Interests
and a bit of history: I am a plant
physiological ecologist, particularly interested in:
* plant
resource use (water use, drought physiology and ecology, mineral nutrition,
photosynthesis) and evolved strategies of resource use
* global
change biology, and extreme events as shaping physiology, ecology, and
evolution of plants
My
background is in chemical physics, so that I take a strongly quantitative
approach to these topics. I construct a lot of mathematical models
(process-based models) to generate testable hypotheses and to interpret
experimental results. I'm more-or-less systematically
posting many of the models - in Fortran, QuickBASIC,
Excel, and BASIC-52 for single-chip computers (Dominos; handy for compact
field dataloggers).
My group
and I work on a variety of systems - virtual/general models "in
silico," as well as in the field in desertified grasslands (including the Jornada Experimental Range, an LTER site – it can be hot, but also beautiful) and riparian forest in New
Mexico.
I teach
or have taught courses in general biology, ecology, plant ecology, biophysical
ecology, plant physiology, physiological ecology, physiology lab (animal
- plant - microbial), biological
modelling, scientific instrumentation, biological numeracy, and global
change. I appreciate the many graduate and undergraduate students who have
co-generated my research along with faculty colleagues. On the other hand,
with no apologies to instructors offering students preparation for (visual)
media careers, I offer some thoughts on impediments to learning, in what
I title
"Television,
fundamentalists,
and
cocaine."
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My full CV is here.
PowerPoint
presentation, The low-carbon, energy-efficient
world: opportunities blossoming
for us in the US, given at NMSU for Focus the Nation teach-in, 31 Jan.
08. It's big (8+ MB), so be prepared to wait as it downloads. It's copyrighted
by virtue of my having written it, so acknowledge me if you use pieces
of it. Thanks. Please note that I used many images from other sources.
The attributions are imbedded
in the JPEG information for many of them. Others are noted at the end of
this paragraph. Abbreviations are: CSM = Christian Science Monitor (the
greatest paper I have found for world news and environmental news; HCN
= High Country News (best paper for news on the U. S. West); NatGeog -
National Geographic; SciAm = Scientific American. Attributions not imbedded:
Radiative forcing bar graphs: SciAm AUg. 07, p. 67. Unplugging a glacier
(1st version): NatGeog June 07, pp. 64-65. Biofuels_good_and_bad: NatGeog
Oct. 07, cover. Malaria incidence: NatGeog July 07, pp. 44-45. Hybrid car
technology: SciAm Apr. 06, p. 75. Ocean acidification map (1st version):
SciAm Mar. 06, p. 64. La Luz power plant, one row of mirrors:. SciAm Jan.
08, p. 65.. US solar power plan for 2050: ditto, pp. 66-67. PV plant, Springerville,
AZ: ditto, p. 68. Solar power map #1: ditto, p. 69. La Luz plant, fuller
view: ditto, p. 72. Geol. injection, Algeria: SciAm July 05, p. 55. Unplugging
glacier (2nd version): SciAm Feb. 08, p. 64. Superconducting grid for elec.
power: SciAm July 06, p. 80
Latest
opinion piece:
Jumping
into biofuels - not such a good idea? An open letter to Senator Jeff Bingaman
(D, NM)
Current emphases:
Nitrogen dynamics in plants and soils
Where are the nitrogen reserves that desert plants can
tap?
Regrowth
of creosotebush (Larrea tridentata)
after detopping is thick and lush; compare the
foreground plant with the sparse, yellow-green undisturbed plants
Coarse roots hold the most N,
inside the plant! Graph from M.S.
student Randy Fowler
What controls nutrient delivery to plants, especially in
our semiarid ecosystem?
Does
mass flow (transpiration) help? No!
The
combined equation for massflow and diffusion
can solved for nutrient concentration at the
root surface; this can then be linked to carrier-uptake
kinetics to estimate , and, subsequently, uptake
The
relevant comparison: uptake with and without massflow à no significant difference
Is N limiting in our desertified grassland with its
islands of fertility under shrubs? Very
unlikely!
Creosotebush
(Larrea tridentata) leaves have 4 to 5 times more N than needed for photosynthesis
We are
starting to track this down in the field – Ph. D. student Shigang Liu
Does investment in roots help with relative growth rate
and ultimate fitness? Surprisingly little,
for nutrients, and the optimum root::shoot ratio is always
near 1 (see Gutschick and Kay, 1995, in my CV)…or is it, when we
consider water also? (Optimization model for RGR,
balancing water uptake and transpiration)
How does plant N content drive growth rate, and how does
growth rate feed back to limit N uptake?
