Title: Modeling Biotic Factors: Testing Understanding
1Modeling Biotic FactorsTesting Understanding
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5)) CO24CO2L(NZ,NY,NX) C4ACIDT0.0
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IF(ARLF(K,NB,NZ,NY,NX).GT.1.0E-64)THEN
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CF(NZ)FC34(NZ,1) DO 500
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0)THEN IF(PAR(N,M,L,NZ,NY,NX).GT.0.0)T
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- Talbot J. Brooks
- Asst. Research Professional
- ASU Dept. of Geography
2Overview and objectives
- Why do we model the biosphere?
- What approaches are available?
- What tools are available?
- What are the limitations?
- Daisy World A simple, but elegant approach to
modeling - Why is it so hard Modeling Photosynthesis
- An introduction to the processes
- Approaches an example
- Summation
3Why do we model biotics?
- To evaluate our understanding of the processes
used within living organisms - To evaluate our understanding of how living
organisms interact with each other - To understand how living organisms cope with
their environments - To understand how living organisms impact our
climate/world
4Approaches
- Empirical
- Based primarily on cause-effect scenarios
- For example, given x number of heating degree
days, a plant will grow by y amount - Mechanistic
- Physics and math based
- Treat like a chemical reaction x number of
reagents with y co-factors yields z product - For example, x photon flux density hits y number
of chlorophyll a molecules which are at a
temperature of z.
5Different approaches serve different masters
- Empirical approach
- Tend to be easier to understand, therefore more
widely used - Relatively inexpensive to run
- Sometimes incorporated into more complex models
- frequently done with climate modeling - Examples
- How much to water you lawn reports
- Crop yield predictions used by financial groups
6Tools of the trade
- Empirical approach
- Programming languages
- Likely use VB, Visual C, Java
- Canned applications
- GIS (ESRIs Model Builder)
- AutoCAD
- Most applications/runs can be performed on a
typical desktop computer - Note that some of these approaches are static!
7Mechanistic tools
- Programming languages
- FORTRAN, C, Pascal, Cobal (business world), and
some Unix scripting - Does not use a canned applications
- Most applications/runs require large computer
resources - Models can be used in a dynamic fashion
8Mechanistic Approach
- Numerically intensive
- More likely to use scaling of processes with the
model - Expensive to run
- Often require a ton of input data to initialize
the model - Similar to Unix expert systems designed and
used by experts environments are not user
friendly - Most frequently used for
- What if scenarios
- Theory validation
- Examples
- Sorkam and Ceres crop models
- Ecosys ecosystem growth model
9Limitations
- Empirical
- Accuracy often rapidly degrades with time
- Limited flexibility of application
- Fixed formats
- Mechanistic
- High overhead/cost
- Nerd factor
- Requires intensive validation for acceptance
10Daisyworld handout and demonstration
- http//www.acad.carleton.edu/ curricular/GEOL/Dave
STELLA/ Daisyworld/daisyworld_model.htm - http//www.gingerbooth.com/courseware/daisy.html
11Photosynthesis
- Introduction to fundamental processes
- An example
- Overview of diversity a few cool case studies
that really screw things up
12Photosynthesis
- The process by which ALL carbon in living things
is captured - It is the capture of light energy and subsequent
storage of that energy in biochemical form - Stored biochemical energy is then used to make
biomolecules (carbs, proteins, etc..) - Generally follows the following equation
- 6 CO2 12H2O light? C6H12O6 6O26H2O
- Start counting the variables that go into
modeling photosynthesis
13Anatomy of a leaf
14Photosynthesis requires energy!
15Actually runs in 2 major steps
- Light reactions light is used to generate a
chemiosmotic gradient across a biomembrane.
Gradient drive production of ATP, the energy
storage molecule of all living things (kinda like
a battery) - Light independent reactions Energy stored in
ATP is used to assimilate carbon into biomolecues
16The light reactions
- Chlorophyll is the primary light gathering
pigment for most photosynthetic organisms. - Carotenoids are protection pigments that prevent
chlorophyll and the photosynthetic apparatus from
being damaged. - Both chlorophylls and carotenoids act in concert
as antenna complexes. - Solar energy, captured by many pigment molecules,
flows to the reaction center, similar to rain
drops collecting on a funnel. - Through a complex set of electron transfers and
chemical reactions, protons are released in the
lumen. - Chemiosmotic gradient dictates that the protons
will flow towards the stroma and drive ATP
synthesis.
