permaculture

["Lawrence F. London, Jr." <lfl@intrex.net>]

:
Horizontal Gene Transfer is between species, which is still in many
place thought impossible.  It's happening, a lot . . .

Gene Ecology Guide to: Measuring Horizontal Gene Transfer
<http://www.inbi.canterbury.ac.nz/Documents/Guides/GE_guide_to_TTEC_2004.pdf>
:
|
:
http://www.twnside.org.sg/title2/service130.htm

THIRD WORLD NETWORK BIOSAFETY INFORMATION SERVICE
6 September 2004

Dear Friends and colleagues,

Re: Papers on horizontal gene transfer point to flaws in monitoring

Two papers recently published in Nature Biotechnology indicate that current 
methods for monitoring horizontal gene
transfer (HGT) from transgenic crops to microorganisms are very problematic 
and too insensitive to detect HGT. As such,
even though monitoring efforts so far have largely failed to observe HGT 
events in the field or have deemed frequencies
too low or too rare to pose risks, this is clearly not the case.

The analysis by scientists from the New Zealand and Norwegian Institutes of 
Gene Ecology critiques contemporary HGT risk
assessment of transgenic crops. [Heinemann JA and Traavik T. “Problems in 
monitoring horizontal gene transfer in field
trials of transgenic plants” Nature Biotechnology 22, 1105-1109 (2004).] 
Using the evolution of penicillin-binding
proteins as an example, they show that current experimental limitations 
preclude measuring HGT with the sensitivity
necessary to dismiss any eventual environmental harm. A major implication is 
that HGT from transgenic crops to soil
microorganisms could still have an environmental impact at a frequency 
approximately a trillion times lower than what
the current risk assessment literature estimates the frequency to be. The 
analysis also suggests that current methods of
environmental sampling to capture genes or traits in a recombinant microbe 
are too insensitive for monitoring evolution
by HGT. Warning that HGT in microorganisms can have significant negative 
health and environmental consequences, such as
increased antibiotic resistance in some bacteria, they conclude: “Contrary to 
the conclusion of others, we believe that
new approaches to monitoring environmental scale applications of transgenic 
organisms are urgently needed.” They suggest
that such an approach would be a decision to consider the scientific 
uncertainty surrounding environmental applications
that introduce HGT risks (e.g. growing transgenic crops) and adjust the pace 
of their release to match developments in
scientists’ ability to monitor at relevant sensitivities, recognising that 
the technology of safety monitoring lags
behind that of genetic engineering.

The second paper, by scientists from the University of Tromso, 
Norway/Norwegian Institute of Gene Ecology, and from the
University of California, Berkeley, also finds flaws in HGT monitoring 
approaches, due to limited experimental
parameters. This paper by Nielsen KM and Townsend JP is on “Monitoring and 
modeling horizontal gene transfer” Nature
Biotechnology 22, 1110-1114 (2004). Using examples of studies that have 
attempted to monitor HGT through field or gut
sampling of bacteria exposed to transgenic plants, they show that real-time 
monitoring of HGT processes in complex
microbial communities has been severely limited by methodological 
constraints. Such attempts have also relied on weak
assumptions of the nature and scale of the process. The scientists state that 
realistic estimates of HGT rates are
rarely obtainable, nor are they predictive of the long-term effects of 
infrequent HGT events. They argue that risk
assessment should not focus on the frequency of HGT, but instead, since rare 
HGT events cannot be excluded, on the
effect of the horizontally transferred transgene on the survival of the 
bacterial transformant. Evidence shows that the
overwhelming majority of HGT events in nature are know to be  eleterious to 
the bacterial transformant, as such it is
also likely that HGT events from transgenic plants would cause deleterious 
effects.