For one,
limitation on meristems caps growth but
lets luxury N accumulate – from a collaboration with Jim Pushnik, Cal
State, Chico
N content has to drop at high CO2, as a simple consequence of functional
balance between root and shoot
Let’s
look deeper from now on
Plant water balance, up to landscape level
Plant roots do “hydraulic redistribution”
between soil layers
This
probably helps store deep water that keeps plants going in long droughts
Does HR
also help support grasses growing under desert
shrubs? Ph. D. student Mark Robertson thinks we need
to look hard
Managed water supplies are getting short; we need
biophysical models of crop water use
that allow explicit optimization of water-use
efficiency, light interception,
and N use – the models need a mechanistic basis but simplification for
real-time use - a raft of people worked on this, including Prof. Ted Sammis,
postdocJunming Wang, and undergraduate Luke Simmons from our companion
Dept. of Plant and Environmental Science, postdoc Alan
Andales (now at the USDA, Fort Collins), and Prof. Dave
Miller (U. Conn.)
What’s the water balance of the landscape?
On
“natural” landscapes, how do runon and runoff redistribute water
and consequently pattern vegetation and its rain-use efficiency? (Example of banded vegetation, though not from the Jornada)
Remote sensing of evapotranspiration is a key need. We are looking to improve the surface energy-balance algorithms to do this
A good
part of remote sensing is also knowing what vegetation is down there, at the
species level of detail.
Can we
use high-resolution aerial imagery in image
analysis (say, Feature Analyst in ArcGIS) to recognize
species (and know their height for aerodynamic roughness)? Ph. D. student Isabella Mariotto works on this in the field and at the
computer
Extreme events, and the rapid rise of atmospheric CO2
as an extreme event
Hormoz BassiriRad from the University of Illinois at
Chicago and I have taken a hard look at
how extreme events can be defined and studied
effectively and how they leave their mark on the physiology and
population genetics of organisms, especially plants
C3 and C4 plants respond
differently to elevated CO2….but
even among C3’s, the diversity of responses is great
None of
this diversity is likely to be adaptive except by accident; selection for
adaptive responses to high CO2 ended long ago
Remanent
diversity in CO2 responses of C3’s à great diversity in multiple performance
measures (photosynthesis, resource-use efficiencies….) à the prospect of wide and
currently unpredictable shifts in distribution – “biogeographic
chaos”
A seasonal extreme: very hot soil and stems on summer
afternoons (the numbers
and thermal IR images tell the story)
Do some
stems die? Yes. Undergraduate Jeanne Tenorio tends field
instruments to find out how hot things get and we also use Mito-Tracker(R) dyes to detail where the damage is
Drought and warm winters stress our SW conifers and give bark beetles lots of opportunity to kill them
off (picture courtesy of DIRENet). The DIRENet collaboration led
by Neil Cobb at Northern Arizona
University has us all
working to understand this
Sharing the concern and the excitement: the course on global change that I teach
Links to courses for Spring 2007 semester
Ecology - BIOL 301
Syllabus is here
MWF
1:30-2:20 PM in Hardman Hall, room 114
Course
registration number (CRN) 12788
Global Change (Special Topics) - Syllabus is here
BIOL
450, Section M03 & BIOL 550, Section M04
TuTh
8:55-10:10 AM in Science Hall, room 111
Course
registration number (CRN) 17704 (BIOL 450),
12847 (BIOL 550)
Some past PowerPoint presentations
(2004): CO2
sequestration; past
climate change; population
growth
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Recent postings
5 June 2007
The
physics of adminstration: 2007 Ignobel Prize
for the discovery that administrators are bosons - also, that they might constitute
the dark matter of the universe.
20 November 2006
Do
we know how plants are affected by elevated CO2 and, thus, where their
distributions are going to migrate in the next decades and centuries? It’s more complex than changes in
temperature and precipitation would indicate, even if we add in the fundamental
differences in responses between C3 and C4 plants. Here’s a preprint of an article in
press in Ecological Modelling.
* You can get a copy:
-
if you subscribe to Science Direct, you can download the entire article;
go to http://dx.doi.org/10.1016/j.ecolmodel.2006.08.013 The article can be cited before print
publication as: doi:
10.1016/j.ecolmodel.2006.08.013
- if you don’t subscribe, email me and I
can send you a copy for limited distribution
A couple of figures from the
article:
Joint
changes in photosynthetic rate, water-use efficiency, N-use efficiency, and
tissue N content, predicted from verified models; changes are diverse,
because plant responses in N uptake, stomatal control, and partitioning of N in
leaves are diverse. The changes cannot
be argued as adaptive; natural selection pressures for adaptive responses to
high CO2 have been absent for about 20 million years!
