NOTE: Pro-GM campaigner Mark Lynas has come up with a predictable attack (item 2 below) on the study by Dr Judy Carman and colleagues, which showed pigs fed GM feed had a higher level of severe stomach inflammation and heavier uteri than non-GM-fed pigs.

The public information website GMOJudyCarman.org has issued a reply to Lynas (item 1).

It may be an interesting barometer of the desperation of the GM lobby that it is reduced to making use of a messenger such as Lynas, who is clearly unfamiliar with basic scientific concepts, as well as with the commercial realities of livestock farming.

On the other hand, it could be that Lynas's lack of knowledge and scientific understanding is considered an advantage, since when he gets it wrong -- as he frequently does -- the GM lobby can simply shrug off his mistakes as the off-the-cuff comments of a non-expert.

Incidentally, Lynas's thesis, expressed below, that GM feed may have had a protective effect on the pigs, since more non-GM fed pigs had moderate stomach inflammation than GM-fed pigs, falls apart when we consider that a number of GM-fed pigs were removed from the "moderate inflammation" category and moved up into the 'severe inflammation' category; they had worse inflammation and so were moved up a notch. So naturally there will be fewer GM-fed pigs in the "moderate inflammation" category -- because they had something worse -- severe inflammation.

Prof David Spiegelhalter makes this same error in his "spoiler quote" circulated by the UK Science Media Centre in its latest attempt to defend GM crops against inconvenient scientific evidence. The SMC spoiler quotes are repeated by Lynas in his article.

As the GMOJudyCarman.org website points out, Lynas also appears to suggest that non-statistically significant findings in the non-GM pigs should be taken as statistically significant, even though enough animals were used in the experiment to obtain statistical significance if there was a significant toxic effect.
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1. A specific reply to Mark Lynas
GMOJudyCarman.org, 13 June 2013
http://gmojudycarman.org/a-specific-reply-to-mark-lynas/

Prominent pro-GM activist Mark Lynas has, as expected, attacked the study by Dr Judy Carman and her colleagues for their recent work titled, “A long-term toxicology study on pigs fed a combined genetically modified (GM) soy and GM maize diet.”

ML:  The authors are GM activists/campaigners and their results shouldn’t be trusted.

Answer Summary:  The authors are not GM activists; they are highly credentialed experts.

Detailed Answer: Two authors are Associate Professors in Health and the Environment, School of the Environment, Flinders University in South Australia.  Another is a Senior Lecturer at Adelaide University in South Australia. Two are veterinarians, one is a medical doctor, and two are farm experts.  The authors have over 60 years of combined experience and expertise in medicine, animal husbandry, animal nutrition, animal health, veterinary science, biochemistry, toxicology, medical research, histology, risk assessment, epidemiology, and statistics.

ML:  The paper’s acknowledgements are a veritable who’s who of anti-biotech activism, including Jeffrey Smith, John Fagan, and Arpad Pusztai.

Answer Summary:  Two of these individuals are scientists with serious qualifications (qualifications Mr. Lynas does not possess). Mr. Smith’s acknowledgement derives from his role in fostering the international collaborations that were necessary part of the study’s completion.

Detailed Answer: There were 38 people in the acknowledgement section, including an ex government Minister, an ex Chief of Staff to the Govt Minister and an ex member of the Board of Australia’s food regulator, as well as numerous scientists with more qualifications than Mr. Lynas has (as author, advisor, and speaker) and numerous farmers who were involved in the research.

Mr. Lynas has picked out three people in that list of 38 and alleged that they are anti-GM activists.  This is not the case.  In fact two of them are scientists with serious qualifications, qualifications that he doesn’t have.

The only anti-GM activist, Jeffrey Smith, is acknowledged simply because he suggested that Howard, who was seeing these effects in pigs and wanted to determine if they were scientifically real, should contact Judy who had the scientific expertise to conduct the sudy.  That simple and singular action resulted in discussions between Howard and Judy which resulted in this research. This starting point was rightfully acknowledged, but importantly, the research was conducted entirely independently of all three people Mr. Lynas mentions.

ML: Funding for the research was derived from anti-GM advocates and therefore biases the results.

Answer Summary: Funding for the study was actually derived from a current supporter of GM technologies.

Detailed answer:  It is clearly stated in the paper that the major funder of IHER’s involvement in the study is the Government of Western Australia, and the current governmentt is a supporter of GM crops.

With regard to IHER’s previous work in opposing Bt brinjal in India and CSIRO’s GM wheat in Australia, IHER conducted a thorough review of the evidence presented and concluded that there were serious safety concerns about GM brinjal and CSIRO’s GM wheat. The organization opposed the release of these based on a review of the evidence, not on ideology.