We reproduce below the abstracts of the two papers in Nature Biotechnology. 
The paper by Heinemann and Traavik can also
be found at 
http://www.nzige.canterbury.ac.nz/documents/Heinemann_Nat%20biotech_2004.pdf

A separate paper “Gene Ecology Guide to Measuring Horizontal Gene Transfer”, 
published by the New Zealand Institute of
Gene Ecology, is a summary critique of the effectiveness of attempts to 
measure HGT from transgenic plants to soil
microorganisms, and of extrapolations of those studies to conclude that the 
risks of HGT are low or can be ignored. As
such, claims that HGT has been studied and found to not be a significant risk 
are not justified. In such cases, the
absence of evidence of risk can easily be explained by extrapolations from 
the results of experiments that were simply
not suited for making a proper assessment of risk. The paper can be found at
http://www.nzige.canterbury.ac.nz/documents/GE-guide-to-measuring-HGT.pdf

With best wishes,

Lim Li Ching
Third World Network
121-S Jalan Utama
10450 Penang
Malaysia
Email: twnet@po.jaring.my
Website: www.twnside.org.sg

REF: Doc.TWN/Biosafety/2004/B

Item 1
Nature Biotechnology  22, 1105 - 1109 (2004)
Published online: 31 August 2004; | doi:10.1038/nbt1009

Problems in monitoring horizontal gene transfer in field trials of transgenic 
plants
Jack A Heinemann1, 2 & Terje Traavik2

1    New Zealand Institute of Gene Ecology, University of Canterbury, 8020, 
Private Bag 4800, Christchurch, New Zealand.
2    Norwegian Institute of Gene Ecology, POB 6418, N-9294 Science Park, 
Tromsø, Norway.

 Correspondence should be addressed to Jack A Heinemann 
jack.heinemann@canterbury.ac.nz

Transgenic crops are approved for release in some countries, while many more 
countries are wrestling with the issue of
how to conduct risk assessments. Controls on field trials often include 
monitoring of horizontal gene transfer (HGT)
from crops to surrounding soil microorganisms. Our analysis of 
antibiotic-resistant bacteria and of the sensitivity of
current techniques for monitoring HGT from transgenic plants to soil 
microorganisms has two major implications for field
trial assessments of transgenic crops: first, HGT from transgenic plants to 
microbes could still have an environmental
impact at a frequency approximately a trillion times lower than the current 
risk assessment literature estimates the
frequency to be; and second, current methods of environmental sampling to 
capture genes or traits in a recombinant are
too insensitive for monitoring evolution by HGT. A model for HGT involving 
iterative short-patch events explains how HGT
can occur at high frequencies but be detected at extremely low frequencies.

Item 2
Nature Biotechnology  22, 1110 - 1114 (2004)
Published online: 31 August 2004; | doi:10.1038/nbt1006

Monitoring and modeling horizontal gene transfer

Kaare M Nielsen1, 2 & Jeffrey P Townsend3
1    Department of Pharmacy, Faculty of Medicine, University of Tromsø, N9037 
Tromsø, Norway.
2    Norwegian Institute of Gene Ecology, Research Park, N9294 Tromsø, Norway.
3    Department of Plant & Microbial Biology, University of California, 
Berkeley, California 947200-3102, USA.

Correspondence should be addressed to Kaare M Nielsen knielsen@farmasi.uit.no

Monitoring efforts have failed to identify horizontal gene transfer (HGT) 
events occurring from transgenic plants into
bacterial communities in soil or intestinal environments. The lack of such 
observations is frequently cited in biosafety
literature and by regulatory risk assessment. Our analysis of the sensitivity 
of current monitoring efforts shows that
studies to date have examined potential HGT events occurring in less than 2 g 
of sample material, when combined.
Moreover, a population genetic model predicts that rare bacterial 
transformants acquiring transgenes require years of
growth to out-compete wild-type bacteria. Time of sampling is therefore 
crucial to the useful implementation of
monitoring. A population genetic approach is advocated for elucidating the 
necessary sample sizes and times of sampling
for monitoring HGT into large bacterial populations. Major changes in current 
monitoring approaches are needed,
including explicit consideration of the population size of exposed bacteria, 
the bacterial generation time, the strength
of selection acting on the transgene-carrying bacteria, and the sample size 
necessary to verify or falsify the HGT
hypotheses tested.
: