Tag Archives: genetics

Book: Genetic Modification in Food

Genetic Modification in Food

Balanced introduction to GM foods for absolute beginners.
<100 pages, ★★★★★

Quick review today. I spent a long time making a table of organic compounds and their smells (view it here).

This book, Genetic Modification in Food, it’s one of the few books that succeeds in conveying a controversial scientific issue to the public while maintaining balance and accuracy. It’s suitable for readers who know nothing about science at all. It appeals to people who are concerned (with good reason) after reading/hearing/seeing reports about GM crops in the news. The concerned British public, for whom this book was intended, has an unusually high resistance to GM foods—so this book, which is free from ‘pro-green’ or ‘pro-science’ extremism, is a welcome addition to the pop-sci literature mix. ★★★★★

12 things I learned from my 23andMe results

Just before Christmas, I spat into a plastic tube and sent it to 23andMe: a genetic testing company in California.

23andMe Logo

 

23andMe tests one million SNPs (minor changes) in a person’s genome, many of which are linked with known, inherited traits. Their results reveal a wealth of information about your health and ancestry, ranging from eye colour and bitter taste perception to the presence of major genetic diseases and your extended family tree. Meaningful results are then sent to you by email within a few weeks.

All this is priced well-below cost, at just $99 plus shipping. It was totally worth it. Here’s a list of the 12 most interesting things that 23andMe revealed about me.

1. No carrier status

Fortunately, I carry none of the 48 diseases for which 23andMe tests. That’s good news! None of these diseases will affect me, nor will they be passed on to my children.

2. HIV-resistance: CCR5 +/Δ32

This is awesome—I carry one copy of the HIV-resistance allele! A very small percentage of people are lucky enough to have this allele.

3. Can’t taste bitter: TAS2R38 -/-

The TAS2R38 gene encodes the receptor that detects PROP and related bitter plant compounds. I have a relatively common mutation that is insensitive to PROP. My version of this gene improves the taste of bitter foods—including poisonous ones.

4. Can digest lactose: MCM6 +/+ (regulates LCT)

I don’t like milk, but at least I can digest it. I have two fully-funcional copies of the lactase enzyme, and both will remain active throughout adulthood.

5. Slow caffeine metabolism: CYP1A2.

Caffeine is primarily metabolized by the liver enzyme cytochrome P450 1A2. My version of this enzyme metabolises caffeine slowly (just like 99% of people). I learned that I’m not one of the 1% of people who are virtually insensitive to caffeine.

6. Ancestry

British and Irish: 67.6%; French and German: 5.8% (4 gen); Scandinavian: 0.1% (10 gen); Northern European: 24.0% (2 gen); Southern European: 1.2% (6 gen); Other European: 1.1% (7 gen); Middle Eastern/North African: 0.1% (10 gen); unknown: 0.1%.

James Kennedy ancestry results
Click to enlarge.

I calculated generations by taking the percentages, log base 2 and multiplying by -1.

Most of my ancestors were from “Britain/Ireland”, or “North Europe”, which includes Britain and Ireland. But interestingly, there was a little more diversity than I expected. one of my (great-?)great-grandparents was either French or German (see number 11). Six generations ago, there was someone from South Europe in the family. Ten generations ago, there was one person from Scandinavia, and one person from the Middle East or North Africa.

7. My blood group: A Rh(-) Di(a-b+) K-k+ Kp(a-b+) Jk(a+b+)

I already knew my blood group, but it was interesting to learn that blood groups are a complicated business. For everyday purposes, though, I’m an A-negative.

8. 3.1% Neanderthal DNA (very high)

Neanderthals looked like caricatures of Celts: white, brutish, red-haired and freckled. The average Caucasian has 2.5% neanderthal DNA, and I have 3.1%, putting me in the 98th percentile. It means that I’m “whiter” than most white people.

9. Maternal haplotype: H3 (Western Europe)

H3 is a minority European haplotype found in Western Europe. (Most natives are H1 haplotype.) Over the last 10,000 years, H3 declined in Europe due to random genetic drift, but remains prevalent today in the Basque region (probably because they mixed less frequently with outsiders). There’s almost no phenotypic difference between H1 and H3, so until further research is done, this is merely an interesting fact.

Maternal haplotype H3 map
Maternal haplotype H3 map
10. Paternal haplotype: R1b1b2a1a2f2 (Ireland)

Obviously. My paternal family is Irish and my paternal haplotype proves it. R1b1b2a1a2f2 is distinctively Irish.

11. One arm of Ch1 is entirely French/German

This is very interesting. I’m British, so while having a little French/German DNA is normal, having it all on one arm of one chromosome indicates that it probably all came from one, recent ancestor (no more than 4 generations ago). Given that French/German DNA is unique in going mostly undetected using 23andMe’s testing methods, and that the possibility of inheriting an entire chromosomal arm halves with each generation, this French/German ancestor was probably a great-grandparent. I didn’t know this.

