August 2010 Archives

The Art of Modeling

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Apparently, the concept made its way into the mainstream scientific journals. The art resides in the numerous educated guesses and assumptions an ecologist faces when building and (as importantly) assessing the validity of his model. From the conceptualization of the scientific question addressed, to the choice of the numerical method(s), the amount and level of precision of the processes to represent, their mathematical formulation, and the determination of the parameters of the equations etc. At each step, some subjectivity, some instinct, some serendipitous success, maybe...

The highest level of certainty an ecological modeler knows is that there are some apparently unavoidable pitfalls. One is mortality (any biological modeler reading this will nod in spite of himself). Sooner or later, in a meeting like the one I am this week, you'll hear something spirited like "...but your mortality function is not based on any mechanism, so what the ... are we (non-modelers) supposed to do with your results..."

Mortality rates of the small plankton are notoriously difficult to measure in the field, and thus, this term is one of the most difficult to constrain. Most single species copepod models have developed empirical relationships with temperature and/or food (for seasonality purpose) and many include some form of density dependence (for numerical purpose). Those choices arise from the trade-offs between the availability of data and the necessity to move forward and do actual modeling.

The case of temperature-dependent functions illustrates this situation: the Gulf of Maine time series suggest that herring predation may limit Calanus finmarchicus abundance. Predation by herring is the highest in the summer and the seasonal changes could then be approximated as a function of temperature. If spring conditions were warmer, we might expect that herring would begin feeding earlier, and thus, the temperature dependent mortality would adequately reflect interannual changes in a mechanistic way. However, it seems unlikely that herring predation would respond to a temperature anomaly of a few days, and it is unclear whether a warming throughout the year would correspond to higher mortality.

A novel approach of mortality in copepod models requires a mortality function that reflects some aspects of the dynamical response of predator populations to copepod abundance. This requirement becomes essential to enable realistic projections under climate variability and change. Our knowledge of copepod predators remains limited, and attempting to model the populations of all of the major predators of the life stages of our copepod would just be unfeasible. Following the "middle-out" framework, in future iteration of our models we want to use a compromise mortality function. This new function will make use of several populations of predators, each representing predation by progressively larger animals preying on progressively larger copepods. We will use classical size-dependent feeding behavior for the predators, namely a type II ingestion function (rapid increase at low food concentrations) for small predators and type III function (depressed feeding at low concentrations) for large predators. The result will be that on one hand, the predation rate on smaller copepods (early life stages) will increase largely through changes in the abundance of the predators, while on the other hand predation on larger copepods (later life stages) will respond to changes in their own abundance through the variable ingestion rate of the larger predators. That, is a bold move!

racoon.jpg This picture has nothing to do with what I just talked about... I just feel that the pictures on the blog are discriminatory toward the earthly mammals ! And raccoons are cute (at 3pm, not 3am, though...).


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You may not buy it, but I swear I did not have the time to make a post earlier ! When scientists gather together, they are a pretty busy bees !

So a typical busy day of workshop looks like that:

1) Wake up early

Early.jpg2) Look for coffee, urgently... smell it, ask for it, but find it !
3) Begin to articulate intelligible English after a hot coffee and socialize in front of a copious breakfast.
4) Gather in a room locked from outside and listen to talks, talks, talks...
5) Wow, first groundbreaking concept of the day !

Curchister.jpg6) After that, everyone is allowed to go eat and socialize before...
7) ... gathering again and listen to talks, talks, talks...
8) After this intense listening, eat, escape to gather somewhere nice and... talk about all those amazing talks !

Group_sunset.jpg9) Finally, because we have to, go to bed and dream about all what we heard counciously and unconsciously during the day.

So be patient, I've already dreamed about some real juicy science blog posts. They are coming soon.

Oceanographer on a ferry

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Since my beginning as a Post-Doc at the University of Maine's EML, I had several opportunities to travel to the west coast... not just to brag about how much more quaint and authentic New-England is, but mostly to share and do my work...  Today I'm back west once again, staying in the Friday Harbor Labs of the University of Washington.  This time is my first participation to a more focused and high-level workshop with seasoned oceanographers under the theme "Global Ocean Ecosystems and Climate".

But before the hardcore science begins, it's time for a short follow-up on a previous blog entry from Andy, while he was traveling this area a year ago.  Andy took an air-borne picture of the northwest part of San Juan Island (Henry Island's shape is unmistakable), and the actual route taken by my own ferry.  Andy is an accomplished oceanographer (and incidentally my boss), so please praise with me his instinctive analysis, in which he correctly guessed that the difference in surface waters' reflectance was caused by oily algae products.

