Tag Archives: biology

(Almost) Nothing is Truly ‘Natural’ – Part 4

Cezanne nothing is natural fruit and vegetables painting still life
Nothing on this table is natural – not even the fruits. The Basket of Apples by Cézanne

Corn isn’t ‘natural’

In 2014, I created a series of infographics to help convey this message. Corn, for example, used to be a spindly grass-like plant called teosinte, which Native Americans farmed and bred through artificial selection until it resembled the yellow corn of today.

In 9000 years, sweetcorn has become 1000 times larger, 3.5 times sweeter, much easier to peel and much easier to grow than its wild ancestor. In the 15th century, when European settlers placed new selection pressures on the crop to suit their exotic taste buds, the corn evolved even further to become larger and multi-coloured. Corn no longer resembles the original teosinte plant at all.

Watermelon isn’t ‘natural’

Watermelon began as a hard, bitter fruit the size of a walnut. It caused inflammation and had an unpalatable bitter taste. Thousands of years of artificial selection (unintentional genetic engineering) have resulted in a modern watermelon that bears no resemblance to its African ancestor. Modern (artificial) watermelons are sweeter, juicier, more colourful and easier to grow than their ancestral varieties.

Peaches aren’t natural, either

Peaches used to be hard, cherry-sized fruits with giant pips. Like corn and watermelon, peaches became larger, sweeter and juicier over thousands of years of inadvertent genetic engineering.

Bananas, wheat, pigs and all farmed animals and plants are not natural

Before agriculture, carrots were white and spindly. Wheat was tall and scrawny with little calorific value. Apples were tiny and sour with giant pips (like crab-apples today). Strawberries were tiny, bananas had stones in them, and pigs were viscous creatures with tiny backsides that made for a not-so-delicious ham. Cows didn’t produce much milk (just enough for their own calves) and chickens were skinny little creatures that laid eggs weekly rather than daily. Every species that’s ever been farmed by humans has been genetically modified over time as a result.

I keep making this point because our ancestors deserve credit for their hard work: they toiled in the fields for thousands of years to breed plants and animals that are suited to our modern tastes and lifestyles. For modern humans to call the results of our ancestors’ hard work ‘natural’ is an insult to the millions of ancient farmers who worked so hard to produce them.

Engineers (including genetic engineers) know that humans have toiled for millennia to change nature and suit it to our own needs – animals became tamer and meatier, and plants started producing more edible portions. I want to counteract the misconception that humans encountered nature in a ‘pristine’ state.

Great documentary snippet – Animal Pharm

[ancient humans] toiled in the fields for thousands of years to breed plants and animals that are suited to our modern tastes and lifestyles. For modern humans to call the results of their hard work ‘natural’ is an insult to our ancestors.

I show the above documentary my Year 10 Science students to demonstrate what is currently being produced using genetic engineering techniques. The video explains all the concepts mentioned in this article and is accessible for and educated audience of any age.

This post is part 4 in a weekly series on chemophobia. Next week, we’ll look at the psychology behind chemophobia.

Chemistry Task Words

Chemistry VCE task words verbs for Chemistry education and instruction
Click for a PDF version of these task words

RTQ! This is one of the most common sources of errors in Chemistry examinations. When I sat 2014’s VCE Chemistry examination, I lost 5 marks in the paper for not reading the question! Your teachers will have told you to ‘read the question’ or ‘RTQ’ as well.

Task word errors can be avoided in two ways. First, learn the exact meanings of each task word. This is particularly important for EAL Chemistry students. Second, highlight the task words in a question (just as you would highlight the important information in a complicated titration question).

For example: “Explain how the different intermolecular forces in butane and butan-1-ol give these two compounds different boiling points. 3 marks

In your answer, you will need to explain the effect of intermolecular forces. This means you’ll need to write why the butan-1-ol forms hydrogen bonds (due to the polar nature of the hydroxyl group) whereas butane forms only dispersion forces with its surrounding molecules (due to the non-polar nature of the molecule). You’ll also need to make some kind of comparison (which is hinted at by the word, ‘different’) in order to get all 3 marks.

