Reproducibility

Originally posted by humy
But there is much established scientific fact without such experiments conducted first because much of valid science comes from just observing how things naturally are.

That was my initial point, a large part of science is pure observation and description and follows completely different rules from experimentation. It is usually best for multiple parties to make the same observation, but that is not the same as calling it repeatable which is a requirement for experimentation. Even in experiments there is a distinction between the observations and the rest of the experiment. Sometimes the observations are tricky and controversial, but much of the time they are straight forward and indisputable. People may argue about why your mouse has white fur, but it is unlikely they will dispute that it has white fur.

Originally posted by DeepThought
It put me off going to the doctors for life! 😉

My own experience with doctors, is that there are some things that they are very sure of, and the medicine undoubtedly works. Then there are other things they don't really know whats causing it, nor what to do to fix it. Then there are some things where they think they know but don't really. And there are somethings that they don't really care, just give you a placebo and it will fix itself.

Originally posted by DeepThought
I've been trying to think of a way to respond to your excellent post. One thing I've seen in medical research papers are the words "marginal significance". They've done a trial and the drug's failed (one even sees the words "the patient failed the treatment" on occasion) but it's right on the borderline so they call it "marginal significance" when it s ...[text shortened]... while ago which is why I've seen these things. It put me off going to the doctors for life! 😉

Yes indeed, and I can do you one better; I've seen "near-marginal significance." Explain that one to me. To be fair, those studies are usually a case of "well, we have to publish it for documentation, disclosure and funding purposes, but the drug probably won't make it to market so it's back to the drawing board in the lab."

I have felt the escalating need recently to defend science from the "perpetual skeptics." (i.e. pseudoscientists) Skepticism is an important skill, however its purpose is to fill in logical gaps/flaws in reasoning, to refine the conclusion. A perpetual skeptic, regardless of what the science demonstrates, will always have a reason to reject the conclusions. They don't take the time to comprehensively review the existing literature before they make definitive statements; rather, they cherry pick certain information and ignore other, solid lines of evidence. They don't think about the experiments. They exploit uncertainty to say that the science overall isn't settled.

Blame it on education systems teaching bad critical thinking skills and the internet where anyone can have a soundboard. Because scientists deal with probabilities and not truths, the lack of any statistical correlation between vaccinations and autism can't definitively rule out arguments that "vaccines might cause some harm". Unfortunately that leaves enough of an open window for people who want to believe that vaccines cause autism.

I think the "reproducibility crisis" fits into this. While it is a legitimate problem, it has been understood for a long time. A very small minority of the unreproducible studies are fraudulent, but that seems to be the implication from media reports. Usually its as simple as an overlooked variable or a bad reagent or a misplaced decimal. But it leaves open that window for the perpetual skeptic to point their finger at the "shameful, biased, selfish scientists".

Again, science is hard. It takes a long time. We just published a story that took 3.5 years to collect data. Repeating all those experiments would be insanity; however, we are following up on it, validating the results in other model systems and hopefully other labs are doing the same. If 5 years goes by with no follow up publications, it was a dead end.

Originally posted by wildgrass
Usually its as simple as an overlooked variable or a bad reagent or a misplaced decimal. But it leaves open that window for the perpetual skeptic to point their finger at the "shameful, biased, selfish scientists".

There do indeed seem to be a plethora of subtle variables that cause an experiment to fail to be reproducible, especially when experimenting on mice:

http://www.sciencemag.org/news/2016/08/mouse-microbes-may-make-scientific-studies-harder-replicate

The "perpetual skeptics" aren't skeptical all the time. Quite a few are only too willing to believe wearing a hematite bracelet will cure their arthritis, or that "Mercury retrograde periods can allow you to increase your productivity and avoid at least some of the frustration they can bring about." (This last I found with a 10-second search in cyberspace.)

Originally posted by wildgrass
Yes indeed, and I can do you one better; I've seen "near-marginal significance." Explain that one to me. To be fair, those studies are usually a case of "well, we have to publish it for documentation, disclosure and funding purposes, but the drug probably won't make it to market so it's back to the drawing board in the lab."

