An Introduction
In this post, I'm going to talk about an experiment we performed to examine alleles of the TAS2R38 gene. I also want to talk about the results I expected, why I expected them, and why this bias was incorrect. For that, I need to begin by talking about race.
On a genetic level, race doesn't exist, or, at least, it's very, very different to how it works on a social level. People from Africa are the most racially diverse, and differ from each other more than, say, someone from England and someone from India do, on a genetic level. That's due to the founder effect; only a small portion of the population of Africa left to populate the rest of the world, representing only a tiny fraction of humanity's genome. The DNA of human beings, in general, is really not all that different. For more info, take a look at A Brief History of Everyone Who Ever Lived by Adam Rutherford.
And yet, even knowing that, it made me happy that the author is the same as me - one parent from India and the other from the UK. I don't get to see people with my heritage that often; basically just East is East, Ben Kingsley, and now, Dr Rutherford. It's the same kind of recognition as seeing women in STEM, for me.
One of my first experiences of studying genetics was when I was fifteen. We learned about punnet squares and eye colour, and I realised that I must be heterozygous for my mother's green eyes and my father's brown eyes. It made total sense to me that I would have inherited different genes from each of my parents; they are completely different people, from different parts of the world. So, knowing that, I walked into the experiment with an expectation; that I would be heterozygous in most of my alleles, including this one.
The Science Bit!
TAS2R38
The TAS2R38 gene was identified in 2003; it's a gene which tastes bitterness in the chemical phenylthiocarbamide, or PTC. People with the T, tasting, allele find it strongly bitter, while people with the t, non-tasting, allele cannot taste it at all. Those with one of each find it mildly bitter.
PTC isn't found in nature, but it does strongly correlate with tasting bitterness in vegetables of the brassica family due to the presence of PTC-like glucosinates. The brassica family consists of those vegetables which have been unnaturally selected from Brassica oleracea. When I say unnaturally selected, I mean humans selectively bred them, like pigeons or dogs, to get specific traits.
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| Genetic Literacy Project |
The amounts of glucosinates found in each one vary; personally, I quite like broccoli, cauliflower, and cabbage, but can't stand Brussels sprouts or kale.
We first began the experiment by separating our own DNA; we'll upload some instructions for that if you want to have a go at home! DNA is a very long molecule; some chromosomes are up to 7cm, so while they're in the cell they're very, very highly condensed so they can fit. The process we used caused the DNA to clump together even more, making it visible to the naked eye. Here's a selfie!
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| #nomakeup #nofilter #selfie |
PCR
We then used PCR to increase the amount of DNA we had. Here's a nice man from Khan Academy to explain how that works, or you can read my explanation below.
PCR is a way of doubling copies of DNA. First, you take some DNA. We did this by swabbing our cheeks for cells and then using a detergent - washing up liquid - to digest the cell membrane, letting the DNA flow wild and free (see my selfie, above).
The first step is to heat the DNA up, so the strands separate. Then we cool it down, and a primer sticks on to the start of the bit we want copies of. We use different primers depending on which bits of DNA we want.
An enzyme called Taq Polymerase then puts in more nucleotides, regenerating the base pairs amd duplicating the DNA!
That cycle is repeated thirty or so times, creating 230 or 1073741824 strands from our original one. That's the power of exponents!
Restriction Enzymes
Restriction enzymes are proteins which cut DNA at specific places.
To go back to the TAS2R38, there are two main alleles that people might have, T and t. Those different by exactly three letters. These single letter changes are called 'SNPs' or single nucleotide polymorphisms. You can translate that name to 'one base differences'. To make that a bit easier to understand, I'm going to compare it to language. Language analogies are used a lot when we talk about DNA, like when we talk about transcribing it and translating it.
You can think of a SNP as the difference between 'grey' and 'gray'. Same word, same meaning, different spelling. Words like colour/color would be deletion mutations, since we've removed a single letter. Adding a single letter would be an insertion mutation.
There are actually three SNPs within the T/t alleles - three single letters which are different between those two versions. Like these two sentences;
The cipher, Mr Grey, accessorised.
Vs
The cypher, Mr Gray, accessorized.
For this experiment, we had a restriction enzyme which cut the middle SNP of the tasting T-allele, but not the non-tasting t-allele. Like if it cut between e and y but not a and y. So, when we use this enzyme on that gene, we get these;
Agarose Gel Electrophoresis
Gel electrophoresis is a method of separating molecules - in this case, DNA - based on size. We get an agarose gel and use electricity to pull the molecules through it. Little molecules move faster and get further, so when we're done, we have visible bands on the gel, showing the sizes of the molecules we had.
That's a very simple explanation; here's a slightly more complex one;
The gels has 'wells' in it, which we loaded with different DNAs. We each had one set that hadn't been treated with restriction enzymes as a control, and one that had. In the first line, we put a set of markers of known sizes, like this;
Normally, there would be ten or so of those, but for the purposes of illustration, I only made three!
Back to Me
All of this takes a while, so while waiting we did some other tests using tasting strips saturated with different strengths of PTC. I found that I could taste them, confirming I had at least one copy of the T allele. I expected the other to be non-tasting; although my mother doesn't like those vegetables, my maternal grandparents both enjoy them. I have no information on my father's taste in brassicas, but I was expecting to be heterozygous based on my own bias, and figuring out why I had that expectation is part of the post. It sounds silly, but I think it's because my parents are from different continents, and they don't really like each other or have a lot in common, and the one allele I definitely know about is heterozygous. Logically, of course, those things have nothing at all to do with genetics.
Our Electrophoresis Results
Here's a graphical representation of our results!
The first lane contains the genetic markers. The second lane contains my undigested DNA while the fourth contains my digested DNA. We do this so Lane 2 can act as a control; it confirms that my DNA was actually present in the original sample, and it was of the original size expected.
I've also included an example of someone who's heterozygous, to show what that would look like. Someone who was homozygous for t/t would have results identical to the undigested DNA in lane 2. However, as you can see from the three bands, I am homozygous for the tasting gene - T/T. And that surprised me, although it shouldn't have, and it amazed me.
I inherited the same allele from two people with hundreds of years of ancestry on totally different continents. Two people with nothing in common except that they once had two children together carried the same allele and passed it on to me. I didn't expect that to happen, even knowing how very similar the DNA of all human beings on the planet is.
I didn't have any reason to think that the alleles would be different, except my own preconceptions, and those preconceptions are exactly what one shouldn't bring into a lab. It's why a lot of tests are conducted as double-blinds, so the examiner can't accidentally bias the results, and you can read more about that in Ben Goldacre's work.
So What Have We Learnt Today?
Today children, we learned about PCR, restriction enzymes, and gel electrophoresis. We also learned about how our biases can even surprise ourselves, and that's important to know. Science and the scientific method is about by finding out what must be true, based on eliminating what isn't. It's impossible to get rid of all our biases, but noticing them and fixing them when they come up is an important attempt.
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