[PCA] Need info on std. template to profile life cycles of angiosperms -- reply to Gena Fleming's comments

[bmacbryde at netscape.net]

Thanks for you inquiry, but no, the impetus for this standard template 
is not to do an ecological evaluation of a crop, either iwithin or 
beyond its planned area of use. Our interest is to have a simple 
profile to characterize the basic life history dynamics of a species. 
Also, we do not plan to have a relational database, simply written crop 
profiles (crop agrobiology templates) based on the standard profile. 
The organizing idea is not to look for species uniqueness, but the 
commonality.

Of course, at some point the standardization will be inadequate, and we 
expect to have minimal text fine-tuned to the crop. The great 
complexity of the potential and likely interactions of a crop with its 
environment, and of particular varietal traits whether the varieties 
have been genetically engineered or conventionally developed, are way 
beyond the scope of a template.

The reason for this inquiry on this listserv is to capture plant 
people's knowledge and experience so that we don't waste time 
reinventing the wheel for a basically simple idea and need. Profiling 
rare plants, or medicinal plants, or weeds and invasives, might 
possibly have a similar high-level standard template.

The many complex and broader topics and issues raised in your email 
would have to be addressed carefully in different ways, not as part of 
the standard plant template idea. I hope this clarifies the subject in 
relation to your thorough and deep c
oncerns.

Thanks,

Bruce MacBryde, Ph.D.
USDA/APHIS
Riverdale, MD

-----Original Message-----
From: Gena Fleming <genafleming at gmail.com>
To: bmacbryde at netscape.net
Cc: peterar at berkeley.edu; native-plants at lists.plantconservation.org; 
bruce.macbryde at aphis.usda.gov
Sent: Mon, 29 Dec 2008 2:01 am
Subject: Re: [PCA] Need info on std. template to profile life cycles of 
angiosperms -- reply to Peter Rauch's inquiry

Noting that all the plants you mentioned have been genetically 
engineered, and APHIS is responsible for processing their
Deregulation 
(see:http://www.aphis.usda.gov/publications/biotechnology/content/printab



le_version/BRS_FS_biodereg_02-06.pdf ), would another more transparent 
way of saying this perhaps be that you are trying to limit (or at least 
justify that you have tried to assess the inevitable) contamination of 
other crops as well as indigenous species (such as guayule) by 
genetically engineered plants (including but not limited to the few you 
mentioned here) that are being evaluated for field trials and 
eventually complete deregulation by the USDA?  Plants that may contain 
vaccines, hormones or other pharmaceuticals;  herbicide tolerance, 
industrial chemicals or pesticides, or have been engineered for partial 
sterility?   So you want to know what other species they might cross 
pollinate with (spreading the contamination, including spreading of 
fertility problems)?  Or whether the genetically engineered seeds might 
lay dor
mant in the ground for years and years and then suddenly pop up 
contaminating other plants unexpectedly?

What about the increased horizontal gene transfer that can be expected 
with transgenic plants?  What about animals that may eat the seeds and 
carry them to diverse locations?  What about pollen and seed dispersal 
through tornadoes and floods?  What about pollen that kills 
pollinators?  What about animals that wander or fly into fields and 
inadvertently consume vaccines and human hormones now growing in these 
plants?  What about cold tolerant eucalyptus and other trees that could 
now become invasive?  What about Bt toxin that kills off beneficial 
soil micro-organisms?  How do we get our heirloom crops back when they 
are contaminated with DNA from other genera and kingdoms?  How do we 
ever reclaim the native guayule?  How do we assess whether a forest 
tree has been contaminated by a genetically altered tree of the same 
species?  How can we trace genetic contamination?  How can you possibly 
account for all the variables when growing these plants in the open?  
And all those genetically engineered trials that are simply designated 
by APHIS as "CBI" (confidential business information), I guess we'll 
never know what they have been genetically engineered to contain.

Nature is an integrated system.   How can a database possibly account 
for all the potential effects from the changes bei
ng introduced by 
genetic engineering:

http://www.isb.vt.edu/cfdocs/isblists2.cfm?opt=8

And yet you write, "We then envision preparing brief (several page) 
biological documents (profiles) on individual species, which would 
adhere tightly to the standard template. The results for a species 
would be something like the Cliffs Notes, but much shorter."

Corporations are corrupting our world's precious life forms, patenting 
them as commodities, placing the entire regenerative and reproductive 
capacity of life on this planet at risk, and your concern is compiling 
documents on species that are "like Cliffs notes, but much shorter"?

The USDA is responsible for allowing this to happen.  But let it not be 
in my name.

Gena Fleming

2008/12/26 <bmacbryde at netscape.net>

Thanks for the inquiry and comments.

