• 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.

…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

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.

For me, today was that day.

Ah, the beauty of Avery Point and the Castle blanketed in a layer of calming white snow. Until the klaxon sounds and sirens wail.

Just to hit the high spots:
Very tired this morning after insomniatic night -> Roads not plowed -> three car pile up on the highway -> highway traffic diverted onto my commute route -> 15 minute commute (+15 for unplowed streets) now takes 57 minutes -> miss Chemistry lecture.

Trying to pack for Ft. Lauderdale trip interupted by two 20 minute fire alarms, both false alarms! Finally got the three crates full of the nav and video systems for the cruise, they are on the way. Hopefully they make it to Ft. Lauderdale and don’t end up in Ft. Leavenworth.

One of three hook and ladder trucks which responds to every Marine Science building alarm. I don’t mean that to imply that there are a lot of alarms.

Laptop died at ~8:40am -> three major projects, all due in next 1-3 weeks on dead laptiop, not to mention three almost complete web site redesigns I figured to complete while on the plane. Fortunately it’s only the video board -> after school Tammy and sick Johann accompany (very tired) me to Genius Bar where they verify, yes it’s the NVidea board. They have replacement mainboard in stock, 3-4 days to replace. Whew! Excellent Indian food from the food court(!!) as celebration.

I managed to get the projects off the laptop before we left for Providence by booting it blind as a firewire harddrive to the iMac. Slow process, but at least I’m safe there. 2 hours sleep in the past 48. This day.. you can have it back (though I’ll keep the vindaloo and nan in the food court, thank you!) Now to sleep perchance to dream, or if not just forget this day.

My co-blogger from the Other95%, Kevin – who is also a member of the Deep Sea Boys who we hope to see make the circuit of Sea Shanty festivals this summer – essentially did just that as he led a session at Science Online ’09 on blogging from the field.

The idea, I believe, was to provide some idea of the level of distraction often present on a ship or field location, a lesson I got a bit of a taste for having “live-blogged” a few posts from the NOAA Ship Nancy Foster.

All I know is I would have loved to have been in the room when Kevin started dancing around with a deep sea angler fish puppet and belting out

Haul away you rolling kings
Heave away, haul away
Haul away youll hear me say
Were bound for South Australia

Please tell me someone got video or audio!!

(for those not familiar with Sea Shanties, Roger McGuinn has the lyrics and an MP3 of the Southe Australia available)

10% cuts came already and now the painful ones are coming… not that the 10% cuts weren’t already painful. Hopefully I can find my way into grad school despite the cuts…

Applications are in to UConn, Rutgers and URI for masters programs. Feelers went to Duke and WHOI but both of those are very long shots since the deadlines for this year have already past and they are Ph.D. only programs.

I had to wonder when Christie at Observations of a Nerd proclaimed that she was actually a man. I mean, I have never met her, but from previous postings etc., I was pretty sure the author of the blog was a female. However it seems her writing is decidedly male, at least according to one analysis.

According to the site GenderAnalyzer.com, which analyzes the gender of the author of a site based on their writings, I also may have an identity issue to deal with on top of GRE’s, Grad school applications, etc…

It seems Eclectic Echoes is decidedly gender neutral. (Technically 53% male).
Larval Images is decidedly male at a ranking of 74% male, and
The Other 95% is comparatively dripping with testosterone at 84% male.

Of course since I blog at TO95% with Kevin, I decided to analyze his other sites as well.
Deep Sea News (with co-bloggers Craig McClain and Peter Etnoyer) scores strongly male, but at 81%
I also tried Kevin’s home page, but according to the analyzer it is not written in English (?!) so it could not complete the analysis.
Unfortunately without a site exclusively authored by Kevin, I don’t think there is a solid way to break out each author’s effects accurately.

Aside from the fact they probably need more training data for increased accuracy, what conclusions can you draw? (While I get back to studying aggregate supply and demand curves and writing a paper on oxygen isotopes and global climate analysis)

He entered a Student Blogger contest that has a $10,000 award and after making the first cut is in a vote-off or the big prize.

(Damn, that would have killed the credit card debt right nicely!)

Seriously, if you all know me and what my family has been doing to make this a reality, you surely know it isn’t easy. Brian is an awesome writer and we need people like him in science and science communications…

Damn, just realized Laelaps isn’t in the science blog links over there —>
must fix.

As for my education… one thing I have learned this week. Bureaucracies are the same wherever you go, and I would still rather be in combat that deal with them – at least in combat you have a fighting chance to survive.

Urinary Tract Wallpaper by Shannon Wright

Hat tip to Miriam at The Oyster’s Garter

While the gents at Deep Sea News get time on some of the best manned and remotely operated vehicles out there, the rest of us don’t have to sit it completely out. I think some time this winter Tammy and Johann and I will build a homebrew ROV to explore some of the local shores. Maybe we can find some of the stomatopods that live in the Mystic estuary for a test cruise.

Mantis Shrimp (Squilla empusa)
Originally uploaded by Littoraria.

We ended up going to Storrs on Sunday to represent the Marine Science Department for the open house, then going down everyday to New Haven related to the surgery. The surgery was on Wednesday. There was a marked difference in the way that everything was handled. The Dr. made sure to talk to us before the surgery and to Tammy afterwards. They released me from the recovery unit as soon as I was able to pee. Amazing how a simple thing like that can become so important yet impossible to do. Basically all the things that were wrong with the first time around were corrected this time. Fortunately they were able to get the stone and use a home removable stent (ACK!!) so there will be no return trip for that.

I was pretty out of it though for the past few days, couldn’t focus enough to get any work or studying done, slept half the day away, so when I was awake I cruised some photography web sites. I was looking for some ways to do some more advanced studio type lighting on the cheap and looking to see if I could find a repair for the focus mechanism on one of my lenses. I ran across a few websites I wasn’t already familiar with so figured I’d share them here…

ProPhotoLife – a site with lots of video tutorials (through YouTube) that is aimed mostly at studio and commercial type photography. Lot’s of good hints here for those specific fields but also for general photography including color management, gear bags, lighting theory, composition, starting and running a business.

Strobist – a site dedicated to photography using off camera flashes and strobes. A lot of good stuff in there including a lot of good DIY ideas for creating complex lighting effects on a beer budget. It covers the range of photography styles including macro, nature commercial, assignment and studio. Their Lighting 101 and Lighting 102 series will get you up to speed with off camera flash photography easily and the On Assignment series (how an assignment shot was created) is always fun to read.

Canon themselves have an interesting Virtual Lens Plant, that shows how their excellent lenses are made including the science behind high quality optics. It’s done in an easy to understand way using graphics and video to best effect. It also has interviews with the lens craftspeople who are responsible for making them. Pretty cool for an optics geek to see how those lenses are actually made.