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In my understanding, there’s nothing “special” in how a GMO product is composed inside compared to a “natural” product. I mean, still, same principles apply to both: some DNA that controls protein building, and so on.

Now, having read about all existing methods of GMO detection, I still can’t understand how it works: e.g., given two potatoes, one GMO and one natural, would you be able to detect which is which without having any samples or knowledge about what parts of DNA to consider engineered by humans?

Once you change someone’s DNA, does it contain any signs that it was changed? Or do we need a database of “natural” products’ DNA to compare with in order to be able to detect DNA ones? Or do we need a database of GMO products to compare with?

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    $\begingroup$ It seems like you'd have to have some way to distinguish between organisms genetically modified by human action and those genetically modified through natural processes. Plausible, maybe, but not trivial. $\endgroup$ – Don Branson Jan 2 '18 at 15:33
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    $\begingroup$ @NathanMerrill Is it? How do you know there aren't naturally occurring (if rare) instances of the traits? $\endgroup$ – jpmc26 Jan 2 '18 at 20:04
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    $\begingroup$ @jpmc26 - You're right, that's not a valid test. First, either one could have a gene replaced by either mutation, natural replacement, or human replacement, and second, there's no assurance that the replaced gene makes the plant better in the particular way you're looking at. It might mutate to be less good, or it might mutate to have better disease resistance at the sacrifice of quality root structure. $\endgroup$ – Don Branson Jan 2 '18 at 20:59
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    $\begingroup$ Check the DNA for a copyright statement. $\endgroup$ – Mark Jan 2 '18 at 23:37
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    $\begingroup$ If two people are floating in outer space, and can only see each other and nothing else... $\endgroup$ – Charles Jan 3 '18 at 14:54
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[G]iven two potatoes, one GMO and one natural, would you be able to detect which is which without having any samples or knowledge about what parts of DNA to consider engineered by humans?

No, you can't distinguish them without knowing a priori the DNA sequence of the wildtype and of the GMO. There is no other mark left within a GMO in the general sense.

Of course, one particular GMO is created with one particular goal in mind. One particular phenotypic effect. If you detect the phenotype of a GMO, then you can recognize it. For example, if you make a GMO tomato that produces a new type of pigment, you can, of course, recognize it by the presence of this pigment! However, there is no general attribute of being GMO that you can recognize. You need to look for something specific that you know about a specific GMO (or specific wildtype).

There are also phenotypic traits that you find (quasi) exclusively in GMO such as Cytoplasmic Male Sterility (CMS) for example. If you find CMS in a plant, then you can be pretty sure it is a GMO. But if you can't find CMS though, you can't be sure it is not a GMO.

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given two potatoes, one GMO and one natural, would you be able to detect which is which without having any samples or knowledge about what parts of DNA to consider engineered by humans?

Possibly, assuming they're the same variety, you might get lucky by simply diffing the sequence data. This also assumes the natural variety doesn't change significantly between generations, such that even if the chromosomes have crossed-over (homologous recombination) you could still do pattern matching to realize correlation. Genes/sequences with no correlation at all would then be suspect as novel/introduced.

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No. Furthermore, the line "once you change someone's DNA" contains a wealth of misconceptions.

Once you have your potato/tomato/whatever, the DNA does not change during the life of that individual specimen. The genetic modifications change the seed before the individual specimen grows, and do not change the individual specimen during its life.

As far as genetic modifications go anyway, each seed inherently has different DNA from its parents. "Normal" breeding has given us a diversity of plants and animals which are so massively different from the originals as to be virtually unrecognisable as the same species in many cases. (If you didn't know better, would you think a dachshund and a husky were the same species?) And whilst we might think of it as "normal" today, when the techniques around selective breeding were first developed, they in turn were seen as highly unnatural, particularly the practise of breeding an individual with a parent or sibling.

This still relies on normal rates of DNA mutation within the same species. More interestingly though, DNA can also be picked up from other sources. This is identical to how scientists insert or replace genetic material for GMO - indeed, GM techniques to carry this out were founded on understanding how this takes place in nature.

This is where objection to GMO falls down. Sure, the result may or may not be healthy. However you are already using/eating/breathing pollen from individual specimens which have carried out gene transfers with other species. The difference between the natural version and what happens in the lab is only the same as the difference between natural breeding and selective breeding - it's simply that someone is deliberately choosing which attributes to pass on to the next generation, using tools which already exist within the organism's DNA.

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It would depend on whether you knew the markers they used to identify the transformed organisms.

When I (briefly) did Genetic Engineering back in the mid eighties we would add antibiotic resistance genes as well as the gene we wanted to insert. The combination would then be incubated with the vector (e.g. bacteria) and the transformed bacteria could be filtered out by growing them on antibiotic laced plates. Then you'd grow up a transformed bacteria and insert it into the target organism.

So, the presence of bacterial antibiotic resistance genes in your hypothetical potato could be an indication but not a guarantee of human modification.

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