It seems that as this discussion continues, more and more concepts become conflated producing all manner of irrelevant comparisons that create more and more confusion.

In the first place, we have the problem of defining what we even mean by food safety.  Truth be told, we don't have any idea what constitutes "safe" food beyond the fact that we may have a history of consuming it without obvious incidence.  Even here, we have a basic problem because many people may have allergies or sensitivites that have always existed, or are now being recognized.

So, the notion of food "safety" is a relative concept suggesting that we have some general states of reaction an individual may experience.  In the first, there is no apparent effect from consuming the food and the individual thrives as well from this source as any other.  In the second instance people may suffer extreme reactions, such as allergies that render such foods toxic.  Again, the difference here is not in the food but in the individual's reaction to it.  In the third instance there is no overt toxic effect, but the individual may simply fail to thrive on the food.  This situation might be considered a kind of low-level toxicity where no overt symptoms are presented, beyond the food not agreeing particularly well with the individual.  One could also consider negative effects that might occur because of long-term exposure to a particular food in this category.

From this it should be clear that any pronouncement of "safety" is a qualified assessment and subject to being wrong depending on the individual exposed.  As a result, we should be cognizant of the fact that whenever food is modified in any form, we may well change the profile of the "risk" for certain individuals.  Food that was formerly "safe" may become problematic, just as food that may have posed a risk previously, may also change.  We simply don't know and, more importantly, we don't actually know how to test for these things beyond a rough approach regarding allergies or overt toxicity.

As has also been stated repeatedly, there is nothing intrinsically wrong with modifying a plant through direct genetic manipulation.  Regardless of the method employed, ALL modifications incur the risk of producing undesired results in some individuals.  There's simply no circumventing that, since it is intrinsic in the nature of food and people's reactions to it.

From this we can see how the concept of "substantial equivalence" arises, since it provides a baseline indicating that if we have a certain level of acceptance [i.e. produces no obvious harm] by people, recognizing that it may cause adverse reactions in others, then any modification [regardless of source] will be no worse than the conventional food.  However, let's also remember that we are specifically talking about the food itself.  This has nothing to do with whether there are pesticide residues, or any other source of contamination to the food item itself.  As a result, we can argue that GM foods, conventional foods, and organic foods all satisfy this baseline requirement of being substantially equivalent to each other regarding their nutritional value and their ability to be tolerated by the average person.  This doesn't preclude adverse reactions from some people with sensitivities or allergies, but we would expect to see no differences in such reactions regardless of whether it was GM, conventional, or organic food.

As a result, food can never be proven to be safe any more than any tests can be conducted from which a claim of safety can be assured.  All that can ever be stated is that there is no evidence to suggest that any food is less safe than its former conventional equivalent.
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The second aspect of food production is post-production handling.  This would involve all manner of activities ranging from pesticide residues on the plants, to the presence of antibiotics, steroids, etc. in animals.  In short, all the elements associated with the product over and above the food itself would be considered in this context.  If conventional foods have pesticide residue that incurs an adverse reaction in individuals, it is important to recognize that this is a processing issue and not something intrinsic in the food itself.  As an example, an E. Coli outbreak from beef doesn't suggest that beef is a problem food for humans, it merely indicates that better post-production processes need to be in place to avoid such contamination.  Similarly when outbreaks of salmonella occur, then they are the result of contamination during food handling and not the food itself.

In not making this distinction it simply confuses the issue around food safety.  Similarly incidences can occur in kitchens when the proper precautions aren't taken with respect to storing meats and vegetables, or cross-contaminating foods during the cooking process.  Each carries a certain risk which can have dramatic consequences, but should not be conflated with the safety of the food source itself.

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From this we can begin to see where some of the controversy surrounding conventional and organic foods comes from.  Clearly a tomato is a tomato is a tomato, and yet when someone wants to allege that one method of growing is superior to another, they are arguing that there is some post-production element that is different.  Invariably this involves issues regarding the use of pesticides or some other "artificial" method of enhancing or producing the final crop.  

The argument that one form of production is "healthier" than another is also based on the idea that there is some artifact present [i.e. pesticide residues] that makes one form of the product more "dangerous" than another.  Of course, if one could ensure that all such residues were removed, then it would be impossible to distinguish between conventional and organic foods.