17A few illustrations to help out
18(No Transcript)
19How photon capture works
20Its predictable Determining energetic
capacitance using fluorescence
21Chlorophyll activity for normal irradiance
22Light reactions take-home message
- The efficiency of photosynthesis, as described by
reaction center activity, is directly dependant
upon pigment concentration. - The rate at which the process occurs is dependent
not only upon light intensity, but the efficiency
of all involved mechanisms and molecules - Environmental stress, eg., limiting NPK and water
will directly impact the formation of
biomolecules used in the above and therefore
reduce photosynthetic capacitance
23Light independent reactions
- Occur in the absence of light
- Require chemically stored energy generated from
the light reactions - Involve carbon fixation from bicarbonate (the
available form in aquatic plants or as dissolved
in the mesophyll in terrestrial plants) - Generally occurs through 1 of 3 metabolic
pathways - C3
- C4
- Crassulacean Acid Metabolism (CAM)
24General pathway
- CO2 enters the leaf through the stomate
- CO2 equilibriates in the mesophyll as bicarbonate
- Bicarbonate is the form of carbon used by the C3
and C4 PCR cycles! - Temperature effects equilibrium of CO2 and
bicarbonate
25C3 Photosynthetic Carbon Reduction (PCR) Cycle
- So named because the primary product is a
3-carbon molecule called glyceraldehyde
3-phosphate
26Significance of RuBisCO
- The primary carboxylating enzyme for C3 plants is
Ribulose 1,5 bisphosphate carboxylase-oxygenase
(RuBisCO) - Rubisco can account for as much as 50 of
soluble leaf protein - as such it is the most
abundant protein in the world! - The active binding site of this enzyme can be
occupied by either CO2 or O2
27C4 Cycle uses carbon concentrating mechanism and
structural modification
28Kranz anatomy
29The geography of it all
- All photosynthetic types have been reported on
every continent except Antarctica, in every
ocean, and in freshwater - Of the 275,000 species of vascular plants, 93
are estimated to be C3 whereas 1, or about 2000
species, are estimated to be C4 (the remaining 6
are CAM) - Land coverage for each subtype are remotely well
documented, but indications are that speciation
percentages are misleading - Corn, sugarcane and sorghum are the major
agronomic crops which use C4 photosynthesis. - These crops may account for as much as 35-40 of
cultivated land in North America (of which 40 of
the land area is estimated to be cultivated). In
other words, as much as 16 of North Americas
land mass is occupied by C4 plants!
30The modelers woes
- Even if we can successfully model and scale
processes from the biochemical to the landscape
level, it is nearly impossible to capture the
diversity - Were we able to capture all of the diversity, no
data exists by which we could validate the model - Modeling living organisms requires an extensive
background - Computer science
- Biology
- Chemistry
- Physics
- Climatology/meteorology
- Mathematics
31C Determine photosynthetic type, implement C4
front end C in loops 900-gt500 or jump to C3 loops
2900-gt2500 C Loop structure is as follows C
900 branch level loop C 800 leaf level
loop C 700 layer level loop C 600
azimuth level loop C 500 inclination level
loop C 400 time step loop C
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IF(ARLF(K,NB,NZ,NY,NX).GT.1.0E-64)THEN
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ARLF(K,NB,NZ,NY,NX))
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,NB) ETGRO4(K,NB)ETMX(NZ)ETDN4(K,NB)TFN1
CBXN4(K,NB)(CO24-COMPL4(K,NB))
/(ELEC(NZ,1)CO2410.5COMPL4(K,NB)) DO
700 LNC,1,-1 IF(ARLFL(L,K,NB,NZ,NY,NX).GT
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IF(PAR(N,M,L,NZ,NY,NX).GT.0.0)THEN
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VL4SURFX(N,L,K,NB,NZ,NY,NX)TAUS(L1,NY,NX)
32World record holders are model killers!
- E. farinosa (brittlebush) highest recorded
transpiration rate up to 10 gallons of water
per day - A. palmerii (pokeweed) highest known
photosynthesis rate up to 304 grams of CO2 per
square meter of leaf area per day (or about 3-4
kg per plant)
33Geographic inspiration Encilia Farinosa
(brittlebush)
- During the winter, E. farinosa has relatively
large green leaves. - Photosynthesis occurs at is annual maximum rate.
- Leaf absorptance of total solar radiation is
0.50 - Leaf surface is said to be glabrate.
34Trichomes!
- During the summer, leaves are small and have a
gray appearance - Trichomes, pictured at right, are three celled
structure that shield the surface of the leaf. - Total solar absorptance is 0.09
35Another cool example Yucca brevifolia (Joshua
Tree)
36Adapted to solar zenith angle
37A prickly final example Cholla
As some of us have had the misfortune of
experiencing, cholla are covered with needles
that reduce incident solar radiation by as much
as 60
38Conclusion
- How many variables did you come up with?
- Modeling is as much an art as a science
- Must learn when to employ which approach
- Must understand assumptions being made
- Must be creative
- Biotic factors greatly impact climate/weather
modeling - Carbon, nitrogen, and water cycles
- Albedo
- Surface energy balance