Seeds of Distrust: The Story of a GE Cover-up explores the potential release of genetically modified (GM) corn in New Zealand in 2000 and alleged attempts by the government to cover it up. As New Zealand has very strict controls on the presence of GE organisms, the publishing of this book made genetic engineering (GE) a hot topic in the 2002 elections. Although Nicky Hager describes some dubious practices from the Labour government, the story in Seeds of Distrust is let down by a lack of science and ultimately loses sense of all proportion.
In late 2000 the Ministry for Agriculture and Forestry (MAF) and the Environmental Risk Management Authority (ERMA) were notified by seed company Novartis of the possible presence of a transgene in a sweet corn seed shipment. Initially Helen Clark took the position that the planted crops needed to all be pulled out and destroyed. Legislation was quickly rushed through in order to give the relevant government agencies the necessary authority. However, after meeting with representatives from the industry, the government became less convinced of any significant transgene presence and moved to adopt new rules allowing seed shipments containing up to 0.5% trangenes to be labelled GE free. The rational for this is PCR - the technique used to detect transegenes - has a certain lower limit of detection (for practical reasons). Additionally, some doubt was cast on the accuracy of the positive results which could have been due to sample contamination or a PCR artifact. Given the positive tests were less than the newly adopted 0.5% threshold, the government allowed the sweet corn to mature and enter the food chain. The Labour government kept the whole situation relatively low key in order to avoid spooking the public as a royal inquiry into GE was currently underway. This is the basic story that emerged for me after reading the facts presented in Seeds of Distrust - and it is a well documented book - however Hager has a different take.
Hager makes a big deal of the government meeting with industry to talk about the possible release of a GMO. Although I share his unease with the influence of corporations on government, in this case it was Novartis who initial detected possible transgene presence and it was their corn seed shipment which may have been recalled or destroyed, they needed to be involved in the early stages. Hager also focuses on the threshold level being set at 0.5%, he says the practical limits of PCR detection were actually 0.1%. Although, in principle, this meant the government was allowing up to fives times more GMOs into the country than was necessary, the overall level of transgene presence in the shipment of seeds was 0.04 - 0.08% and therefore below either measure. There was one test which reported a 0.5% transgene level but here his lack of science really lets Hager down as the rigour of the test is not defended at all. The story then continues with Hager doing everything he can to spin the downplay of the possible GMO release by the government into a deliberate cover-up of a definite GE food contamination. This is the weakest part of the book and I was not convinced anything particularly sinister was being perpetrated by the New Zealand government.
After reading this book I wanted to find out more about the science of the PCR tests that had gone on during this process. I found this press release by Dr Russell Poulter (now a professor of genetics at Otago University) who explains where the positive results came from. The ‘transgene’ detected was actually the nos terminator which can be associated with the actual transgene but can also be found in the common soil bacteria Agrobacterium. If this was an actual case of transgene presence then a 35S promoter sequence should have also been found by PCR as it is associated with the transgene but is not present in soil bacteria. It wasn’t. Given that Hager notes two of the samples were opened in the field, it seems likely these positive results were from contamination of the sample rather than due to a GMO. Removing these as false positives brings the presence of transgene down to an undetectable amount and eliminates most of the force in Seeds of Distrust.
Overall, Hager has written a book detailing behind-the-scenes decision making when governments behave in a less than exemplary manner. But given that the major premise of his book - GMOs were knowingly released by the government - is not well defended and likely false the whole thing reads like a storm in a teacup. Only worth reading if you are interested in the GMO scandal that hit around the 2002 election.
2/10.
Showing posts with label Biology. Show all posts
Showing posts with label Biology. Show all posts
September 09, 2011
September 01, 2011
Free GE
A recent story in the Dominion Post (Commercial benefits lacking in GE trials) reveals the genetic engineering trials being carried out by Crown Research institutions have lead to very few commercial gains. Plant and Food and AgResearch have paid over half a million dollars in application fees to ERMA and only one of the trials has resulted in royalty generating IP. To those familiar with New Zealand's restrictive requirements for GE research, this outcome is hardly a surprise.
