• Tomorrow's Table for Nature by Pamela Ronald

    On this web log I explore topics related to genetics, food and farming

    • Who Can We Trust?

      Thursday, 06 Aug 2009 - 20:15 UTC

      Discussions about genetic engineering with the general public inevitably lead a to concern that scientists cannot necessarily be trusted. It seems that to successfully make decisions on how to use GE for the betterment of humankind and the environment, the public will need to understand the scientific process and learn to distinguish high-quality scientific research that has stood the test of time and can largely be relied on from simple assertions or unsubstantiated rumors.

      Jim Holt, a writer for the New York Times Magazine, cites a survey indicating that less than 10% of adult Americans possess basic scientific literacy. For nonscientists, it may be the sheer difficulty of science, its remoteness from their daily activities, “that make it seem alien and dangerous” (Holt 2005). Yet, the societal values that science promotes—free inquiry, free thought, free speech, transparency, tolerance, and the willingness to arbitrate disputes on the basis of evidence—are exactly the qualities needed when debating the future use of GE in generating new plant varieties. In the words of Ismail Serageldin, Director of the Library of Alexandria and past Vice President for Environmentally and Socially Sustainable Development of the World
      Bank, an understanding of the scientifi c process is important “not just to promote the pursuit of science, but to yield a more tolerant society that adapts to change and embraces the new” (Serageldin 2002).

      Misrepresentation of science for ideological or political purposes simply muddies the debate, and sadly, with respect to the GE foods, this often occurs. For example, to suggest that genetic engineering is dangerous, proponents of the California initiatives to ban the process often cite a book called Seeds of Deception (Smith 2004), written by a former Iowa political candidate f or the Natural L aw Party with no scientific training. This book is the likely source for information on another Sonoma county flyer suggesting that “Lab animals fed GE food develop stomach lesions,” in reference to a fundamentally fl awed experiment carried out in 1999 that was never confirmed (Ewen and Pusztai 1999). To lend credence to those irreproducible results, Smith cites the experiment of a seventeen-year-old student who fed mice genetically engineered potatoes. According to the referenced Web site, “ . . . [the mice] fed GM ate more, probably because they were slightly heavier on average to begin with, but they gained less weight.” In addition, “ . . . marked behavioral diff erences” were observed though the boy admitted, “these were ‘subjective’ and not quantitative.” Smith argues that this experiment demonstrates that GE food may have negative eff ects on the “human psyche” and concludes that the boy “has put the scientists to shame.” The implication is that the public can trust this experiment carried out by a student, unhampered by scientific training but not those of the scientific community who pointed out the flaws in the original experiment. Smith ignores the fact that this experiment conducted by a teenager was not subjected to the rigorous methods that are inherent to the scientific process.

      So how can the public distinguish rumors from high quality science, determine what an established scientific “ f act” i , and what is still unknown? Here are some useful criteria:

      1. Examine the primary source of information. Is there a reference to the source of information? If not, it cannot be verified. If so, is the source reputable? In the case of the boy and the mice, I found that the reference given for the boy’s work was to another Web site, and that that web site referred to even another Web site (Ho 2002). It turned out that the only documentation of this “experiment” was a chance meeting with the boy’s mother, who was the source of the “scientific information.” “Mum Guusje is very proud of her son. . . .” Why would someone would cite a conversation with a boy’s mother as a good scientific reference? Either the authors of the book and the Web site lack a basic understanding of science and cannot assess the accuracy of the work, or they
      simply do not care, or both. But they should care; for this kind of deception only confuses and frightens people. And laws are being passed based on this kind of information.

      2. Ask if the work was published in a peer-reviewed journal. Peer review is the standard process for scientific publications. Peer-reviewed manuscripts have been read by several scholars in the same field (called peers), and these peers have indicated that the experiments and conclusions meets the standards of their discipline and are suitable for publication. In the absence of peer-review the significance and quality of the data cannot be assessed. With no peer-reviewed, published record of the boy’s subjective experiment, it is doubtful that normal standard scientific methods were applied.

      3. Check if the journal has a good reputation for scientific research. If a peer-reviewed paper is cited, where was it published? Is the journal widely respected? One tool that is commonly used for ranking, evaluating, categorizing, and comparing journals is the frequency with which the “average article” in a journal has been cited in a particular year or period. The frequency of citation reflects acknowledgment of importance by the scientific community. High-impact and widely respected journals include Science and Nature. Therefore, a citation in Science generally suggests scholarly acceptance, whereas publication in a nonscientific or little-known journal does not.

