I say beautiful) fish with some great characteristics and a face only a mother, or a crazy marine biologist, could love! They feed mainly on molluscs, crustaceans and echinoderms using their huge canines. They are a large benthic fish, growing up to 5 feet and weighing up to 40 pounds.
They are also a slow growing and late maturing species. Growth and maturity varies with temperature fluctuations, but generally they are reproductively mature by 6 years or about 16 inches total length. Spawning pairs of male and female form in the spring with actual spawning period varying, possibly as a function of temperature. As with many species, reproductive success increases as females grow larger and older, producing both more eggs and more viable eggs (ranges from 5,000 to 12,000 eggs per season). The female lays her eggs in holes and around boulder reefs. The male then begins a fast, loses his teeth, and guards the eggs for four to nine months of egg incubation (again a function of temperature). Four to nine month fasting and guarding the eggs. Think about that one guys!
One of the cool things about wolffish is the presence of anti-freeze in their body, which allows them to survive, even thrive, in extremely cold waters. In the wild they have been caught in trawl surveys in waters from -1.9°C to 14°C. In the laboratory they survived temperatures as high as 17°C, but feeding was strongly negatively correlated with the higher temperatures.
So temperature is a major factor on the wolffish, but so is habitat. Wolffish are most often found in rocky reefs or seaweed beds on hard substrate from 80m to 180m depths, but range as deep as 650m and can, on occasion, be found in coastal shallows. My most memorable dive in New England remains being about 3 feet away from a 4 foot wolffish in the cove just off Avery Point in late November.
Young wolffish keep to the deeper, colder part of their range where temperatures remain -1°C to 4°C. Only mature fish are found in shallower ranges and higher temperatures with an upper temperature limit of 10°C.
My thoughts recently have related mainly to mapping the current and potential future ranges of some of these animals using habitat suitability modeling techniques in geographic information systems (GIS), including especially ecological niche factor analysis (ENFA). Using what we know of their habitat requirements (for the wolffish: -1°C-10°C, boulder reefs for spawning, 80m-200m depth, and abundance of lobster, crab, urchin or molluscs) we can map the current optimal and sub-optimal ranges. It doesn’t mean they’ll be there, but it is where the potential for finding them should be highest, based on our understanding of their requirements. By altering the temperature and depth components to match forecasts based on climate change models, we can look ahead to forecast the likely range of the animals, and even the decade by decade march or retreat of suitable habitat.
An example of using mulitple habitat factors with multipliers to determine ecological niche. From http://www2.unil.ch/biomapper/
For some animals the outlook is pretty bleak. The combination of habitat requirements and temperature requirements will drive them completely out of the Gulf of Maine and potentially out of the Western Atlantic entirely. There are many fish that are at their breeding temperature limits in the Gulf of Maine already, including many commercially important species. Some marine animals are existing in virtual islands of suitable habitat formed by complexities of depth, substrate type and complexity, currents and temperature, among many other factors.
The challenge is to identify, for each species or community, which of these factors are most important for both the organism’s survival and our modeling efforts. Unfortunately, especially in the marine realm, there is still so much we don’t know about the ecological requirements of may of the animals and communities. Even mapping the seafloor at resolutions comparable to our maps of terrestrial areas continues to be challenge. It often surprises many people I talk to when they find out that almost all our knowledge of marine animal populations and habitat characteristics comes from commercial fisheries and from sample trawls by the NMFS. Most species that are not targets of fisheries or considered commercially important have not been studied extensively, if at all.
Trawler bringin up it's haul - from http://en.wikivisual.com/images/f/fb/Fish_on_Trawler.jpg
In the marine environment it is very challenging to accurately predict how communities will respond to warming waters and how individual species ranges will change, simply from lack of direct observation. We are getting better at using the important data we do have, and have identified proxies for the data we simply do not have, but we need more time in the water with ROV’s and DSV’s for direct observations, especially of the continental shelf and deep sea ecosystems.
Burreson, E., & Ford, S. (2004). A review of recent information on the Haplosporidia, with special reference
to Haplosporidium nelsoni (MSX disease) Aquating Living Resources, 17 (4), 499-517 DOI: 10.1051/alr:2004056
Hagen, N., & Mann, K.H. (1992). Functional response of the predators American lobster Homarus americanus (Milne-Edwards) and Atlantic wolffish Anarhichas lupus (L.) to increasing numbers of the green sea urchin Strongylocentrotus droebachiensis (Müller) Journal of Experimental Marine Biology and Ecology, 159 (1), 89-112 DOI: 10.1016/0022-0981(92)90260-H
Jonasson, J., Thorarinsdottir, G., Eiriksson, H., & Marteinsdottir, G. (2004). Temperature tolerance of Iceland scallop, Chlamys islandica (O.F. Muller) under controlled experimental conditions Aquaculture Research, 35 (15), 1405-1414 DOI: 10.1111/j.1365-2109.2004.01159.x
King, M.J., Kao, M.H., Brown, J.A, & Fletcher, G.L. (1989). Lethal freezing temperatures of fish:
limitations to seapen culture in Atlantic Canada. Proc Ann Aquacult Assoc Can., 89 (3), 47-49
Ordás, M., & Figueras, A. (1998). In vitro culture of Perkinsus atlanticus, a parasite of the carpet shell clam Ruditapes decussatus Diseases of Aquatic Organisms, 33, 129-136 DOI: 10.3354/dao033129