ML:  All the animals were in very poor health. Weaner mortality rates indicate inadequate husbandry standards, and higher rates of abnormalities of the heart and liver in non-GM fed pigs were conveniently ignored.

Answer Summary: Mr. Lynas does not appreciate the role of statistics in ascertaining scientific certainty.

Detailed answer:  Mr. Lynas is incorrect. These are not the mortality rates for weaners.  The rates presented are for the entire lifespan of the animal. Furthermore, animal husbandry was the same for both the GM and non-GM fed groups. This effect has been randomised-out as an effect on the results. Therefore, animal husbandry is not a factor in the difference between GM and non-GM-fed pigs.

There are hundreds of numbers in the paper. Mr. Lynas has “cherry-picked” a few of these numbers that were not statistically significant and tried to allege that they are. Carman et al only discuss statistically significant findings because this is the scientifically credible approach.  GM-fed animals had smaller livers, more pneumonia and more abnormal lymph nodes, but the researchers did not make any statements about these findings because they were not statistically significantly different when compared to non-GM fed animals.

ML: The authors used “statistical fishing” in their interpretation of the results, clearly attempting to skew or exaggerate their findings.  What visual evidence is presented is done so to justify this statistical fishing experiment.

Summary:  The authors executed careful and comprehensive statistical analysis to answer two hypotheses that had been generated by previous observations by the researchers in the U.S. piggeries.

Detailed answer:  The authors performed statistical tests on all of the parameters that Mr. Lynas mentions, and none of them were found to be statistically significantly different. These analyses are clearly presented in the paper. Mr. Lynas either did not read the paper well enough or saw the analysis but did not understand them.

The counter argument from supporters of Mr. Lynas suggests that the study was not designed to test and statistically evaluate a sole hypothesis.  If the authors had measured just the variables associated with the hypotheses being specifically tested (stomach inflammation and reproductive problems) and nothing else, few statistical tests would have been done and little to no statistical adjustment would have been suggested.  The significant results that the authors found around the hypotheses that were tested should not be made invalid simply because the authors took some other measurements.

Furthermore, the level of inflammation in the non-GM fed group was concentrated in the mild to moderate range of inflammation. Feeding GM crops boosted that to severe inflammation, and this was a significant finding. Importantly, inflammation is a graded variable; the more inflammation, the more biologically impactful it can be to the animal. So, you cannot equalize the biological consequence of nil or mild inflammation to severe inflammation. Doing so goes against scientific knowledge on the effects of inflammation.

ML: This study subjects animals to inhumanely poor conditions.

Summary:  The pigs in both groups were treated equally, humanely and within commercial piggery standards. Any assumption otherwise would be contesting the standards of the U.S. government and should be directed as a complaint to U.S. legislators.

Detailed answer:  Pigs in commercial piggeries are not like laboratory animals that are raised and housed in specific-pathogen-free environments, sometimes only one animal to a cage.  On the contrary, pigs in commercial piggeries are part of an industrialised food chain.  Pigs are born in commercial farrowing facilities housing many sows at a time.  Once weaned, pigs are housed communally in large pens.  The result is a real-world experiment that is closer to the interactive, infectious-disease-transmitting and messy school yard than than the more controlled environment of a laboratory animal house.  Commercial pigs can and do get infectious diseases and there are indeed a number of infectious diseases that tend to occur in US commercial piggeries.  Furthermore, pigs fight, bite and harass each other.  As a result, some pigs, particularly runts, can, and do, die.  Piggery owners expect some pigs to die and they factor this into their financial returns.  Indeed, if no pigs had died in this study, many US piggery owners would have found our results rather incredible.

The number of pigs was essentially the same between the GM-fed and non-GM-fed pigs.

All pigs that died underwent autopsies.  In all cases, death was found to be due to things such as infectious diseases, ie things that were piggery-related.  At no time did any pig handler or veterinarian note, or autopsy indicate, that there was anything treatment-related associated with any pig’s death, including intestinal or stomach problems.  Moreover, the number of deaths were the same between groups, which adds weight to the evidence that there was no treatment-related aspect to these deaths.

All pigs, regardless of dietary group, were fed and treated the same way by experienced pig handlers that were blinded as to the dietary group of the pig so that any differences between the two dietary groups can only reasonably be due to the effect of the GM component of the diet.
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2. GMO pigs study – more junk science
Mark Lynas
marklynas.org, 12 June 2013
www.marklynas.org/2013/06/gmo-pigs-study-more-junk-science/‎

When I saw on Twitter that a "major new peer-reviewed study" was about to reveal serious health impacts from GMO corn and soya, I was intrigued to say the least. Would this be Seralini 2.0, a propaganda effort by anti-biotech campaigners masquerading as proper science, or something truly new and ground-breaking?