      4. Determine if there is an independent confirmation by another published study. Even if a study is peer-reviewed and published in a reputable journal, independent assessment is critical to confirm or extend the findings. Even the best journals or scientists will occasionally make mistakes and publish papers that are later retracted. Sometimes there may be outright fabrication that is overlooked by the reviewers and not detected until later (Kennedy 2006). In other cases, the scientific report may be accurate but its significance may be misrepresented by the media. A good example is that of genetically engineered corn and the monarch butterfly controversy that erupted in 1999. A Cornell entomologist, John Losey, published a short paper in the scientific journal Nature reporting that monarch butterfly larvae died after eating milkweed plants dusted with pollen from GE corn (Losey et al. 1999). The paper generated intense national and international news coverage transforming the monarch butterfly overnight into a dramatic symbol of what some consumers saw as the dangers of agricultural biotechnology. Subsequent scientific studies, including field trials, showed that the exposure of monarchs to GE corn is fairly small and that the threat to monarchs pales in comparison to risks presented by conventional pesticides (Pew Initiative on Food and Biotechnology 2002). Such misrepresentations or errors are usually discovered by other researchers because most reports, especially if it is exciting news such as a suggestion that genetic engineering kills monarch butterflies or makes mice sick, will be rapidly retested by other scientists. If the data are challenged, the first author then has the opportunity to write another paper refuting the challenge.

      Although it is a slow process to establish a scientific “truth,” a particular scientific conclusion will eventually either gain broad acceptance or be discarded.

      5. Assess if a potential conflict of interest exists. Most people would agree that a mother usually believes the best about her son, and that pesky details such as lack of scientific training may not bother her. Therefore, a mother’s recommendation represents a clear conflict of interest in such a case. Studies tainted by such undisclosed conflicts of interests are a major concern in the debate about genetic engineering. If governmental regulators were to rely solely on data supplied by parties whose primary concern is not the public good but private interest, then the public would have reason to question the integrity of the research. Similarly, if a person with a strong stance on the use of GE in agriculture is an employee of a for-profit biotechnology or organic industry, such employment should be disclosed because a conflict of interest may exist. . Transparency is a wonderful disinfectant when honesty is needed. (Full disclosure: neither Raoul nor I presently have financial relationships with for-profit food biotechnology or organic industries; nor have we for the last 10 years).

      6. Assess the quality of institution or panel. Does the report emanate from a University accredited by the U.S. Department of Education or equivalent society? Such information is generally more reliable than that issued from a single individual putting information out on the web. In the United States, government research arms such as the National Science Foundation and the National Institute of Health and professional scientific societies generally provide up-to-date, high-quality information. For example, the American Society of Plant Biologists is a nonprofit professional society devoted to the advancement of the plant sciences. It publishes two world-class journals and organizes conferences and other activities that are key to the advancement of the science. K e National Academy of Sciences (NAS) is “an honorific society of distinguished scholars engaged in scientifi c and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare.” (NAS 2006). Election to the Academy is considered one of the highest honors that can be accorded a U.S. scientist or engineer. These types of nonprofit organizations provide a public service by working outside the framework of government to ensure independent advice on matters of science, technology, and medicine.

      7. Examine the reputation of the author. Do the author(s) have training in science?
      If so, have they had formal training leading to an advanced degree such as a Master’s degree or doctorate, and have they published widely in reputable journals? If not, then are they working with a reputable scientist(s) to evaluate the data? In the case of the boy and the mice, a university affiliation is hinted at, but it seems that the “experiment” was carried out at home and reviewed primarily by his mother.

      You, the consumer, are now ready to delve into issues surrounding genetic engineering.
      Applying these tips about the scientific process, you can now more easily assess the accuracy of media reports. Checking scientific sources can be time consuming, but it is worth the effort because such sources will get you closer to accurate facts about GE than rumor or unconfirmed reports.

