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robfatland committed Aug 21, 2024
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4 changes: 3 additions & 1 deletion book/chapters/data.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"[Jupyter Book](https://geo-smart.github.io/oceanography/chapters/data.html) and [GitHub repo](https://github.com/geo-smart/oceanography).\n",
"[Jupyter Book](https://geo-smart.github.io/oceanography/chapters/data.html) \n",
"<br>\n",
"[GitHub repo](https://github.com/geo-smart/oceanography).\n",
"\n",
"\n",
"# Data\n",
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167 changes: 123 additions & 44 deletions book/chapters/oceanscience.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"[Jupyter Book](https://geo-smart.github.io/oceanography/intro.html) and [GitHub repo](https://github.com/geo-smart/oceanography).\n",
"[Jupyter Book](https://geo-smart.github.io/oceanography/chapters/oceanscience.html) \n",
"<br> [GitHub repo](https://github.com/geo-smart/oceanography)\n",
"<br> [RCA Learning Site](https://interactiveoceans.washington.edu)\n",
"\n",
"\n",
"\n",
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"> But I now leave my cetological System standing thus unfinished, even as the great Cathedral of Cologne was left, with the crane still standing upon the top of the uncompleted tower. \\[For small monuments\\] may be finished by their first architects; grand ones, true ones, ever leave the copestone to posterity. God keep me from ever completing anything. This whole book is but a draught—nay, but the draught of a draught. Oh, Time, Strength, Cash, and Patience! <br><br> -Herman Melville\n",
"\n",
"\n",
"**Note: until images inline for both the Jupyter Notebook *and* the Jupyter Book: I will double up.**\n",
"**Note: Until fixed: Not appearing properly: Inline images in both the Jupyter Notebook and the Jupyter Book ontext: Temporary solution is to simply double up.**\n",
"\n",
"\n",
"```{figure} ../img/revelle.jpg\n",
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"starting at the chapter on **`data`** goes into the technical means behind the science.\n",
"\n",
"\n",
"Let us begin, then, by attempting to frame the science, beginning \n",
"with an ambitious question:\n",
"Let us begin with an ambitious question:\n",
"<br>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"${\\Large \\textrm{How stable is the epipelagic ocean?}}$\n",
"###### ${\\Large \\textrm{How stable is the epipelagic ocean?}}$\n",
"\n",
"\n",
"This question by itself is simplistic so let's qualify its meaning.\n",
"With that let's qualify what we mean.\n",
"\n",
"\n",
"\n",
"### *Epipelagic ocean* defined\n",
"\n",
"\n",
"Pelagic refers to the ocean water column, particularly away from the shore. \n",
"*Epipelagic* is then the *upper* water column and the term is synonymous with \n",
"*sun illuminated* or *photic*. The most common expressions are \n",
"*epipelagic zone* and *photic zone*.\n",
"This is the upper 200 meters of the water column subjected \n",
"to downwelling sunlight. Sunlight is in turn the energy source of primary \n",
"production: Photosynthesis primarily by plankton. So we are looking at\n",
"the ecosystem of the upper ocean: The biological engine powering\n",
"life in the ocean.\n",
"Pelagic refers to the ocean water column, surface to sea floor, and \n",
"specifically some distance away from the shore. \n",
"*Epipelagic* is then the *upper* water column and the term coincides \n",
"with *sun illuminated* or *photic*. In fact the most common expressions \n",
"are '*epipelagic zone*' and '*photic zone*':\n",
"This is the upper 200 meters of the water column subject to \n",
"downwelling sunlight. Sunlight is the energy source for primary \n",
"production, i.e. photosynthesis primarily of plankton. *Epipelagic*\n",
"is then the ecosystem of the upper ocean including this biological \n",
"engine that powers much of the life in the ocean.\n",
"\n",
"\n",
"Our observational starting point is three observing sites located in the \n",
"northeastern Pacific Ocean. \n",
"\n",
"\n",
"```\n",
"Site name Latitude Longitude\n",
"------------------ -------- ---------\n",
"Oregon Offshore 44.37415 -124.95648\n",
"Oregon Slope Base 44.52897 -125.38966 \n",
"Axial Base 45.83049 -129.75326\n",
"``` \n",
"Site name Latitude Longitude Depth (m) D-offshore (km)\n",
"----------------- -------- --------- --------- ---------------\n",
"Oregon Offshore 44.37 -124.96 577 67\n",
"Oregon Slope Base 44.53 -125.39 2910 101\n",
"Axial Base 45.83 -129.75 2620 453 \n",
"```\n",
"\n",
"\n",
"\n",
"Our initial observational focus is a\n",
"Our initial focus is a\n",
"[shallow profiler](https://interactiveoceans.washington.edu/technology/shallow-profiler-moorings/) \n",
"maintained and by the Regional Cabled Array program located at the Oregon Slope Base site. \n",
"The shallow profiler generates a record of the state of the upper ocean with both time and \n",
"depth at fine scale. From this observational starting point we proceed to add other resources\n",
"including ARGO drifters, satellites, and NOAA buoys."