Despite decades of safe use around the world, GE and GMOs remain contentious issues in New Zealand. The regulatory environment alone makes it difficult to carry out even basic research, let alone the commercial research which scientists are now being criticised for not producing. Anti-GE spokeswoman Claire Bleakley decries that the benefit of GE research being completed in New Zealand is lost to the overseas companies. But if private companies are the only ones paying for the research to be carried out then it makes sense they are the ones who reap the economic benefit. Basic funding for GE research is simply not available in New Zealand, the funding bodies know there is little chance any innovation made will be allowed to be used.
If New Zealand wants its scientific organisations to produce applied science using GE technology then it must:
1) relax the regulatory environment so that research time and money is not being consumed navigating expensive legislation
2) fund GE projects so the IP is not captured by overseas companies
3) open the New Zealand market to GMOs so that the benefits of this technology can be accrued here
There is very little risk and huge benefits to allowing GE research to be conducted more freely. The longer New Zealand clings to the anti-GE label, the more we miss out on the exciting commercial opportunities. Rather than be GE-free, let's free GE!
Despite decades of safe use around the world, GE and GMOs remain contentious issues in New Zealand. The regulatory environment alone makes it difficult to carry out even basic research, let alone the commercial research which scientists are now being criticised for not producing. Anti-GE spokeswoman Claire Bleakley decries that the benefit of GE research being completed in New Zealand is lost to the overseas companies. But if private companies are the only ones paying for the research to be carried out then it makes sense they are the ones who reap the economic benefit. Basic funding for GE research is simply not available in New Zealand, the funding bodies know there is little chance any innovation made will be allowed to be used.
If New Zealand wants its scientific organisations to produce applied science using GE technology then it must:
1) relax the regulatory environment so that research time and money is not being consumed navigating expensive legislation
2) fund GE projects so the IP is not captured by overseas companies
3) open the New Zealand market to GMOs so that the benefits of this technology can be accrued here
There is very little risk and huge benefits to allowing GE research to be conducted more freely. The longer New Zealand clings to the anti-GE label, the more we miss out on the exciting commercial opportunities. Rather than be GE-free, let's free GE!
May 28, 2010
Could you patent the sun?
One of the biggest enemies facing critical thinking and scepticism is that of personal bias. Bias is extremely easy to spot in other people, but notoriously difficult to spot in yourself. No one likes to think that they may be biased but everyone is, in one way or another. Bias often appears in science denialism where someone may be religiously biased towards a Biblical interpretation of the fossil evidence (for example) rather than towards the scientific explanation. The best we can do about our biases is recognise them and be extra vigilant when we come across evidence that conforms to our biased pre-judgements. Because bias has such an affect on our interpretation of evidence, scientists especially should try to limit the influence of such outside factors on their impartial research. Yet we see precisely the opposite occurring. As research and industry snuggle into a cosy relationship, scientists have become enamoured with their commercial partners.
The commercialisation of research has exploded in the fields of biomedical science and biotechnology, with industry poised to make millions, scientists are all too happy to take a cut of the action. However, money is a powerful motivator and researchers now have an added incentive to find certain result. The result which favours whatever corporation provides the funding. If scientists are being influenced by their source of funding, then it should be apparent in their results. Industry funded projects should find positive results more often than non-profit funding. Indeed, taking the example of pharmaceutical research, that is what we find.
Many scientific journals require the submitting authors to declare any conflicts of interest, for example being funded by the same company who owns the patent on the drug in question. Several statistical analyses have been done on the outcomes of these studies and the results should not be surprising to anyone who understands the effects of bias. In 2001 an analysis of 314 drug trials found that non-profit funded research was 3.5 times more likely to find a negative result than industry sponsored trials1. A 2002 study of 159 articles in the British Medical Journal, which requires that funding be declared, found that the authors' conclusions were significantly more positive in trials funded by for profit organisations compared with trials without competing interests (mean difference 0.48, P=0.014)2. A 2004 study showed that in 158 drug trials published in five leading medical journals results favoured industry funded studies by an odds ratio of 1.93. Finally, in 2003 a review selected 37 of the most rigorous studies and pooled their data. They found a statistically significant odds ratio of 3.6 favouring industry funded research4. This review also found that industry funding was associated with restriction on publication and data sharing if the results were negative.