      Ewen, S.W.B., and A. Pusztai. 1999. Effect of diets containing genetically modified potatoes expressing Galanthus nivalis lectin on rat small intestine. The Lancet 354:1353–1354.
      Holt, Jim. 2005. The Way We Live Now: “Madness A bout a Method.” New York Times
      Magazine, December 11. www.nytimes.com (accessed March 29, 2006).
      Ho, Mae-Wan (ed.). 2002. Mice Prefer Non GM. Institute of Science in Society: Science
      Society Sustainability. ISIS 13/14 (February). w ww.isis.org.uk/Mice Prefe rNonGM.php?
      (accessed March 31, 2006).
      Kennedy, Donald (ed.). 2006. Retraction of Hwang et al., Science 308:5279.
      Re traction of Hwang et al., Science 303:1669. Editorial Re traction. Science
      (Letters) 301:335.
      Losey, JE, LS Rayor, ME Carter. 1999.Transgenic pollen harms monarch larvae. Nature 399:214.
      NAS (National Research Council and Institute of Medicine of the National Academies).
      2006. Washington D.C.: < e National Academy Press. www.nasonline.org/site/
      PageServer?pagename=ABOUT_main_page (accessed May 2, 2006).
      Pew Initiative on Food and Biotechnology. 2002. “Three Years Later: Genetically
      Engineered Corn and Monarch Butterfl y Controversy.” University of Richmond, < e PEW
      Charitable Trusts. pewagbiotech.org/resources/issuebriefs/ monarch.pdf (accessed May 8,
      2006).
      Serageldin, Ismail. 2002. The rice genome: world poverty and hunger—the challenge for science.
      Science 296(5565, April 5): 54-58.
      Smith, Jeffery M. 2004. Seeds of Deception. Exposing Industry and Government Lies About the Safety of the Genetically Engineered Foods You Are Eating. Portland: Chelsea Green Ltd.

      Last updated: Thursday, 06 Aug 2009 - 20:15 UTC

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      • Comments

        • Date:
          Friday, 07 Aug 2009 - 11:16 UTC
          Lee Turnpenny said:

          That’s a nice read, Pamela. And your criteria are, of course, applicable to many other examples of naysayers and interest groups and businesses and lobbyists who court the media in order to exploit public gullibility and foster doubt. (I’m sure Michael will find this of interest.) But I wonder that your list is a tall order for much of the lay public; even for the ‘educated.’ We’re all ‘lay’ outside of our own particular field. And rather than make the effort to scrutinise in the ways you suggest, because it takes time, we grab our info from the media and cognitively file it with what we (think) we already know. And an emotional reaction will glue it to the shelf.

          Don’t get me wrong – I’m with you all the way. And we should continue to make these points. It’s just that we live in an age of media manipulation.

        • Date:
          Friday, 07 Aug 2009 - 16:34 UTC
          Pamela Ronald said:

          Thanks Lee. Most of the public will not scrutinize carefully in this way but I do hope that some can at least understand how science is done. I want people to understand what broad scientific consensus means as opposed to something they hear on TV.

          Thanks also for sending me to Michael’s post. I can see he is on the same bandwagon!

        • Date:
          Monday, 10 Aug 2009 - 14:04 UTC
          Henry Gee said:

          Lee said – And rather than make the effort to scrutinise in the ways you suggest, because it takes time, we grab our info from the media and cognitively file it with what we (think) we already know. And an emotional reaction will glue it to the shelf.

          Amen. Who, except a diligent person such as yourself, Pamela, is going to take the trouble to examine your checklist? No – they’ll get it from the Daily Mail or the Naional Enquirer or their local creation museum.

        • Date:
          Monday, 10 Aug 2009 - 15:34 UTC
          Pamela Ronald said:

          You are right most people will continue to consume what is most readily available. Still, there are some that really do want to know the “truth” about global warming, plant breeding etc but dont understand how scientific conclusions are drawn. If we can reach some of that crowd, we will have made some progress.

          And it is true. It takes an emotional reaction or personal involvement for some before science can be seen as a force for good. There was an OpEd in the NYT yesterday by a chef who said that he and his friends always felt science when applied to agriculture was suspect (not realizing that virtually everything they eat was developed through scientific breeding). Now, however, when his favorite farmer can no longer supply tomatoes because they all died from blight, he is reconsidering his position. Still, he didnt dare use the word “gene” in his article. Instead he said the new varieties have “natural resistance”. I will try to find time today to post it on my blog.

        • Date:
          Tuesday, 18 Aug 2009 - 18:25 UTC
          Jennifer Henry said:

          It makes me sad that many in the general public still find it easiest to lump those scientists involved in genetic modification into one big ‘evil scientist’ category. There are some brilliant projects out there, many of them aimed at alleviating hunger, disease and malnutrition in the developing world, so please judge each case on its merits and don’t assume we are all out to make a buck (or that we all work for Monsanto!).

        • Date:
          Tuesday, 18 Aug 2009 - 19:13 UTC
          Pamela Ronald said:

          well-said!

        • Date:
          Tuesday, 20 Oct 2009 - 20:28 UTC
          Yi-Ning Chen said:

          No national body exists in Australia to handle research misconduct allegations. Each institution sets its own procedures in compliance with relevant state employment or anti-corruption laws.
          Several months ago, I raised my concerns about Belinda Herring, a lecture at Department of Infectious Disease and Immunology, Sydney Medical School, Sydney University, for her research misconducts.