Extraordinary claims require extraordinary evidence – and it would take a lot of extraordinary evidence to confound the hundreds of studies showing that GMO foods are just as safe as conventional, as summarised in this recent AAAS statement:

“The science is quite clear: crop improvement by the modern molecular techniques of biotechnology is safe. The World Health Organization, the American Medical Association, the U.S. National Academy of Sciences, the British Royal Society, and every other respected organization that has examined the evidence has come to the same conclusion: consuming foods containing ingredients derived from GM crops is no riskier than consuming the same foods containing ingredients from crop plants modified by conventional plant improvement techniques.”

So when I found the paper, again via Twitter, I determined to read it as I would a climate "denier" paper which aimed to overturn the scientific consensus in that area – with an open mind, but a sceptical one. I could see that it was already generating news, and the anti-GMO crowd on Twitter were also getting excited about some new grist to their ideological mill. Here’s what Reuters wrote:

“Pigs fed a diet of only genetically modified grain showed markedly higher stomach inflammation than pigs who dined on conventional feed, according to a new study by a team of Australian scientists and U.S. researchers.”

Really? Time to have a look at the study. It is by a Judy Carman and colleagues, entitled "A long-term toxicology study on pigs fed a combined genetically modified (GM) soy and GM maize diet" and published in a minor Australian journal I have never heard of called 'Journal of Organic Systems". (This journal does not appear in PubMed, suggesting it is not taken very seriously in the scientific community. It only publishes about twice a year, mostly with research touting the benefits of organic agriculture.)

I skimmed the paper first, and the conclusions seemed doubtful enough (see below) to try to find out who was beind it. So I looked at the sponsors of this journal. They include the Organic Federation of Australia, which seemed odd for a journal presumably aiming to be independent. Imagine the hullaballoo if Nature Biotechnology was sponsored by Monsanto!

I also wondered who Judy Carman and her colleagues were. She turns out to be – as I feared – a long-time anti-biotech campaigner, with a website called "GMOJudyCarman", which says it is supported by GMOSeralini.org. She is a founding member, according to this website, of the scientific advisory council of the Sustainable Food Trust. The Sustainable Food Trust was the UK outfit set up by former organic lobbyist Patrick Holden which stage-managed the media release of the infamous Seralini GMO rats study to the Daily Mail and other credulous outlets.

What about the co-authors? One is a Howard Vlieger, who seems to have made some wild allegations about GMOs in the past if this source is to be believed. Vlieger is president and co-founder of Verity Farms, a US "natural foods" outfit which markets non-GMO grain. Despite this, the paper declares that the authors have no conflicts of interest, although it seems to me that he would have a very clear commercial interest in scaring people about GMOs in order to drum up business of his GMO-free offerings.

What about funding? The paper states that funding came from Verity Farms, the natural product outfit mentioned above. Carman and her colleagues are also funded by and associated with the Institute of Health and Environmental Research, an Australian not-for-profit which seems to be entirely dedicated to anti-GMO activism. Recent activities have included opposing Bt brinjal in India and CSIRO’s GMO wheat in Australia. Funding sources are not disclosed, although donations are solicited. The paper’s acknowledgements are a veritable who’s who of anti-biotech activism, includin Jeffrey Smith, John Fagan and Arpad Pusztai.

So, that’s the context. Now let’s look at what raised my suspicions about the actual study. Well, Carman and colleagues claim significant differences in a long-term study of pigs fed GMO and non-GMO diets. But if you look at the data they present (and the data presentation is at least a step better than Seralini) there are obvious problems. Clearly all the animals were in very poor health – weaner mortality is reported as 13% and 14% in GM-fed and non-GM fed groups, which they claim is “within expected rates for US commercial piggeries”, a vague statement intended to justify what seem to have been inadequate husbandry standards.

This picture is even more stark in the data presented in Table 3. 15% of non-GM fed pigs had heart abnormalities, while only 6% of GM-fed pigs did so. Similarly, twice as many non-GM pigs as GM ones had liver problems. Why no headlines here? “Pigs fed non-GMO feed 100% more likely to develop heart and liver problems, study finds” – I can just see it in the Daily Mail. But of course negative results were not what Carman et al were looking for.

So we fast-forward to the stomach inflammations. This is where Carman et al got their headline. As Reuters reported:

“But those pigs that ate the GM diet had a higher rate of severe stomach inflammation – 32 percent of GM-fed pigs compared to 12 percent of non-GM-fed pigs. The inflammation was worse in GM-fed males compared to non-GM fed males by a factor of 4.0, and GM-fed females compared to non-GM-fed females by a factor of 2.2.”