One point to make about these analyses is that they are correlative only, causation could not be determined. Although the quality of the studies was controlled for (often poorer quality in industry funded trials) one possible explanation is that industry interests somehow pick pharmaceuticals that are more likely to succeed in trials. I can’t imagine how they would know beforehand which drugs have better prospects, but it is a possibility. More likely, however, is that the scientists performing these studies are influenced by the commercial factors at play in their research. These results are very reminiscent of ‘tobacco science’ where, for example, 94% of industry funded inquiry found no harm from second-hand smoke compared to just 13% of non-profit funded research. If correct, this interpretation is quite troubling. First, it means that consumers are being bombarded by new pharmaceuticals which are of questionable value over the old versions and in some cases, downright dangerous. Second, the reputation of science for impartiality and following evidence is being ruined by commercial interest by both outside companies and the scientists themselves. When the commercial bias of scientists is revealed, say through a drug recall or hidden financial contributions, the public starts becoming suspicious of these intellectual elites. In fact, the commercialisation of research could be contributing to the distrust of science, the growing interest in alternative medicine, and the rejection of genetic engineering.
Believe it or not there was a time when industry and academia where more or less separate. Scientists with relevant expertise might be given an honorarium to help overcome a particular problem or speak on a certain topic, but that was about it. Funding was largely provided by governments and scientists were free to explore myriad lines of inquiry, whether it might lead to a practical application or not. Even when there research could be commercialised, the scientists themselves would rarely have much to do with it. Their results were given away into the public domain. In 1954, Jonas Salk developed his vaccine against polio, when asked whether he would patent it he found the idea ridiculous replying, “Could you patent the sun?” Unfortunately, this attitude is found rarely in the field of biotechnology. Many exotic genes and interesting methods are often patented by the researchers who first discover them either preventing further inquiry or driving the cost of research even higher. This also makes the funding of science less attractive to the public sector that now sees less return for its investment.
Unfortunately, I don’t have any solutions for the problem. I just think the commercialisation of research makes an important contribution to the growth of science denialism and was worth highlighting. Patent law clearly needs a complete overall. I dislike attempts to own parts of nature - “to patent the sun” - but companies do need protection for their intellectual property. Similarly, industry funding research is having a negative impact on the impartiality of science, but there is no denying the benefits that have emerged from such partnerships. Perhaps blinding individual scientists to the source of their funding and preventing patents on natural products could go some way to removing this troubling commercial bias from academic scientists.
1. Yaphe J, Edman R, Knishkowy B, Herman J. The association between funding by commercial interests and study outcome in randomized controlled drug trials. Fam Pract. 2001 Dec;18(6):565-8.
2. Lise L Kjaergard & Bodil Als-Nielsen. Association between competing interests and authors' conclusions: epidemiological study of randomised clinical trials published in the BMJ. BMJ 2002;325:249 ( 3 August )
3. Bhandari M, Busse JW, Jackowski D, Montori VM, Schünemann H, Sprague S, Mears D, Schemitsch EH, Heels-Ansdell D, Devereaux PJ. Association between industry funding and statistically significant pro-industry findings in medical and surgical randomized trials. CMAJ. 2004 Feb 17;170(4):477-80.
4. Justin E. Bekelman, AB; Yan Li, MPhil; Cary P. Gross, MD Scope and Impact of Financial Conflicts of Interest in Biomedical Research: A Systematic Review JAMA. 2003;289:454-465
The commercialisation of research has exploded in the fields of biomedical science and biotechnology, with industry poised to make millions, scientists are all too happy to take a cut of the action. However, money is a powerful motivator and researchers now have an added incentive to find certain result. The result which favours whatever corporation provides the funding. If scientists are being influenced by their source of funding, then it should be apparent in their results. Industry funded projects should find positive results more often than non-profit funding. Indeed, taking the example of pharmaceutical research, that is what we find.