The first picture below shows the intricate smooth and rough surface water features he talked about from a ferry's deck point of view.


The second, though a little blurred, shows what's in the slicks: algae washed off from the shore!


Add these two blog entries and you get the idea behind modern oceanography. Just replace the iPhone shot from a plane by a few $M satellite sensor and a couple of unreliable Canon PowerShot pictures with a few $100K scientific sampling cruise. Now you know how oceanographic knowledge is acquired and validated.  Next step, integrate everything and fill the gaps with models... Hey, that's what we happen to do in the EML!


Stay tuned for daily updates on this workshop (that's my resolve, for now...).


Atlantic white-sided dolphins

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Here's a quick video of a few Atlantic white-sides escorting us into casco bay last weekend.

Darkstar dolphins from peter stetson on Vimeo.


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I went snorkeling in Kettle Cove today and managed to get this picture of a ctenophore:
You can clearly see the rows of reflective cilia called "ctenes" that give the phylum it's name.  You can also see one of the tentacles dangling down to the left.  It uses these sticky threads to entangle zooplankton.  The stomach is in the middle of the ball, and the bald thing with the snorkel is me.  I'm not a jelly expert, but I'm pretty sure this guy is Pleurobrachia, a known copepod predator.
Week 3 since the cruise, and the pieces of the puzzle are beginning to come into focus.  Cameron's incubation experiments indicate a presence we've not sensed since last year--the presence of diapausing copepods deep in the abyss.  As I typed earlier, I'm getting a similar signal in the laser data: an anomalously large aggregation of particles at just the size and depth we would expect to find C. finmarchicus.  Here is another view:


While it is possible that this deep aggregation of particles is some mysterious, and as yet undiscovered presence in the gulf, the evidence points to one plausibility: if it quacks like a copepod, it's probably a copepod.

I returned to my personal microcomputer to plot up quasi-silhouettes from the lasers, showing these particles.  Here are the preliminary results:

A glance at this image is far from conclusive, and it remains to demonstrate that the blobules we see are actually diapausing copepods.  I conjecture that they are indeed that, and I am presently taking steps to convince myself that I'm correct.

Nick Record, signing off.

With the thrill of the lobster molt wearing off, the time has come to crunch some numbers.  A few weeks ago--the 22nd of July, 2010 to be more precise--we spent a full day on our deep station in Wilkinson Basin.  For six relentless hours, we sampled profile after profile at the same station.  What began as a routine and sunny carefree day slowly morphed into grueling repetition, and as twilight descended upon us, so did the madness of tedium.  (I won't speak here of what that madness led to.)


The driving motivation behind this long series of profiles was to capture the twilight transition in Wilkinson Basin.  Every night, an unfathomable host of plankton emerges from the depths of the world's ocean to feed at the surface under the cloak of darkness.  This transition occurs, for the most part, during the twilight hours--hence the name of this sampling series.  Our objective is to sort out some of the major players in this massive migration, and to pinpoint as well as we can their preferred depths.

Naturally, we are in the early stages of unraveling this depth-stratified tapestry of plankton, but some curious signals are already appearing.  The plot shown below is taken from a night sample, well after the sun has set.  On the left is a plot from our laser optical plankton counter.  It shows the depth concentration of each size class of plankton--divided by equivalent spherical diameter (ESD).  You can see that most of the critters we observed are near the surface, with the concentration tapering off around a depth of 20-40 meters.  What stands out is the strong signal at the size range 1000-2000 microns (1-2 mm) at depths below 120 meters.  I have labeled this "Diapausing finmarks"-- what I believe to be the copepod Calanus finmarchicus, gathered in large numbers in its deep hibernation.  This is something that we hope to confirm with the net tows.

It is interesting to note that, while we think of this species as a cold-water animal at the southern edge of its range here in the Gulf of Maine, it appears to be actively avoiding the coldest depths at this station.  The right-hand plot shows a temperature profile, with a classic Maine-intermediate-water signal. I've labeled that.  It's a cold layer that forms between two warmer layers in the ocean, due to a combination of processes.

The other curiosity to this temperature plot is the blip of warmer water around 50 meters depth.  This I've labeled with a question mark.  It appears in nearly all of our profiles, at the same depth, and I've since noticed it in other temperature profiles from the Gulf of Maine.  I have yet to find an explanation.  Thus, another mystery has bubbled up to the surface.


PS in response to Pete's comment, I've posted some of the LOPC shapes on the LOPC blog:

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