When GM foods are considered, the problem changes slightly because the modification involves the manipulation of a plant's genes directly.  In the case of Bt toxin, the bacterial gene, normally present in soil bacteria, is placed in the plant so that the toxin can be produced protecting the plant from a particular insect pest.  Bt toxin is not toxic to humans, so by the assumption of "substantial equivalence", there is no fundamental change in the plants nutritional qualities, and no apparent risk increase because of the presence of the toxin.  Certainly many people object simply because of the word "toxin" which invariably conveys the idea that some poison is being introduced into their food supply, but in fairness, there are many toxins routinely produced by bacteria, in and around us, which simply have no effect on humans.  As a result, there is no indication that Bt toxin present in a plant should carry any higher risk than its normal occurrence in the soil and our routine exposure to it.

While it is always possible that the presence of Bt toxin could induce an allergic reaction in some individuals, the 90-day animal studies have demonstrated that there appears to be no toxic effect in the animals, and no indication that any allergic-type reactions are present.  Since Bt toxin is not associated with any allergies, the principle of "substantial equivalence" suggests that there is no compelling reason to presume that it has allergenic properties in humans.

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So what is the problem or controversy surrounding GM foods?

The simple fact is that when we examine all the data and consider all the studies, we simply don't know whether such modifications may produce unexpected effects later or not.  Regardless of how unlikely such events are, we simply don't know.  In the absence of any actual human studies we are simply extrapolating the results of animal studies.  Is this a reasonable approach?  Again, we simply don't know since there is no real precedent for this in our food supply. 

While Bt toxin may not be harmful, can the same be said of glyphosate [Roundup]?  Even if not harmful to humans, might they be harmful or affect the ecology of the human microbiota?  How about in infants, or pregnant women?  Might some of these genes be transferred by Horizontal Gene Transfer (HGT) to other microbes that would increase their persistence in the environment?  After all, antibiotic resistance in pathogens is often provided by our own gut bacteria that have the antibiotic resistant trait.  These questions aren't intended to provide fodder for the precautionary principle, but rather to illustrate that there are no "free lunches" in nature, and that for every action we take, there will be a dozen we didn't anticipate.  So when we elect to take a risk, let's not do it naively and presume that we've already planned for all the possibilities.

Certainly arguments have been made that genetic modification is more precise than plant hybridization and other methods that have been used over the centuries.   Since humans have typically fared well, it is often presumed that past results will be reliable indicators of future results.  It may be true, but it isn't scientific.  Similarly we are discovering that perhaps some of our plant hybridization methods have already produced unintended consequences in some people, particularly as is being observed with respect to the presence of gluten in wheat.  

Changes of any sort have the potential to create problems.  Consequently regardless of how confident we are that something won't cause a problem, we should have learned by now that there are far more subtleties in biology that we may be unaware of.  

Does this mean that we should just invoke the precautionary principle and avoid all technological changes?  Of course not, but I think that we do need to be clear on what specific problems we are going to solve.  Making changes simply to be making changes is not an option.  The practice of science is not the practice of public policy and regardless of what science demonstrates, that is no basis for making arbitrary public policy changes that aren't warranted.  Unfortunately, the implementation of scientific policies is often economic, and economics invariably lacks the nuances that are often presented in scientific theories.

As an analogy, we can certainly recognize that insects are an excellent source of protein in a diet.  There's no scientific dispute on the matter, so one could easily make the argument that insect protein would potentially be healthier for us than many of the animals we currently consume.  Yet, I can't imagine anyone being in favor of the government or corporations arbitrarily introducing insects into our diet and not tell us about it.  There are many aspects of our food that have nothing to do with science, but rather are based on our cultural beliefs.  Regardless of the science, individuals have the right to pursue their personal beliefs regarding food.  It doesn't matter what science says about nutritional equivalence, since such a food choice isn't about nutrition alone.

When we examine the overall controversy about GM, conventional, and organic foods, we should recognize that one aspect of it involves personal beliefs for which no science will ever change minds.  The other aspect of it involves businesses striving to gain market share and control the markets.  Whether one is fully satisfied with the studies involving the safety of consuming GM foods, I expect that these products are substantially equivalent and don't present a clear risk at this point.  I also don't believe this is a condition that will persist, but there are for more significant problems that need to be addressed which appear to be ignored because of this distraction regarding food safety.  It is these issues that I will address in my next post and outline my own opposition to GM foods.