This is statistical fishing of the most egregious sort, and I would put money on the Reuters summary above being lifted near-verbatim from a press release written by Carman et al. Table 3 actually shows that many more pigs fed non-GMO feed had stomach inflammations than those with GMO feed. So 31 non-GM pigs had "mild" inflammation, while only 23 GM pigs had it. For "moderate" inflammation, a GMO diet again seemed to be beneficial: 29 non-GM pigs had moderate inflammation of the stomach, while 18 [GM] had it. So that’s 40% vs 25%. Do Carman et al perform a test for statistical significance to see if GMO feed has a protective effect on pigs stomachs? Of course not – that’s not the result they are after. These findings are ignored.

Instead, it is the next line of data that they play up: for "severe" inflammation 9 non-GM pigs were determined to have it, while 23 GM-fed pigs had it. Shock, horror. You can immediately see how the data is all over the place from the previous results, which also rule out any causal mechanism with GMO feed – if GMO feed is causing the severe inflammation, why is the non-GMO feed causing far more mild to moderate inflammation? It’s clearly just chance, and all the pigs are not doing well and suffering stomach problems: about 60% of both sets had stomach erosion.

Yet the paper slyly presents photographs of inflamed pigs stomachs, with non-inflamed and mildly inflamed from non-GM fed pigs, and moderate and severe inflammation presented from GM-fed pigs. Yet 38 of the non-GM pigs, more than half of the total of 73, were suffering moderate or severe inflammation – why not present photos of their stomachs? This is rather reminiscent of how Seralini presented shocking pictures of GM-fed rats with massive cancerous tumours, but did not present pictures of the control rats (non-GM fed) which also developed cancers.

Indeed, if you add together the "moderate" and "extreme" categories – which from the photos are not easy to tell apart, involving a value judgement on the part of the vets employed to do the post-mortems – then the non-GM fed pigs have 38 affected individuals (52% of the animals studied), while the GM-fed pigs have 41 affected individuals (56% of the total). Statistical significance? My ass. This is propaganda dressed up as science, which is why it didn’t make a proper peer-reviewed journal. (Update: Andrew Kniss makes this point better, using an appropriate statistical technique, here.)

My judgement is that, as with Seralini, this study subjects animals to inhumanely poor conditions resulting in health impacts which can then be data-mined to present ‘evidence’ against GMO feeds. Most damning of all, close to 60% of both sets of pigs were suffering from pneumonia at the time of slaughter – another classic indicator of bad husbandry. Had they not been slaughtered, all these pigs might well have died quickly anyway. No conclusions can be drawn from this study, except for one – that there should be tighter controls on experiments performed on animals by anti-biotech campaigners, for the sake of animal welfare.

Thanks are due to the numerous Twitter correspondents who provided insight and links which have been useful in this post. You know who you are.

Update: I received the following expert commentaries courtesy of the UK Science Media Centre:

Prof David Spiegelhalter, Winton Professor of the Public Understanding of Risk at the University of Cambridge, said:

“The study’s conclusions don’t really stand up to statistical scrutiny. The authors focus on ‘severe’ stomach inflammation but all the other inflammation categories actually favour the GM-diet. So this selective focus is scientifically inappropriate.

“When analysed using appropriate methods, the stomach inflammation data does not show a statistically statistical association with diet. There are also 19 other reported statistical tests, which means we would expect one significant association just by chance: and so the apparent difference in uterus weight is likely to be a false positive.”

Prof Patrick Wolfe, Professor of Statistics at University College London, said:

“I am not an expert on animal health, husbandry, toxicology etc, and therefore I cannot comment on these aspects of the study. As a statistical methodologist I can however comment on the data analysis undertaken and presented in the article.

“The biggest issue is that the study was not conducted to test any specific hypothesis. This means that the same sample (in this case nearly 150 pigs) is, in effect, being continually tested over and over for different findings.

“The statistical tests employed assume that a single test is done to test a single, pre-stated hypothesis; otherwise the significance levels stemming from the tests are just plain wrong, and can be vastly over-interpreted.

“Thus there is a higher-than-reported likelihood that the results are due purely to chance. The number of pigs being in the low hundreds (instead of, say, the thousands, as is often the case in large medical studies) can make this effect even more prominent.

“Bottom line: a better-designed study would have hypothesized a particular effect (such as changes in stomach size), and then applied a statistical test solely to check this hypothesis. Perhaps another independent team of researchers will go down this path. Until then, this study definitely does not show that GM-fed pigs are at any greater risks than non-GM fed pigs.”

- See more at:                                                                                            http://www.marklynas.org/2013/06/gmo-pigs-study-more-junk-science/#sthash.kV4io7Ny.dpuf