Example 3-mark answer: “Butan-1-ol forms intermolecular hydrogen bonds with the surrounding molecules due to the polar nature of the hydroxyl group (O-H bond). Butane forms only dispersion forces with its surrounding molecules due to the non-polar nature of the molecule. Hydrogen bonds are stronger than dispersion forces and thus require more energy to break. This results in a higher boiling point for butan-1-ol than for butane”.

One mark would be awarded for each of:

  • Explaining the intermolecular bonding of butan-1-ol
  • Explaining the intermolecular bonding of butane
  • Comparing the relative strengths of the two and relating this to boiling points

In a 2-mark answer, the student might omit the comparison step:

Example 2-mark answer: “Butan-1-ol forms intermolecular hydrogen bonds with the surrounding molecules due to the polar nature of the hydroxyl group (O-H bond). Butane forms only dispersion forces with its surrounding molecules due to the non-polar nature of the molecule.”

In a 1-mark answer, the student might only mention one of the two molecules, or might only make a comparison without explaining why these two compounds display different types of intermolecular forces.

Example 1-mark answer: “Hydrogen bonds formed by butan-1-ol are stronger than dispersion forces formed by butane and thus require more energy to break. This results in a higher boiling point for butan-1-ol than for butane”.

In that latter example, the student didn’t explain the reasons for the differences in intermolecular bonding – they merely stated them.

Task word Chinese Description
Calculate 计算 Write the value of a number (include equations)
Compare 比较 Write the similarities and differences between
Evaluate 评价 Write arguments for and against
Define 确定 Write the exact meaning of
Describe 描述 Write details about (a thing or a process)
Discuss 讨论 Write reasons for and against
Distinguish 区分 Write the differences between two or more things
Explain 讲解 Write details to give the reader an understanding of
Find/State Write (sometimes by doing calculations)
Identify 鉴定 Write which one
Illustrate 说明 Write something and draw a labelled diagram as well
Indicate 表明 Write which one (usually on a given diagram)
List 列出 Write a list
Outline 轮廓 Write a summary
Suggest 建议 Write a reason for a phenomenon
To what extent 到什么程度 Write whether a reaction is complete (→) or incomplete (↔).

Watch task words in the examination… and make sure you answer the question!

Veritasium image

10 Best Science Channels on YouTube

1. Veritasium blows your mind by breaking misconceptions

2. Periodic Videos: experiments you’d love to do but can’t

3. SciShow blasts fun facts

4. Numberphile makes you LOVE mathematics

5. AsapSCIENCE: fascinating hand-drawn mini-tutorials

6. MinutePhysics: fascinating mini-Physics tutorials

7. Vsauce investigates fascinating questions

8. SmarterEveryDay explains cat-flipping, and more

9. Science Channel gives you the latest Science news

10. NASA gives you real-life science inspiration

Are there any that I missed from this list? Add them in the comments section below.

Ingredients of All-Natural Cherries

Cherries are extremely sweet, and are unusual in that they contain more glucose (52%) than fructose (42%). Their bright red colour comes from the carotenes and capsanthin (the E160 colourings) that are present in high quantities throughout the fruit.

Cherry flavour comes from a huge collection of aroma compounds produced naturally by the cherry. To make all of these compounds in the lab, then mix them together in the correct proportions would be ridiculously time-consuming and expensive.

When making artificial cherry flavourings, only the first two compounds are usually added: (Z)-3-hexenol and 2-heptanone. Artificial cherry flavouring thus tastes absolutely nothing like real cherries: it lacks most of the ingredients that give real cherries their delicious flavour.

It’s quite a different story with oranges and lemons, though. Most of the flavour of oranges and lemons comes from (+)-limonene and (-)-limonene, which, by themselves, smell like orange and lemon, respectively.

Ingredients of All-Natural Cherries
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Ingredients of An All-Natural Peach

I enjoyed reading the discussion that last week’s Artificial vs Natural Peach spawned on Tumblr and Facebook. People discussed the meaning of “natural” versus “domesticated”, and debated whether humans have really “improved” fruits in the last few millennia or just evolved them into giant candy.

I hope that people now see the irony in the title, “Ingredients of an All-Natural Peach”. The fruits we grow aren’t natural at all—but I still love to eat them!

