diff --git a/book/chapters/data.ipynb b/book/chapters/data.ipynb index 1c47c92..0ed6044 100644 --- a/book/chapters/data.ipynb +++ b/book/chapters/data.ipynb @@ -4,7 +4,9 @@ "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", + "
\n", + "[GitHub repo](https://github.com/geo-smart/oceanography).\n", "\n", "\n", "# Data\n", diff --git a/book/chapters/oceanscience.ipynb b/book/chapters/oceanscience.ipynb index f21957e..ee8bd84 100644 --- a/book/chapters/oceanscience.ipynb +++ b/book/chapters/oceanscience.ipynb @@ -4,7 +4,9 @@ "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", + "
[GitHub repo](https://github.com/geo-smart/oceanography)\n", + "
[RCA Learning Site](https://interactiveoceans.washington.edu)\n", "\n", "\n", "\n", @@ -15,7 +17,7 @@ "> 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!

-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", @@ -45,8 +47,7 @@ "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", "
" ] }, @@ -54,25 +55,26 @@ "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", @@ -80,21 +82,49 @@ "\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." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "67.06354079832528 101.96806724387616 452.8567919405785\n" + ] + } + ], + "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)" ] }, { @@ -162,10 +192,32 @@ "\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", @@ -194,14 +246,32 @@ "### 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+ | pH sensor\n", + "|1|Hydrogen cation H+ | pH sensor\n", "|17|Hydroxide ion OH- | -no direct observation-\n", - "|18|Water H2O | temperature and salinity sensors\n", + "|18|Water H2O | temperature, salinity, light sensors\n", + "|?|Calcium| -no direct observation-\n", + "|?|Silica| -no direct observation-\n", "|46|carbon dioxide CO2 | 'partial pressure' pCO2 sensor\n", "|62|carbonic acid H2CO3 | by inference\n", "|61|bicarbonate anion HCO3- | by inference\n", @@ -218,22 +288,31 @@ "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", " " ] },