Tuesday, November 19, 2013

Assay


I've basically stolen this post from Dr. Siouxsie Wiles (but added storm troopers). I have asked for permission. She replied back with "it's not stealing. It's reworking". Except that reworking makes me feel like less of a rebel (and we all know the rebels are the heroes). To be fair, it really is a great big simplifying reworking. This post shouldn't be taken as an indication of Dr. Wiles work unless of course you see this post for what it is - my mind map and reworking of a blog post as well as my little dig about animal testing.

Please note: no storm troopers were harmed in the writing of this blog post.

I haven't made a typo... Assay is a word... Who knew? Wikipedia defines it thusly:
An assay is an invesitigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
Boring!... So let's describe one using not animals (because we seem to be hung up on animal testing). Instead, I propose we use storm troopers. Why storm troopers? Because whoever designed their uniforms decided to abstract any sense of humanity out of them. Look at them! They look like robots. Which makes testing on them okay (though, given what we'd be testing for, if they were robots, would make them ultimately useless.... details details).

Imagine you want to figure out if a food has been contaminated with a toxin. If it is harmful, you want to know why it's harmful (i.e. which toxin) to perhaps prevent other batches from being contaminated. Please note: this is an extreme simplification. If it were real, we'd probably be talking about injecting "storm troopers" rather than merely feeding them... oh and we wouldn't be talking about storm troopers.

The first step, the lite version, would be to take 3 groups of storm troopers. Why is there a first step? Storm troopers are expensive. Look at them. You have to build a robot type thing and mould (or 3d print) the uniform. They eat, contrary to being robot type things. Besides which, no one likes having to put the damn things out of their misery at the conclusion of the tests.

One group of Storm Troopers gets the food that you're testing. The second group is fed their regular food and the third group is fed food that is definitely infected.

What does this tell us?

The second group is a control group. They attest to the general health of the storm troopers. There's always the chance that you have a bad batch of storm troopers. If some storm troopers show symptoms - death, illness etc. - in this group, then the storm troopers need to be "disposed" of and the experiment repeated.

The third group is a "positive control". It shows you what to expect if the first sample is infected with what you're looking for or gives you clues if there's something wrong - like the storm troopers are immune to the toxin you're testing for. This apparently doesn't make any sense for this example... But it's there anyway. Take this as an infantile explanation

If a few of the storm troopers in the first group get sick, and the control groups have done what you'd have expected them to have done, then there's quite likely something wrong with the food. Further testing needed...

You could always repeat this first test - perhaps with a bigger sample size (read: more storm troopers!) - just to rule out a botched test. And if it is replicable, then it's time to move on and get a whole lot more focused...

And this is where the costs go up... Because now we need quite a few more storm troopers:

Group 1:
Eat the infected food and Antitoxin A

Group 2:
Infected food + Antitoxin B

Group 3:
Infected food + Antitoxin C

So on and so forth.... And your control groups:

Group CG1:
Inert food (definitely not infected)

Group CG2:
Definitely infected food.

This allows the sort of verbosity that would allow you find out what strain of a bug a food is infected with. If the strain is toxin B for example, you'd expect to see Groups 1, 3 etc. and GC2 to get sick.

Of course, I talked about the fact that science generally isn't conclusive or rather, it's a lot more rigorous in what it considers conclusive. An important step to getting to some confidence in your conclusions is being able to replicate the results. Giving someone else enough information to replicate the results is probably even better. Basically more and more storm troopers. Actually - there's a whole process here around getting an article published. Peer review, discussion (about the conclusions drawn from the results) - basically an academic battle royale where EVERYTHING is brought into question.

Now we can start in on the ethical questions... is it okay to sacrifice robotic looking storm troopers if it could save lives? and if we didn't test on "storm troopers", what would we not know about the world around us and the effects the world around us has on us?

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