Many scientific journals require the submitting authors to declare any conflicts of interest, for example being funded by the same company who owns the patent on the drug in question. Several statistical analyses have been done on the outcomes of these studies and the results should not be surprising to anyone who understands the effects of bias. In 2001 an analysis of 314 drug trials found that non-profit funded research was 3.5 times more likely to find a negative result than industry sponsored trials1. A 2002 study of 159 articles in the British Medical Journal, which requires that funding be declared, found that the authors' conclusions were significantly more positive in trials funded by for profit organisations compared with trials without competing interests (mean difference 0.48, P=0.014)2. A 2004 study showed that in 158 drug trials published in five leading medical journals results favoured industry funded studies by an odds ratio of 1.93. Finally, in 2003 a review selected 37 of the most rigorous studies and pooled their data. They found a statistically significant odds ratio of 3.6 favouring industry funded research4. This review also found that industry funding was associated with restriction on publication and data sharing if the results were negative.
One point to make about these analyses is that they are correlative only, causation could not be determined. Although the quality of the studies was controlled for (often poorer quality in industry funded trials) one possible explanation is that industry interests somehow pick pharmaceuticals that are more likely to succeed in trials. I can’t imagine how they would know beforehand which drugs have better prospects, but it is a possibility. More likely, however, is that the scientists performing these studies are influenced by the commercial factors at play in their research. These results are very reminiscent of ‘tobacco science’ where, for example, 94% of industry funded inquiry found no harm from second-hand smoke compared to just 13% of non-profit funded research. If correct, this interpretation is quite troubling. First, it means that consumers are being bombarded by new pharmaceuticals which are of questionable value over the old versions and in some cases, downright dangerous. Second, the reputation of science for impartiality and following evidence is being ruined by commercial interest by both outside companies and the scientists themselves. When the commercial bias of scientists is revealed, say through a drug recall or hidden financial contributions, the public starts becoming suspicious of these intellectual elites. In fact, the commercialisation of research could be contributing to the distrust of science, the growing interest in alternative medicine, and the rejection of genetic engineering.
Believe it or not there was a time when industry and academia where more or less separate. Scientists with relevant expertise might be given an honorarium to help overcome a particular problem or speak on a certain topic, but that was about it. Funding was largely provided by governments and scientists were free to explore myriad lines of inquiry, whether it might lead to a practical application or not. Even when there research could be commercialised, the scientists themselves would rarely have much to do with it. Their results were given away into the public domain. In 1954, Jonas Salk developed his vaccine against polio, when asked whether he would patent it he found the idea ridiculous replying, “Could you patent the sun?” Unfortunately, this attitude is found rarely in the field of biotechnology. Many exotic genes and interesting methods are often patented by the researchers who first discover them either preventing further inquiry or driving the cost of research even higher. This also makes the funding of science less attractive to the public sector that now sees less return for its investment.
Unfortunately, I don’t have any solutions for the problem. I just think the commercialisation of research makes an important contribution to the growth of science denialism and was worth highlighting. Patent law clearly needs a complete overall. I dislike attempts to own parts of nature - “to patent the sun” - but companies do need protection for their intellectual property. Similarly, industry funding research is having a negative impact on the impartiality of science, but there is no denying the benefits that have emerged from such partnerships. Perhaps blinding individual scientists to the source of their funding and preventing patents on natural products could go some way to removing this troubling commercial bias from academic scientists.
1. Yaphe J, Edman R, Knishkowy B, Herman J. The association between funding by commercial interests and study outcome in randomized controlled drug trials. Fam Pract. 2001 Dec;18(6):565-8.
