February 2009 Archives

working with AESTUS

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The model I'm using to look at internal wave dynamics was created by Daniel Bourgault and Dan Kelley (see Aestus on Daniel Bourgault's website, or Bourgault and Kelley 2004). It is a laterally averaged non-hydrostatic model. This means two things:
  1. In a laterally averaged model, we assume that advection perpendicular to the primary flow is minimally significant. This allows us to reduce the number of dimensions in the model and reduce the time necessary to complete each run (i.e. more experiments in the same amount of time).
  2. A Non-hydrostatic model does not hold the hydrostatic assumption as true. This means the system does not have to be in hydrostatic balance, where the pressure gradient is balanced by the buoyancy forces,Istantanea 2009-02-24 22-14-56.jpg.  Generally, this makes sense: the deeper you go the denser the water and the greater the pressure. But when you want to investigate the dynamics of water that is being mixed, by internal waves for example, the denser water mass is not always deeper. This makes the math for solving the model more complicated and a non-hydrostatic model is capable of handling that.
A big part of running any model is setting up initial conditions that will accurately recreate your system. This is something I'm still fine tuning, and perhaps I'll talk more about that in a later post.

For now, here's what a sample output looks like:

The figure above shows an internal wave traveling from left to right aross Platts Bank (43°10'N  69°40'W). The colorbar on the right shows density (sigma). Red = less dense water and Blue = denser water. The leading packet of waves (right-most dip of red) is relatively organized in comparison with the trailing wave, especially near the left edge of the bank. This is not only aesthetically pleasing (at least to the author), but it's interesting in terms of what it means for energy dissapation, mixing, and advection. The isobaths 4 km before Platts and 2 km after were artificially created in order to look at the dynamics of the internal waves with the bank not the bathymetric features before and after.

Next time, I'll talk about how we populate the model with krill-like particles to examine the interactions between krill (euphausiidae) and the waves.

First unofficial forecast

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Since there have been delays in getting out our first Cape Cod Bay forecasts (i.e. still waiting for satellite data and flow fields), I decided to attempt a crude forecast using the limited information that we do have.  You'll see that the forecast isn't too bad, but there is quite a bit of room for improvement.  As we incorporate more data (see below), and more advanced methods (e.g. ensemble Kalman filter), we should expect to see marked improvement in the accuracy of our forecasts.

Disclaimer: As you read on, bear in mind that these are not finalized results.  This description is to provide insights into the forecasting process.

First, the data that we have:
- flow fields from previous years
- satellite data from previous years
- zooplankton samples for 2009 from the Provincetown Center for Coastal Studies (PCCS)

What's missing:
- flow fields from 2009 (coming soon)
- satellite data from 2009 (coming soon)

As the weeks roll by, we'll also be getting zooplankton updates from the PCCS, as well as updated flow and satellite data.  The missing data, however, is critical to a good forecast, so this exercise should be taken with a grain of salt.

Now for the forecast:

There's not a whole lot we can do about the missing 2009 data.  Our computation requires sea surface temperature and chlorophyll values from satellites and flow fields, so I've used representative values from previous years.  I then tuned the output to a collection of zooplankton sample data, and scaled the values to correspond to what the PCCS has been seeing in the water this year to give us our forecast (Fig. 1).

Figure 1 Forecast zooplankton abundance (ind. m-3) at selected dates.

An important note: for simplicity's sake, I'm just using the Pseudocalanus parameterization to forecast all zooplankton, omitting for now the Calanus and Centropages groups.  The forecast will lose validity, therefore, as the assemblage changes later in the winter.

PCCS.gifIf we compare the forecast to the maps from the PCCS through the end of January (Fig. 2), there are a couple of points to make.  The first part of the temporal signal appears to come through, with populations rising to high levels by late January.  Whether or not the decline toward Feb. 21 is observed in the net samples remains to be seen.  The second point is that the spatial pattern is incorrect.  That is, the high concentration that appears in the forecast should be located more toward the southeastern part of the bay.  This is likely due to the fact that the 2009 flow field is missing from the calculation.