First the easier clarification:  We've no plans to have a relational 
database for this, just static information. However, databases can help 
to narrow down categories to a functional minimum, which is what we'd 
like to start with in a standard agrobiology template. So, maybe 
someone has done the general profile work for a plant database, and a 
manual would give the summary.

Second, the basic use envisioned is just internal guidance, so that an 
array of people with different backgrounds can quickly and 
simplistically understand the basic dynamics of the species, which are 
often major crops such as corn, rice, co
tton, rapeseed/canola, onion, 
etc., but include a range of other species, e.g. safflower, guayule, 
plum, and poplar. Reproductive concerns relate to placement of crop 
varieties (experimental or breeding strains) so they don't 
cross-pollinate with other varieties, don't come up as volunteers in 
subsequent crops, and whether they could be dispersed beyond the 
agricultural area.

The idea is not to go far into agroecological aspects, but recognize 
potentials. When fine-tuning refinements are needed for a particular 
species or planting situation, the idea is that they would just be 
added beyond the template. Also, if some new major fact became know, 
e.g., long seed dormancy in a crop thought to not have it, the crop 
profile would be changed, but by some internal staff review process, so 
that each staff person wouldn't be morphing the crop profile into their 
own version.

Thanks.
Bruce MacBryde
USDA/APHIS
Riverdale, MD

E-mail: bmacbryde at netscape.net

-----Original Message-----
From: Peter Rauch <peterar at berkeley.edu>
To: native-plants at lists.plantconservation.org
Sent: Tue, 23 Dec 2008 11:46 am
Subject: Re: [PCA] Need info on std. template to profile life cycles of 
angiosperms, emphasis on reproductive dynamics

Just two brief comments...

You say:
"The impetus behind this idea is to organize and focus internal 
information
better, and limit the categories to those we really need."
and,
"just to capture the main categories to 
profile the potential dynamics 
of such
species."
and in the subject line,
"to profile life cycles of angiosperms, emphasis on reproductive 
dynamics".

But, organize and focus better for what purposes ?   What is it that 
you really
need the data for ?  The "potential dynamics" of a (mainly common crop 
plants
and several plantation trees) species includes a world of possibilities 
--how is
this information intended to be used ?

That will help (you and others) determine what might constitute a 
"relatively
standard set of parameters to indicate basic life cycles of flowering 
plants in
the United States, focusing mainly on common crop plants and several 
plantation
trees".

"...envision preparing brief (several page) biological documents 
(profiles) on
individual species..."

Who is expected to read (be served by) these documents, and for what 
purpose(s)?

Second, you refer a couple of time to "relational database".  I suggest 
that
_how_ the information is stored and accessed is a far second (but then 
very
important) consideration, after the full details are understood of "what
purposes" and "what data will serve those purposes."

Peter

At 09:48 08/12/22, you wrote:

Where I work (USDA/APHIS), we are in early stages of planning to
prepare and/or fine-tune and adopt a relatively standard set of 
parameters (which
we are calling a template) to indicate basic life cycles of flowering 

plants in the
United States, focusing mainly on common crop plants and several 
plantation
trees. The impetus behind this idea is to organize and focus internal
information better, and limit the categories to those we really need. 
This would
not be for a relational database. We then envision preparing brief 
(several
page) biological documents (profiles) on individual species, which 
would adhere
tightly to the standard template. The results for a species would be 
something
like the Cliffs Notes, but much shorter.

I would appreciate information on existing standard formats or 
templates of
this general type. For example, parameters of interest to put in the 
standard
template include: native or introduced; annual, biennial, herbaceous or 
woody
perennial; modes of pollination (wind, insects, both, percentages,
characteristics); outcrossing, selfing, both (and rough percentages); 
isolation
distances to maintain genetic separation between cultivated strains 
(cultivars);
vegetative propagation (kinds, extent); modes of dispersal (and
characteristics); seed dormancy (practical characteristics, longevity);
potential free-living strains (weedy strains or relatives, other taxa); 
etc.
Details on morphology are not a focus.

Occasionally others have made thorough efforts to capture life history
variation in flowering plants, for example in standardizing categories 
for a
relational database. I'd much appreciate suggestions on major 
comprehensive
papers or similar efforts, whet
her they relate to wild plants (native or
naturalized), horticultural plants, silvicultural plants, or 
agricultural
plants. The idea is not to elaborate on the infinite variation, but 
just to
capture the main categories to profile the potential dynamics of such 
species.

Thanks, Bruce MacBryde, Ph.D.
USDA/APHIS
Riverdale, MD

E-mail: bmacbryde at netscape.net

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