A diagram of the elaborate links of environmental conditions +
physiological parameters to final plant performance - why it has been a bit
difficult to make performance predictions
Title: Plant acclimation to elevated CO2 - from simple
regularities to biogeographic chaos
Abstract: Upon
exposure to altered levels of CO2,
plants express a variety of acclimations to CO2
directly, over and above acclimations to indirect changes in
temperature and water regimes. These acclimations commonly include increased
photosynthetic CO2
assimilation and increased water-use efficiency with reduced N content and
reduced stomatal conductance. The robust generic acclimations are explicable by
combining simple models of carboxylation, stomatal control, energy balance, and
functional balance. Species- or genotype-specific acclimations are overlaid on
these generic acclimations. Several such specific acclimations that are often seen
are readily incorporated in an extended model. These specific acclimations
generate a great spread of values in key performance measures of
photosynthesis, water- and N-use efficiencies, and rates of water and N use,
even among C3 species
that are the focus of this work. These performance measures contribute strongly
to relative fitness and thus to evolving biogeographic distributions. The
spread in fitness values is so large as to impend “chaotic” shifts
in biogeography (and, ultimately, evolution) that are not understandable with
models specific to species or functional groups; rather, a systematic study of
key physiological and developmental parameters is merited. Also merited is a
coherent extension of the model used here, or similar models, to include other
phenomena, including mycorrhizal associations, transience in resource
availability, etc.. The composition of useful approximate fitness functions
from physiological and allocational responses is a major challenge, with some
leads originating from the model. In the search to extract patterns of
responses, arguments based on the responses being close to optimal or adaptive
will be misleading, in view of the absence of selection pressure to perform
adaptively at high CO2 for
over 20 million years. I offer suggestions for more useful research designs. Keywords: CO2; acclimation;
models; biogeography
31 March 2006
Spreadsheet for estimating the contribution of mass
flow to nutrient uptake. The adaptive value of transpiration for aiding
nutrient uptake by roots is controversial - transpiration per se, and
especially nocturnal transpiration in arid systems that seems so
maladaptive. I developed an uptake model
with both diffusion and mass flow, to quantify the role of mass flow. I also developed a schema for estimating all
the parameters in the model, from a wide variety of alternative data
sources. The model and the data schema
are embodied in a spreadsheet posted here.
A manuscript with full discussion has been submitted to Plant, Cell
& Environment.
29 August 2005
Excavating plant roots with the AirSpade
We have used the AirSpade to excavate entire root systems of
creosotebushes (Larrea tridentata). The ads at Concept Engineering
(http://www.air-spade.com) and the testimonials therein indicate that fine
roots are retained, while bulk soil is blown away by air bursts at Mach 2 (ca.
2500 kph!), generated by what appears to be the air equivalent of a hydraulic
ram. It really works! Here are images of fine roots left after the
bulk soil is blown away. Here, too, is a movie (.avi format, commonly
used; about 4.5 MB) showing graduate student Randall Fowler enjoying fun with
the dirt.
26 October 2004
A primer on
carbon-isotope discrimination in studies of plant performance, from leaf to
globe: how
discrimination works, and what it tells us
about plant performance - including some novel simple
formulae for plant responses to the
environment (PDF:
click here)
15 October 2003
Tansley
review, Extreme events as shaping physiology, ecology, and evolution of plants:
toward a unified definition and evalution of their consequences [New
Phytologist 160 (2003): 21-42]. Please note that there are a few
typos in the final article:
*
Page 26, column 2, line 10: "changes of
-50% in A and +70%in E" -> "changes
of -50% in A and 70%in E"
* Page 26, column 2, line 22: "raising W to13%" -> "raising W by13%"
* Page 28, column 1, line 29: "Costs of acclimation are also" -> "Costs of adaptation are
also"
*
Page 31, column 2, last line: "modest average value of
0.16" -> "modest average
absolute value of 0.16"
Gas-exchange data, from studies at the
Chequamegon National Forest, Wisconsin, 1997-2000
*An
overview of the project is given below.
*The
data, and a detailed discussion of the data (fields, methods of calculation,
locations in data directory), are in the directory linked here. You'll need
a password to get here; please email me at the address above. The
data are mostly in Excel, spreadsheets, with a few in Quattro Pro).
- For a guide to the types of data we have, look in the file data_explan.txt.
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Full curriculum vitae
Other postings
* A short course on color theory
(PDF format), for analyzing digitized images. It's intended as a tutorial
for students in our research group; it
may be useful more widely.