Ingredients of an All-Natural Peach POSTER

jameskennedymonash.wordpress.com

Over the next few weeks, I’ll be posting more Ingredients posters onto this blog. I have a whole stash of them lined up, ready for you to eat…

I’m also looking for your ideas. What would you like to see the “ingredients” of next? Vanilla? Tea? List them in the comments below.

Stay up-to-date by following @VCEasy on Twitter, where I tweet about Chemistry for visual learners. These posters usually appear there first.

Enjoy 🙂

Meet the Terpenes: A Visual Introduction from Isoprene to Latex

Inspiration for Meet the Terpenes came from the rhetological fallacies graphic over at Information is Beautiful, while motivation came from a 45°C heat wave this week that prevented any sensible Australians from going outside. So I stayed at home and did this.

Meet the Terpenes - A Visual Introduction from Isoprene to Latex
Click to download 200dpi JPEG (5.4Mb)

It took about three days to sketch, research and create.

Three days ago, I knew nothing about terpenes. My undergraduate phytochemistry class was really difficult. The teacher was a genius, and put huge amounts of effort into his tutorials, giving us thick booklets at each seminar filled with his hand-written notes and dozens of chemical structures. But for some reason, I just didn’t get it.

So this week, I decided to make the graphic I wish I’d had when I took the phytochemistry class many years ago. Having this poster on my wall would have answered all my questions and made the class much more enjoyable. I hope you find it useful, too.

As always, I welcome all feedback, corrections, suggestions and comments, etc.

Enjoy 🙂 James

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. ★★★★★

Essay: Student alternative conceptions in secondary level plant science

After much deliberation, I’ve decided to put this online. Here’s the first essay I wrote during teacher training. Monash University was kind enough to award it the top grade 🙂  Continue reading Essay: Student alternative conceptions in secondary level plant science

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. The virus which heterosexual, monogamous vegans almost never encounter just got even harder to get.

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: Stories of the Invisible

Stories of the Invisible: a guided tour of molecules
A modest cover for a modest book.

Rapid tour of the sciences, from Chemistry to Biology.
380 pages, ★★★★★

Reading this, I feel like one of those busy tourists who takes a coach-tour of 17 European countries in the same number of days.

The book’s travel plan looks like this:

  • Pure Mathematics (smallest)
  • Statistics
  • Theoretical Physics
  • Particle Physics
  • Applied Physics
  • Theoretical Chemistry
  • Inorganic Chemistry
  • Organic Chemistry
  • Biochemistry
  • Genetics
  • Cell Biology
  • Physiology
  • Psychology
  • Medicine
  • the Social Sciences
  • Philosophy (largest)

By reading this book, you’ll get a glorious tour of all the subjects in bold above. Equate that to dozens of stamps in your passport.

You’ll learn why spider silk becomes insoluble when it solidifies as it comes out of the spider (and thus can’t be re-constituted like dried vermicelli can). You’ll learn the history of some chemical discoveries (all of which occurred by accident). You’ll learn why bacteria can ‘swim’, and how this technology can be harnessed to make nano-robots. You’ll learn how ambiguous names such as “A-bands” and “H-zones” (in muscle sarcomeres) indicate that the discoverers hadn’t the faintest clue as to their purpose. On top of all that, you’ll even learn how nerves work (that’s physiology).

This book even dispels my two favourite high-school lies: first, that mitochondria are round (actually, they are long and blobby, like the wax that drips down the side of a burning candle); and second, that ATP has a “high-energy phosphate bond” (actually, it’s only a high-energy bond under normal cellular conditions because cells manufacture a strong intracellular disequilibrium in favour of ATP).

This book is a quick primer to Chemistry and Biology. It’s clearly-written, and big diagrams are used when necessary. I recommend Stories of the Invisible for all prospective chemistry, biochemistry, or biology students. You all have time to read it. ★★★★★

Book: Molecular Biology of the Cell (Alberts’)

Molecular Biology of the Cell
Each edition changes colour. Fifth edition is red. Fourth edition is grey.

The KitchenAid of biology. All other biology textbooks are just accessories.
1392 pages, ★★★★★

Molecular Biology of the Cell, or “Alberts'”, as it’s known colloquially, is the cornerstone of a university education in biology. All biology undergraduates will have seen it, most of them will buy it, yet none of them will actually read it. They should.