2. Lise L Kjaergard & Bodil Als-Nielsen. Association between competing interests and authors' conclusions: epidemiological study of randomised clinical trials published in the BMJ. BMJ 2002;325:249 ( 3 August )
3. Bhandari M, Busse JW, Jackowski D, Montori VM, Schünemann H, Sprague S, Mears D, Schemitsch EH, Heels-Ansdell D, Devereaux PJ. Association between industry funding and statistically significant pro-industry findings in medical and surgical randomized trials. CMAJ. 2004 Feb 17;170(4):477-80.
4. Justin E. Bekelman, AB; Yan Li, MPhil; Cary P. Gross, MD Scope and Impact of Financial Conflicts of Interest in Biomedical Research: A Systematic Review JAMA. 2003;289:454-465
May 21, 2010
May 14, 2010
Lizard competition drives evolution
In a large manipulation of the environment two researchers have used entire islands in the Bahamas to test evolution. The biologists focused on the traits of running and body size of native lizard populations to test whether intra- or inter-specific competition was the greater driver of evolution.
On different islands these researchers alternatively used bird-proof netting to limit predation, introduced snakes to increase predation, or added more lizards to increase competition. They found that predation was essentially random with neither body size or overall speed making much difference to who would be eaten for lunch. On the other hand, when intra-specific competition increased having a larger body size and faster movement allowed certain lizards to access scare resources more effectively. It was this force, the researchers found, that drove the lizards evolution and not the predation.
While this is fascinating research and provides yet more evidence that evolution does actually occur (and within our lifetime) the biologists are quick to point out that this finding may not be replicating in other predator/prey relationships where predation could be more of an evolutionary factor.
Ryan Calsbeek, Robert M. Cox. Experimentally assessing the relative importance of predation and competition as agents of selection. Nature, 2010; DOI:10.1038/nature09020
On different islands these researchers alternatively used bird-proof netting to limit predation, introduced snakes to increase predation, or added more lizards to increase competition. They found that predation was essentially random with neither body size or overall speed making much difference to who would be eaten for lunch. On the other hand, when intra-specific competition increased having a larger body size and faster movement allowed certain lizards to access scare resources more effectively. It was this force, the researchers found, that drove the lizards evolution and not the predation.
While this is fascinating research and provides yet more evidence that evolution does actually occur (and within our lifetime) the biologists are quick to point out that this finding may not be replicating in other predator/prey relationships where predation could be more of an evolutionary factor.
Ryan Calsbeek, Robert M. Cox. Experimentally assessing the relative importance of predation and competition as agents of selection. Nature, 2010; DOI:10.1038/nature09020
May 08, 2010
Neanderthal genes in human genome
DNA sequencing of Neanderthal genome has provided evidence that Neanderthals and humans may have interbred. The 40,000 year old DNA was was decoded by Svante Pääbo, a palaeogeneticist at the Max Planck Institute in Leipzig, Germany. The researchers manged to decode about two thirds of the genome in duplicate.
The team also compared the Neanderthal DNA to genomes form various human populations including French, Chinese, Papua New Guinean, and San. They found fragments of Neanderthal DNA in all modern human populations except those descended from African populations. As Neanderthals only lived in Europe and the Middle East this finding suggests that Neanderthals and human interbred some 45,000 years in the past.
Although none of the Neanderthal DNA contributed to expressed genes in modern humans comparison of the two Homo genomes with those of chimpanzees may reveal uniquely human traits that arose after the human/Neanderthal split and provided an evolutionary advantage to early humans. This was a crucial time in the evolution of humans and any discoveries in this area will be fascinating.
So with everyone of European, Asian, American, or Polynesian descent having 1-4% Neanderthal DNA in their genomes, this means that Africans are now the most racially 'pure' population. I wonder what white supremacists would have to say about that?
Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, et al. A Draft Sequence of the Neandertal Genome. Science, 2010; 328 (5979): 710-722 DOI: 10.1126/science.1188021
The team also compared the Neanderthal DNA to genomes form various human populations including French, Chinese, Papua New Guinean, and San. They found fragments of Neanderthal DNA in all modern human populations except those descended from African populations. As Neanderthals only lived in Europe and the Middle East this finding suggests that Neanderthals and human interbred some 45,000 years in the past.
Although none of the Neanderthal DNA contributed to expressed genes in modern humans comparison of the two Homo genomes with those of chimpanzees may reveal uniquely human traits that arose after the human/Neanderthal split and provided an evolutionary advantage to early humans. This was a crucial time in the evolution of humans and any discoveries in this area will be fascinating.
So with everyone of European, Asian, American, or Polynesian descent having 1-4% Neanderthal DNA in their genomes, this means that Africans are now the most racially 'pure' population. I wonder what white supremacists would have to say about that?
Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, et al. A Draft Sequence of the Neandertal Genome. Science, 2010; 328 (5979): 710-722 DOI: 10.1126/science.1188021
May 01, 2010
Jumping genes
The transfer of genetic material is well known to occur in a vertical orientation. Parents pass their genes on to their children, and their children pass those genes on to the next generation. This fact allows scientists to analyse particular genes and to use the pattern of inheritance to build the tree of life.
It is also well known that the bacteria at the base of this tree form more of a fuzzy bush. This is because bacteria are much more promiscuous than their mammalian counter-parts. While invertebrates stick exclusively to members of their own tribe, bacteria are happy to have sex with a completely different species and will even engage in necrophilia if the occasion arises. This swapping of genes between species is called horizontal gene transfer and was thought to be the purview of bacteria (and some fungi) only.
But now scientists have discovered that transposons (jumping genes) can be transmitted from parasite to host - at least in some special cases. The parasite in this case is the blood-sucking triatomine, a parasite which regularly bites humans and can carry Chagas disease. Researchers found the invertebrate had transposon DNA which was also found in some vertebrate hosts, namely the opossum and the squirrel monkey (but not humans - yet). These jumping genes were 98% identical between the different hosts.
Although this is a clearly a rare and special case, it does demonstrate that genetic transfer between different species is possible. This finding increases the risk associated with genetic engineering and emphasises that once a gene is released into the ecosystem total control of the set of instructions cannot be guaranteed. On the other hand, what scientists do when genes are artificially transferred from one species to another is not much different to this newly discovered natural process. Perhaps this finding may help to ease the environmentalists' fear that genetic engineering is bringing Dr Frankenstein's monster to life.
Clément Gilbert, Sarah Schaack, John K. Pace II, Paul J. Brindley, Cédric Feschotte. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature, 2010; 464
It is also well known that the bacteria at the base of this tree form more of a fuzzy bush. This is because bacteria are much more promiscuous than their mammalian counter-parts. While invertebrates stick exclusively to members of their own tribe, bacteria are happy to have sex with a completely different species and will even engage in necrophilia if the occasion arises. This swapping of genes between species is called horizontal gene transfer and was thought to be the purview of bacteria (and some fungi) only.
But now scientists have discovered that transposons (jumping genes) can be transmitted from parasite to host - at least in some special cases. The parasite in this case is the blood-sucking triatomine, a parasite which regularly bites humans and can carry Chagas disease. Researchers found the invertebrate had transposon DNA which was also found in some vertebrate hosts, namely the opossum and the squirrel monkey (but not humans - yet). These jumping genes were 98% identical between the different hosts.
Although this is a clearly a rare and special case, it does demonstrate that genetic transfer between different species is possible. This finding increases the risk associated with genetic engineering and emphasises that once a gene is released into the ecosystem total control of the set of instructions cannot be guaranteed. On the other hand, what scientists do when genes are artificially transferred from one species to another is not much different to this newly discovered natural process. Perhaps this finding may help to ease the environmentalists' fear that genetic engineering is bringing Dr Frankenstein's monster to life.
Clément Gilbert, Sarah Schaack, John K. Pace II, Paul J. Brindley, Cédric Feschotte. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature, 2010; 464
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