* An article on the pros and cons of digital cameras and
film-based cameras in ecological research. This appeared in the Bulletin of the Ecological Society of
America in July, 2002. This preprint is posted, with the OK of the
ESA. Note of March, 2007: the
information is dated! For an updated
view, please feel free to contact me.
Technological Tools editor, David
Inouye. It's here as a Word 97 file,
or as a PDF file, or as a PostScript
file, or as an HTML file.
* A model of stomatal conductance (and CO2 assimilation
and transpiration) as controlled by
1. the leaf aerial environment (the
Ball-Berry model, coupled with leaf energy balance and the Farquhar - von Caemmerer - Berry model of CO2 assimilation) and
2. a water-stress signal (ABA) from roots (Francois Tardieu's model,
basically).
Fortran 77 code (flat
ASCII file)
Sample
data input for Fortran program (flat ASCII file)
Narrative:
explanation of the model (PDF format; 10 pages -
or PostScript)
* A functional-balance model of plant mineral nutrition,
particularly aimed at predicting plant performance at elevated CO2
1. Narrative description of the model (PDF format, or pages in GIF format: 12345678)
2. The Fortran-77 code,
as flat ASCII text
Recent presentations, some of which include
graphics (not active yet; sorry)
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What else is on this site?
Extended descriptions of some models
and other research projects
A functional-balance
model of mineral nutrition and photosynthesis, applicable to
predict plant responses to elevated CO2; supports our publication in Oecologia
Color theory: a
guide to color and its digital representation; used to teach members of
our research group about analyzing digitized images to estimate vegetative
cover
and (we hope, soon! species identities of shrubs in aerial photos
Many computer programs
in Fortran, QuickBASIC, Excel, and BASIC-52
URLs for some Web sites that I've found to
be very useful
Math and more:
SOS math site: can't remember some key bit
of analytic geometry, differential equations, etc.? Find tutorials here
Geography:
The equation of
time (correcting local mean solar time to real solar time)
Magnetic declination
- the ins and outs of using it in field work, and more
Maps, maps,
maps
World time zones
Telephone country
codes and city codes
Patent information: find out how the
principles on which the device you're buying is really based
Weather site - its for New Mexico as far as
data go, but there are extremely useful programs to calculate ET, etc.
Funding agencies - pages
where they post RFP's for their programs
NSF (they can be coy, and old
programs may continue with what look like outdated postings)
NASA
DOE (sometimes it
comes up "no opportunities;" this is misleading)
USDA
(their server linked to research opportunities has been abolished 23 Nov. 2001;
look for a new one)
Computing:
Software: GNU (free, high-quality software
for LINUX, UNIX, and UNIX look-alikes)
Freeware for Solaris OS
Numerical recipes in C...and in Fortran
Sun documentation
Fortran-to-C
interface (instructions...and a tutorial in Powerpoint)
Fortran
to C converter (shareware, $10; I haven't tried it yet)
ANSI C library for CGI programming (I
haven't used it yet)
Fortran interface to
HTML, via CGI (ditto)
X-windows available for
PC's, I hope (haven't installed these yet)
Hardware,
mostly: Comparison
shopping Psion palmtops (neat devices for field
datalogging and more)
Electronics parts: Newark Electronics
Digi-Key PartMiner (find parts from many
distributors)
And if you're a bit
bored: La ferme aux
crocodiles My wife and I visited la ferme in 2006; it is a
fascinating place.
The co-owner/founder,
Luc Fougeirol, talked with us about 20 minutes.
They don’t seel croc skins or meat; Luc and his staff love
live crocodiles.
They sell some
adults to zoos and some eggs to embryologists.
The
place is huge, immaculate, and fascinating, with lots of documentation.
Computer programs in
Fortran, QuickBASIC, Excel, and BASIC-52 (not ready yet - 23 Nov. 2001)
For modelling water and nutrient fluxes in
plants and whole stands, light interception,
energy balance, and more
For designing and operating novel sensors,
including those we have built ourselves
(very small leaf-mountable light
sensing; branch sapflow gauges; weather station with
radiative sensing of soil T and
more; thermistor-based T-profilers; multiplexed
thermocouples)
For processing data (leaf gas exchange data,
to photosynthetic capacity and stomatal
control parameters)
Useful subroutines, for solar angles, Julian
date, water-vapor pressure, etc.
Some are "production models" we use in
our work, others are debugged but not
prettified, though most are extensively
commented internally
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**** No animals were harmed in the creation of this Website1 ****
1Except those affected by CO2 emissions at power plants2
supporting my laptop's operation, and yours
2 Unless they used renewable sources such as wind or
biomass3
3 But biomass takes land area, so there go some animals,
and wind turbines kill birds...so,
next time, I'd better
power this all from a stationary bicycle
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