          In particular, Belinda Herring misrepresented or falsified the bootstrap values used for testing the reliability of bootstrap trees, as those for testing phylogenetic relationships. She also misrepresented or falsified the bootstrap confidence intervals as ranges in the following 6 papers as well as her PhD thesis entitled “Molecular investigation of variation in HIV-1 genes”:

          1. Herring BL, Tsui R, Peddada L, Busch M, Delwart EL (2005), Wide range of quasispecies diversity during primary hepatitis C virus infection, Journal of Virology 79(7): 4340-4346

          http://jvi.asm.org/cgi/content/full/79/7/4340

          2. Herring BL, Ge YC, Wang B, Ratnamohan M, Zheng F, Cunningham AL, Saksena NK, Dwyer DE (2003), Segregation of human immunodeficiency virus type 1 subtypes by risk factor in Australia, Journal of Clinical Microbiology 41(10):4600-4604

          http://jcm.asm.org/cgi/content/full/41/10/4600

          3. Herring BL, Cunningham AL, Dwyer DE (2004), Potential drug resistance polymorphisms in the integrase gene of HIV type 1 subtype A, AIDS Research and Human Retroviruses, 20(9):1010-1013

          4. Herring BL, Bernardin F, Caglioti S, Stramer S, Tobler L, Andrews W, Cheng L, Rampersad S, Cameron C, Saldanha , Busch MP, Delwart E (2007), Polygenetic analysis of WNV in North American blood donors during the 2003-2004 epidemic seasons, Virology 363(1): 220-228

          5. Tsui R, Herring BL, Barbour JD, Grant RM, Basshetti P, Kral A, Edlin BR, Delwart EL (2004), Human immunodeficiency virus type 1 superinfection was not detected following 215 years of infection drug user exposure, Journal of Virology 78(1): 94-103.

          6. Herring BL, Page-Shafer K, Tobler LH, Delwart EL, Frequent hepatitis C virus superinfection in injection drug user, Journal of Infection Disease 190(8): 1396-1403.

          Statistically, bootstrap is a way of testing the reliability of the dataset. It is the construction of pseudo-replicate datasets by re-sampling. Bootstrap enables us to evaluate whether or not the distribution of characters has been influenced by stochastic effects. In phylogenetic analyses, the pseudo-replicate datasets are generated by randomly sampling the original character matrix to generate new matrices of the sample size as the original. The frequency with which a given branch is found is recorded as the bootstrap proportion. These proportions can be used as a measure of the reliability of individual branches in the optimal tree. Therefore, bootstrap analysis is a statistical method for obtaining an estimate of error. It is used to assess the reliability of a tree, and is used to examine how often a particular cluster in a tree appears when nucleotides are re-sampled. There is no distance information in this tree. It can only tell use how reliable some groupings are.

          If the entire data is compatible and has not been biased by stochastic effects, all bootstrap trees should in principal have the same topology. However, if the original dataset is biased, a cluster may be regarded as statistically significant, even if it is a wrong one!

          To learn how to interpret bootstrap phylogenetic trees, we can refer a number of first-hand statistical papers; e.g.

          1. Bootstrap confidence levels for phylogenetic trees, Efron B et al, Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7085-90.
          http://www.pnas.org/content/93/14/7085.full.pdf

          2. Bootstrapping phylogenetic trees: Theory and Methods, Susan Holmes, Statistical Science, Volume 18, Issue 2 (2003), 241-255.
          http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.ss/1063994979
          3. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, JD Thompson, TJ Gibson, F Plewniak, F Jeanmougin and DG Higgins, Nucleic Acids Research, Vol 25, Issue 24 4876-4882, Copyright © 1997 by Oxford University Press
          http://nar.oxfordjournals.org/cgi/content/abstract/25/24/4876
          4. Multiple sequence alignment with the Clustal series of programs, Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins and Julie D. Thompson
          http://nar.oxfordjournals.org/cgi/content/abstract/31/13/3497
          Unfortunately, the Deputy Vice Chancellor Professor Jill Trewhella at the University of Sydney engaged in serious and systematic corruption with the aim of concealing Belinda Herring’s research misconducts. The Vice Chancellor Dr Michael Spence at the University of Sydney was a lawyer, and therefore he cannot understand anything about statistics and medical research. Yesterday, Jane Coulter, a staff at the University’s Audit and Risk Management made her hardest efforts to suggest me concealing Belinda Herring’s research misconduct.

          It is really a pity!!!


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