This is a good jumping off point, but more than that, it illustrates the importance of the missing data layers.  Stay tuned for a more refined forecast in the next week or so.

Figure 2 Measured zooplankton abundance (ind. m-3) from PCCS surveys.

Science: minimizing interpretive variance

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All of us in science are challenged with the question of how to explain our work to those outside of our field. Over the weekend I was asked by a performance artist to explain the meaning of the sentence fragment "doing research".  When explaining the ways and the whys of math and science, I often come back to a claim made by my undergraduate linear algebra professor - "mathematics is about the communication of ideas".

I liken research to the work of an artistic painter. Imagine beginning with a blank canvas in the studio.  Leave your studio, toodle around town, grab a couple of cups of coffee and find combinations of sights, sounds and feelings that inspire you.  Internalize your experience, return to the studio and recreate your experience with paint, brush and canvas.  Voilà! - an unambiguous record of your impressions of the day.  Not so (not the way I paint, anyway).  Art is open to to interpretation (is Mona Lisa frowning or smiling?).  In science, the intent of the artist or investigator should be clear to all.  If a scientific manuscript were represented as a painting, the color and texture of each brush stroke would (ideally) be deliberate and defensible. Each stroke placed in an effort to reduce ambiguity and increase the uniformity with which the painting is interpreted. This goal of uniformity of interpretation is one of the primary reasons that mathematics has become the language chosen by scientists to communicate their ideas.

maxentExample.jpg On a less abstract note, images are created and used in science to convey information. I generate images of areas likely to host right whales.  In the image shown, blue represents an area where you would be unlikely to find a right whale, and red areas are likely to be a temporary home for the animals. The right whale habitat map below was generated with the maximum entropy species distribution modeling software. In the next post I'll talk about the methodology behind these "paintings".

Sea Surface Time Lapse

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Here is an example of the results of the georectified time lapse photogrammetry.  This is still rough around the edges, but you can see some neat phenomena.  As in the earlier entry, the photo on the right is the original (a bit stretched), and the image on the left is the rectified, top-down version.  This is one day of images, taken once per minute.  Anything on the surface of the water is rectified correctly, but anything with height, such as tankers and buildings, will be skewed.  There are some very coherent and complex marine surface films.  It's also interesting to watch the boat traffic.  We have a really busy harbor.

There is almost a year's worth of data to analyze--that's one image per minute, every day--so I've got my work cut out for me.  We can use the movement of the surface films to infer flow velocities, and examine these under different wind and tidal regimes.

Just a quick note: marine surface films are generally not the result of spilled oil.  They are caused by oils generated by living organisms in the ocean.

Right whales, climate change, and the press

If you believe the old maxim that "all press is good press", then It's been a good couple of weeks for EMLab.  While I'm usually pretty happy to be the center of attention, I'm beginning to think that maybe all press is not so good.  

Last week, the Ellsworth American ran a story titled "Is Climate Change Keeping Whales in the Gulf of Maine?", that reported on a lecture I gave at the Marine Environmental Research Institute in Blue Hill.  The article did a good job describing many themes I discussed. Unfortunately, my talk did not address the question posed in the headline, namely whether climate change is keeping whales in the Gulf of Maine.  Given the strong feelings that right whales evoke along the coast of Maine, I was worried that this would create some negative feedback for our work, especially for some of my colleagues who are more actively engaged in the entanglement issues.  Thankfully, it didn't draw a lot of attention--no angry letters to the editor that I can find, but our local public radio station did pick up the story.  MPBN actually interviewed me and others to get the straight story.  My only complaint is that they only mentioned my GMRI affiliation.  