Alberts’ details every aspect of cell biology, and delves deeply into physiology, neurology and pharmacology as well—rendering some undergraduate textbooks in those fields redundant.

Illustrations are crisp, clear and never excessive. Colour is used for clarity but not for aesthetics. The text is prose-heavy and reads like a story so it can be read cover-to-cover quite comfortably (albeit slowly). And that’s exactly what students should do.

Many students will use Alberts when they need to learn about something quickly, such as, “what shape is a mitochondria?”, “what does kinesin do?”, or “in what order does the electron transfer chain take place?” If you haven’t read this book from cover-to-cover already, then finding those answers is going to take much longer than you think. Alberts is not a reference book—it’s a comprehensive background story. Quick answers can be found on Google, but genuine understanding comes from a cover-to-cover reading of Alberts. ★★★★★

Book: The Brain that Changes Itself

Yes, I read a photocopied version of this book. This is commonplace in China.

Modern update to Sigmund Freud’s
The Interpretation of Dreams

426 pages, ★★★★★

I’ve changed many times. At 17, I used to drive at 130 mph and get searched by police for “looking suspicious” (a vicious cycle). At 19, I became a Cambridge student, at 21 became a raving Communist, and just one year later became an ideological capitalist. Now, at 23, I’m studying Chinese and Buddhism at home with Silver Needle Pekoe tea, or as the Buddhists would say, “I’ve stolen my monkey brain”. I recommend it.

I can therefore connect easily with the thesis of this book: that the brain is plastic.

Reading neuroscience usually brings one of two outcomes: I either self-diagnose a plethora of conditions (this occurs when the descriptions are flattering, such as the OCD in Steve Jobs or the Aspergers’ Syndrome in The Essential Difference); or I am disgusted by the patients described and thus feel more normal than ever. This book is certainly the latter.

The book is enlightening throughout. Here are some highlights:

  • new brain theory (plasticity)
  • a theory of autism (BDNF, white noise)
  • support for Buddhist teachings
  • a theory of love (oxytocin, memory loss)
  • insights into depression (hypothalamus shrinkage)

The Brain that Changes Itself is mostly an enlightening (rather than disturbing) read. It makes advances on many books I’ve read. It uses scientific animal models and human case studies to ‘prove’ the new, emerging theory of brain science: that the brain is plastic.

The Brain that Changes Itself is more insightful on autism and Aspergers’ Syndrome than Simon Baron-Cohen’s The Essential Difference. Improper release of BDNF (brain-derived neurotrophic factor); and excessive white noise during brain development could cause autism. This was even proven using rats! This book stops short of explicitly stating a cure for autism, but the reader can infer a cure from the information given in this book. The author doesn’t write the cure due to its “capability for misuse”. You’ll have to decode it for yourselves, which is infinitely more exciting.

The Brain that Changes Itself usually agrees with Buddhist teachings. On page 171, we see a direct parallel with The Heart of Buddha’s Teaching with, “Buddhists will observe the effects of anger, rather than the cause, and therefore separate themselves from it”. Both books tell us how learning only arises from “focussing”, “being present” and giving “undivided attention”. (The “deliberate practice” in Malcolm Gladwell’s Outliers is essentially the same phenomenon.) Buddhism has been teaching us this for 2,600 years.

Happiness by Buddhist monk Mathieu Ricard tells us that “love wipes out previous memories, especially bad ones”. The Brain that Changes Itself uses science to tell us exactly how this happens. Oxytocin is released when we fall in love, which makes us feel warm and trusting of our new partner. Since falling in love requires simultaneously “falling out of love” with previous partners, oxytocin also wipes parts of our memory. This has been proven using studies in using rats.

Finally, The Brain that Changes Itself tells us that long-term depression was found to cause hypothalamus shrinkage, especially in the “critical period” of brain development. Short-term depression had almost no effect on hypothalamus size. The hypothalamus shrinks to decrease our sensitivity to the negative effects around us. The result is, unfortunately, a desensitisation of pleasure as well as pain. Schizophrenia, ADHD and bipolar disorder are all implicated.

This book lends itself very well to being taught in schools. Each chapter would take one or two lessons, and the students can simulate the human and animal experiments with each other in class. ★★★★★