I have felt the escalating n ...[text shortened]... r labs are doing the same. If 5 years goes by with no follow up publications, it was a dead end.

Knocking science for political ends is hardly a new strategy. There are a number of interest groups, most famously tobacco and oil companies, who want to undermine science so that it generates the answers that they want, rather than the truth. What is new is the co-opting of the opinion of ordinary people. So groups like the Patriot movement try to undermine trust in the scientific method because it suits their interests to have people not believe it.

The other edge of the sword is that accepting the validity of scientific method does not entail that one should accept any given new technology. Whether there is a problem with GM crops or not, there are strong financial interests pushing them so there's an argument along the lines of "accept this technology or be labelled as anti-science.". Which tends to feed the problem we are talking about, science used as an authority to win what is essentially a political argument can cause people to reject science as a whole.

I agree with your point about education. Philosophy should be taught in schools, with an emphasis on logic, both symbolic and informal. There's a recent trend to talk about education in the same vein as training, the point being to produce individuals who are able to perform tasks but not think for themselves.

Just as an aside about vaccines. If there is a problem I think it is likely to be connected with the use of mercury rather than anything intrinsic to the vaccine. Use of mercury is being cut out, although I don't know how far down the process we are.

Originally posted by DeepThought
The other edge of the sword is that accepting the validity of scientific method does not entail that one should accept any given new technology. Whether there is a problem with GM crops or not, there are strong financial interests pushing them so there's an argument along the lines of "accept this technology or be labelled as anti-science.". Which tend ...[text shortened]... y to win what is essentially a political argument can cause people to reject science as a whole.

I must say that the GM issue goes both ways. There are strong financial and political interests pushing against GM. The thing is, the only rational argument against GM has to be a scientific one, so when you say it is an essentially political argument, that is a little inaccurate. It is a political argument that in theory could be decided by science and for which science is held up as the deciding factor by both sides. For most ordinary people, the science of it IS what matters, ie they are concerned about possible health and environmental risks. For governments and farmers, the concerns are more about exports and imports, monopolies of seed producers, pesticide and herbicide use and more and science and scare tactics are used to achieve political aims.

Originally posted by twhitehead
I must say that the GM issue goes both ways. There are strong financial and political interests pushing against GM. The thing is, the only rational argument against GM has to be a scientific one, so when you say it is an essentially political argument, that is a little inaccurate. It is a political argument that in theory could be decided by science and f ...[text shortened]... ide and herbicide use and more and science and scare tactics are used to achieve political aims.

I don't see how you can separate the point about seed monopoly from GM crops. It'll be a while before peasant farmers can do their own genetic tinkering (but see [1]). In the meantime bio-technology companies have a de-facto monopoly on them.

[1] http://www.nature.com/news/crispr-the-disruptor-1.17673

Originally posted by DeepThought
I don't see how you can separate the point about seed monopoly from GM crops.

why can't GM crops be made to allow, as they currently often are, peasant farmers to propagate them from seed themselves for next year with the next generation of crop also having the same active GM genes? That way the peasant farmers don't have to do any genetic tinkering of the own for that. They would only have to initially source their seed from bio-technology company just once and then from then on each year propagate the GM crops themselves for next years crop.
In fact, if monopoly from GM crops really is an issue, why not simply make it a none issue by introducing a law saying the bio-technology companies MUST by law GM their crops so that they are such that it is practical for the poor peasant farmers to propagate the plants for themselves? Problem solved. Of course, that might take away much of the incentive for bio-technology companies to do the GM in the first place thus prevent the poor peasant farmers from benefiting from such GM. But perhaps the governments can pay the bio-technology companies to make GM seed to benefit the poor peasant farmers thus solving that issue?

Originally posted by DeepThought
I don't see how you can separate the point about seed monopoly from GM crops.

I didn't think I did. My point was that it is a political concern not a scientific one but it does not directly affect the average consumer. Therefore, although that is one of the major concerns of political groups either for or against GM crops, they tend to try to use scientific claims (health risks) to push their agenda.