So what do we know about right whales and climate?  The Gulf of Maine, which extends from the coast of New England and Canada south to Georges Bank, is a special place for right whales.  All of the known right whale feeding grounds are found in this region, and all of the approximately 400 right whales in the North Atlantic spend some time in the Gulf during the spring and summer.  During the winter, pregnant females migrate to the calving grounds off of Florida.  We know very little about where males and nonpregnant females go during the winter.  This is why the recent sighting of 44 whales in the central Gulf of Maine in December was such big news.  While their presence was news to us, these animals were probably doing what right whales have done for thousands of years.  The fact that scientists only recently found them is more likely due to increased efforts to find whales than to a changing climate.  While it is unclear exactly how the Gulf of Maine will respond to a shifting climate, the coming changes will challenge the animals in the Gulf.  Scientists are learning more every year about how animals move in relation to environmental conditions.  Further research in this area will allow more precise predictions about how right whales and other animals will behave in a changing ocean.  

whales and internal waves

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     The methods by which animals take advantage of their environments to increase foraging and locamotive efficiency are sometimes astounding. Albatross (family Diomedeidae) can lock their wings and surf the pressure gradients in front of surface waves for days (see dynamic soaring). Striped bass (Morone saxatilis) are known to sit in one location, swimming in place, facing the current (this, by the way, is called positive rheotaxis, for those of you looking for your $2 word of the day) with their mouths agape, waiting for the current to bring them the food.
    A recent paper by Moore and Lien (2008) documents a pod of pilot whales (Globicephala macrorhynchus) following internal waves through the South China Sea. Moore and Lien suggest that the Globichephala may do this to take advantage of the increased concentrations of prey entrained in the physical mixing generated by the waves. (In fluid dynamics, to be entrained, literally, is to be picked up by and carried with a flow).
     While I think the ideas within the paper are very interesting, I'm disappointed that the authors didn't go further. How about some prey sampling in the waves? No nets? If the data was collected with a depth-sounder, there is post-processing software that can be used to estimate plankton and fish abundances. The other papers cited, Ramp et al. (2004) and Lien et al. (2005), describe methods used to investigate the internal waves in the South China Sea. Data collection methods included: ADCP, moored current, temperature, conductivity, and pressure sensors as well as other acoustically gathered data. If the pilot whale were observed by chance during the course of the internal wave research-cruises, Moore and Lien would have the capacity to describe the (probable) presence or absence of prey for the whales that was aggregated by the waves. Such inferences could be made from the available acoustic data.
     Although the authors mention that the shoaling waves bring nutrients and plankton to the surface, there is no mention of plankton in the cited paper by Lien et al. (2005) describing the internal waves in the area.
     Basically, my issue with the paper is that Moore and Lien don't offer any evidence that prey were present in the waves. They merely say the waves are capable of entraining likely prey for the pilot whales. That said, I think the phenomenon is interesting, and I agree with Moore and Lien's conclusion that the issue merits further study.

Super-surface Planktivores

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I'm not an ornithologist, but I played one for three months in Costa Rica (interesting bird research). Though I've moved from terra to aqua, I maintain an interest in happenings where the z-axis is positive, and in particular where it is small. Marine Ecology Progress Series published a theme section titled "Seabirds as indicators of marine ecosystems" (Volume 352).  In this blog entry, I'll going to chat about one of the articles from that section.

In Hot oceanography: planktivorous seabirds reaveal ecosystem responses to warming of the Bering Sea, Springer et al. looked at the diets of least auklets (Aethia pusilla) in the Pribilof Islands. Like some whales, these birds eat copepods! Upwards of 80% of their diet may be composed of Neocalanus spp. and Calanus marshallae. The former is a deep water species, and the latter is more often found in shelf waters. The authors examined the diet of birds on two of the Pribilof Islands - one in "shallow" shelf water, and the other closer to the "deep" basin water. The relative proportion of Neocalanus spp. to C.marshallae found in the birds is assumed to be representative of the availability of each copepod in the vicinity of each island. 

YanNetTow.jpgOne of the really neat things about this study is the methodology: that one can let the birds do the sampling. In the absence of an "indicator" such as the lesser auklet, we humans would need to hop on a boat and sample the water column with a net or with acoustic instrument(s). Finding indicator organisms is, in effect, biological remote sensing. Another aspect of this study that makes it interesting is it's location - tiny mountainous islands at high latitude. Look forward to a future post containing a list of super-surface planktivores.

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This page is an archive of entries from February 2009 listed from newest to oldest.

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