James Kennedy French/German DNA
My French/German DNA (dark blue) is mostly on one chromosome.
12. Eight chromosomes contain one arm with no British/Irish DNA at all.

Chromosomes 1, 8, 9, 10, 11, 18, 20, and 22 contain one arm with no British/Irish DNA at all, and one arm with almost 100% British/Irish DNA. Given that one arm is inherited from each parent, this indicates that either I (or each of my parents) had one parent who was purely British/Irish, and one who was a more mixed “Northern European”.

James Kennedy's British/Irish DNA from 23andMe
Eight chromosomes have one arm with no British/Irish DNA (dark blue) at all. This indicates one recent family member of mixed, Northern European origin, not just from Britain and Ireland.

Additionally, 23andMe found 833 distant cousins who have also had their DNA tested. I share great-great-grandparents with the closest of these cousins, but none of them have surnames that I recognise. Some of them live in Wales, but that’s probably just a coincidence. The process of trying to link the family trees, if I do it, would be a long one.

I wanted to do this years ago, but it used to be too expensive: $999 plus a monthly subscription (whatever for?) The price then dropped to $499, $299 then $249 (last year), before finally hitting $99 before Christmas 2012—without any monthly fees. That final price drop prompted me (and nearly a million others) to buy the test.

I highly recommend 23andMe. The data arrives little by little, so there’s something to look into (and reference papers to read) each day. Anyone interested in their own health or ancestry should give it a go.

Book: A Life Decoded

This is the book I was looking for when I ordered Jay-Z's "Decoded". I've admired Craig Venter since the first year of university, and have finally found time to read his book.

Chronicles of an adrenaline junkie
400 pages, ★★★★★

A Life Decoded portrays a benevolent, macho J. Craig Venter.

When most of us were playing with toy cars, trains and planes, Venter was playing with the real thing. He satisfied his thirst for adrenaline by pressing pennies on railway tracks (to his disappointment, new U.S. pennies are too robust to be flattened by trains); by using bicycles to chase airplanes during takeoff (before the runway area was protected by an unscalable fence); and built engines with his friends and their parents.

His science career got off to an unusual start as a medic in Vietnam. He writes that the grotesque scenes of violence and disease spurred his desire to work in the field of medicine after his return from duty. But his actions toward the end of the book indicate that his desire to “help people” would always remain subordinate to his giant ego: an attribute that benefitted both him and his companies later (and, arguably, the sequencing industry) in the political and ethical minefields of human genomics. Evidence shows that it was not a “medic’s benevolence” but a relentless desire to win that would keep him so motivated.

Venter is best-known for sequencing the first human genome (his own genome!) with Celera Genomics. A more popular, publically-funded initiative to sequence the human genome was already underway, but Venter’s company was first to claim victory. On the day of Venter’s historic announcement (which was at the White House, with heads of state present via video-link), 46 per cent of Americans in a CNN/Time poll responded that Venter’s efforts bore “negative consequences” because his superiors ruthlessly patented the genes they discovered (on an unrelated note, biological patents have gotten out of hand: one patent was granted for a peptide sequence so short it could fit onto Twitter). Venter’s rebuttal can be summarised as, “I have always known that only a tiny proportion of human genes have yielded profits. The only viable alternative to patenting those genes would have been to keep the codes secret—which would have benefitted no-one”. Basically, “I could have done worse”.

Venter has always known that only a tiny proportion of human genes have yielded profits. The only viable alternative to patenting those genes would have been to keep the codes secret—which would have benefitted no-one.

Venter’s own genes are interesting. He starts by joking that his billion-dollar genome scan revealed the gene SRY (the gene for testes), which make him (as a man), “more likely to commit crimes, go to prison, be depressed, be addicted, get cancer, be violent, get rich, and die young”. He continues intermittently with descriptions of his genetic makeup: OAC2 gave him blue eyes, DAT1 contributed to his ADHD, MAO created his thirst for adrenaline (expressed through ever-larger yachts in later life), his DRD4 makes him less susceptible to addiction and schizophrenia, and his FTO type helped him keep a lean figure. His 5’HTTLPR made sure he didn’t get long-term depression, and while he prefers to work in the evenings, he’s not a “night owl”, which we can tell by looking at his Per2 and Per3 genes. Most interestingly, he is one of the lucky 1% of individuals who possess the rapid caffeine degradation gene CYP1A2, which eliminates the long-term side-effects of drinking coffee (cancer, heart problems) almost entirely. He describes many more.

Now, I really want to get my own genome analysed. It’s only $399 for a basic SNP scan from http://www.23andme.com. Genetic research is now advanced enough to make the investment worthwhile. For the insight it provides, it’d be money very well spent. ★★★★★