"maintained and by the Regional Cabled Array program at the Oregon Slope Base site. \n",
"The shallow profiler generates a record of the state of the upper ocean at fine scale \n",
"both in time and in depth. Once we have a handle on shallow profiler observations\n",
"we can proceed to add other sensor resources such as ARGO drifters, satellites, and NOAA buoys."
]
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"67.06354079832528 101.96806724387616 452.8567919405785\n"
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"source": [
"# using a spherical earth approximation here are offhore distances \n",
"from math import cos, pi\n",
"re=6378.\n",
"d_oof = .95648 - .10448\n",
"d_osb = 1.38966 - .09422\n",
"d_axb = 5.75326 # using shore lon = -124\n",
"d2r = pi/180\n",
"km_per_rad = (cos(pi/4)*(2*pi*re))/(2*pi)\n",
"s_oof = d_oof*d2r*km_per_rad\n",
"s_osb = d_osb*d2r*km_per_rad\n",
"s_axb = d_axb*d2r*km_per_rad\n",
"print(s_oof, s_osb, s_axb)"
]
},
{
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"\n",
"\n",
"*Coincidence* refers to ocean structure that persists across multiple sensor streams. \n",
"*Persistence* refers to structures that persist in time, i.e. for multiple consecutive observations.\n",
"*Persistence* refers to structures that persist in time, i.e. for multiple consecutive observations. Let's take a moment to anticipate both (coming up in the next chapter).\n",
"\n",
"\n",
"Suppose a smooth data curve concerned with temperature has a noticeable 'jag' or\n",
"anomaly in measurement at a depth of 100 meters. Perhaps this reflects actual \n",
"water temperature or it may be due to a temporary sensor issue. We can turn to\n",
"another sensor -- say salinity or chlorophyll -- and look for a matching anomaly \n",
"at a comparable depth. If present: We have evidence that the anomaly is in fact\n",
"due to the water via coincidence. \n",
"\n",
"\n",
"Continuing onward from this point: Temperature data is collected on both ascent and\n",
"descent over the course of more than an hour. Seeing the above anomaly in both profiler\n",
"phases is an example of persistence of a signal of interest. Even stronger evidence:\n",
"The anomaly appears over the course of multiple profiles (of which there are nine \n",
"per day).\n",
"\n",
"### How stable is the epipelagic ocean?\n",
"\n",
"To take this one step further: We will find that the shallow profiler also measures\n",
"water velocity as a function of depth. Suppose an anomaly persists for two days and\n",
"the upper water column has a consistent velocity of 2 kilometers per hour southward.\n",
"This suggests a water mass 100 kilometers across has drifted past the profiler site;\n",
"an estimate that could be compared with satellite data, both spectral and sea level anomaly. \n",
"\n",
"\n",
"### Returning to the question *How stable is the epipelagic ocean?*\n",
"\n",
"\n",
"The water column is well understood as stratified. The upper layer is\n",
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"### Ocean chemistry\n",
"\n",
"\n",
"Let's begin with a table of molecules.\n",
"Let's motivate a very simple table of atoms and molecules distributed \n",
"in the ocean. We have on the one hand the physical ocean with tides and \n",
"currents and sunlight; we have ocean chemistry including pH and salinity (salt concentration); \n",
"and we have biology: Life in the ocean from plankton to apex predators.\n",
"These topics are interconnected and the \n",
"umbrella term invented for all of it -- with a particular eye to how\n",
"carbon is transported and stored -- is **biogeochemistry**. (For \n",
"a great deal more on the topic visit this\n",
"[ocean carbon and biogeochemistry website](https://www.us-ocb.org/).)\n",
"\n",
"\n",