Originally posted by humy
But perhaps the governments can pay the bio-technology companies to make GM seed to benefit the poor peasant farmers thus solving that issue?

Well there is more to it than just seed monopolies. Many governments don't want GM crops for other reasons. Zambia and the EU for example are against GM crops because it is a good excuse for banning US imports.

Many Monsanto produced crops are designed to work with Monsanto products and reduce the need for certain other products such as pesticides or fertilizers. So competitors will be against the crops because it will put them out of business.

Zambia also has its own organisations that develop and sell seed designed for the local conditions, and they would probably not want competition from international companies.

Originally posted by twhitehead
I didn't think I did. My point was that it is a political concern not a scientific one but it does not directly affect the average consumer. Therefore, although that is one of the major concerns of political groups either for or against GM crops, they tend to try to use scientific claims (health risks) to push their agenda.

With health risks there isn't any proof that there are health risks, they've done laboratory tests for toxins, but what they haven't done, as far as I know, is a randomized controlled trial to make sure.

Originally posted by DeepThought
With health risks there isn't any proof that there are health risks, they've done laboratory tests for toxins, but what they haven't done, as far as I know, is a randomized controlled trial to make sure.

But what would they test? One plant? Every plant?

The fundamental error you are making is to group all GM products into a single entity. That is like saying 'they haven't yet done randomised controlled trial to make sure that fish are not dangerous to eat'. The very fact that GM crops are almost always grouped this way demonstrates that the real issues are political not scientific - but it remains the case that science gets dragged into it.

And what would they be testing anyway? One of the concerns about one specific group of GM plants is that the farmers use much more herbicide on them. So the danger is not the plant but the herbicide.

Originally posted by DeepThought
Knocking science for political ends is hardly a new strategy. There are a number of interest groups, most famously tobacco and oil companies, who want to undermine science so that it generates the answers that they want, rather than the truth. What is new is the co-opting of the opinion of ordinary people. So groups like the Patriot movement try to un ...[text shortened]... trust in the scientific method because it suits their interests to have people not believe it.

But at least with tobacco, while there were industry-funded scientists trying to prove that cancer causes smoking (?), there was mounting evidence that the opposite was true, and eventually the data overwhelmed the skeptics. The anti-vax movement, however, has been going on for at least 50 years. Without any evidence, a lot of intelligent people actually believe that vaccines cause autism, despite [1]. School systems have been forced to mandate vaccinations to prevent measles outbreaks. It's 2017.

[1]https://www.aap.org/en-us/Documents/immunization_vaccine_studies.pdf

Originally posted by DeepThought
I don't see how you can separate the point about seed monopoly from GM crops. It'll be a while before peasant farmers can do their own genetic tinkering (but see [1]). In the meantime bio-technology companies have a de-facto monopoly on them.

[1] http://www.nature.com/news/crispr-the-disruptor-1.17673

This is a legal issue, not a scientific one. Apparently, if a GM seed blows into your non-GM field from an adjacent farm, you are still legally required to pay the company for that seed. That seems ridiculous.

Originally posted by twhitehead
But what would they test? One plant? Every plant?

The fundamental error you are making is to group all GM products into a single entity. That is like saying 'they haven't yet done randomised controlled trial to make sure that fish are not dangerous to eat'. The very fact that GM crops are almost always grouped this way demonstrates that the real issues ...[text shortened]... t the farmers use much more herbicide on them. So the danger is not the plant but the herbicide.

They'd have to use organic crops as a control. I assume you mean insecticide, using herbicides on crops is going to defeat the objective of the farmer. If the plant produces its own insecticide then I'd prefer it to be tested. One of the points with CRISPR is that they can actually control where the new gene is inserted, which wasn't possible in the earlier set of GM crops so that there were more potential gotcha's from gene interactions. Other foods aren't new, the risks are known.

With medical trials they don't just test one drug from a class of drugs and allow them all through, they test each one. So I am suggesting that each one should be tested.