"The following table is sorted in terms of molecular mass in Daltons.\n",
"(One Dalton is effectively the mass of a single hydrogen atom.) \n",
"The last three entries are life-based or *organic* compounds. \n",
"[Chlorophyll](https://en.wikipedia.org/wiki/Chlorophyll) is of particular\n",
"interest as the central agent in photosynthesis: Absorbing and transferring\n",
"light energy within a structure called a photosystem. \n",
"\n",
" \n",
"| Mass (Daltons) | Substance | Comment on measurement\n",
"|---|---|---\n",
"|1|Hydrogen ion H<sup>+</sup> | pH sensor\n",
"|1|Hydrogen cation H<sup>+</sup> | pH sensor\n",
"|17|Hydroxide ion OH<sup>-</sup> | -no direct observation-\n",
"|18|Water H<sub>2</sub>O | temperature and salinity sensors\n",
"|18|Water H<sub>2</sub>O | temperature, salinity, light sensors\n",
"|?|Calcium| -no direct observation-\n",
"|?|Silica| -no direct observation-\n",
"|46|carbon dioxide CO<sub>2</sub> | 'partial pressure' pCO2 sensor\n",
"|62|carbonic acid H<sub>2</sub>CO<sub>3</sub> | by inference\n",
"|61|bicarbonate anion HCO<sub>3</sub><sup>-</sup> | by inference\n",
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"source": [
"### Ocean structure\n",
"\n",
"In addition to chemical composition here are some further attributes of the ocean.\n",
"\n",
"- The ocean is 3700 meters in depth on average\n",
"- Locations in the ocean are given precisely in terms of latitude and longitude\n",
" - Informally we discuss location using historical terminology\n",
" - Example: The Coral and Tasman Seas are regions of the southwestern Pacific Ocean \n",
"- The ocean is 3700 meters deep on average, covering 70% of the earth's surface\n",
"- Coastal ocean water (shelf water) is six times as productive as the deep ocean\n",
"- The photic zone is about 200 meters so 90% of the ocean is perpetually dark\n",
"- Heat capacity of seawater versus atmosphere\n",
"- Water temperature decreases with depth\n",
" - Geothermal heat at the sea floor\n",
"- Salinity increases with depth\n",
"- Ocean water has greater capacity for dissolved oxygen (DO) with lower temperature\n",
" - Dissolved oxygen concentration is affected by biological respiration\n",
"- Carbon dioxide is complicated\n",
" - A more appropriate term to use is carbonate chemistry\n",
"- The photic zone is the upper 200 meters of the ocean\n",
" - Consequently 90% of the ocean is in perpetual darkness\n",
"- Remark on the heat capacity of seawater relative to that of the atmosphere, to land\n",
"- Water temperature decreases with depth and is fairly constant below the thermocline\n",
" - Geothermal heat emanates from the earth's interior: At the sea floor\n",
" - Ocean spreading centers feature hydrothermal vents\n",
"- Salinity increases with depth, typically stable below the halocline\n",
"- Ocean water has the capacity to hold oxygen: A dissolved gas\n",
" - This holding capacity increases with lower water temperature\n",
" - Dissolved oxygen is depleted by biological respiration\n",
"- Carbon dioxide is an atmospheric gas that dissolves in the ocean\n",
" - Within the ocean: Carbon dioxide is converted to carbonic acid\n",
" - Carbonic acid in turn dissociates to bicarbonate and hydrogen ions\n",
" - Collectively this is called *carbonate chemistry*\n",
"- Productivity primarily refers to photosynthesis by phytoplankton\n",
" - Photosynthesis is bounded on the low side by limited availability of nutrients and sunlight\n",
" - Photosynthesis is bounded on the high side by saturation\n",
"- Nutrients: Nitrate and \n",
" - Photosynthesis is bounded on the low side by availability of nutrients and sunlight\n",
" - Photosynthesis is bounded on the high side by saturation (availability of chlorophyll)\n",
"- Nutrients: Nitrate \n",
" "
]
},
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