Saturday, 19 April 2014

Slavery and Exploration



My children love the TV cartoon series "Octonauts". They are a collection of ocean explorers/ adventure heroes who live on a submarine called the Octopod, and undertake missions generally involving one real marine/aquatic species at a time, and something to do with their Mission Statement: "Explore - Rescue - Protect".

It's nice - boppy music, nothing violent, and now my kids have a reasonably comprehensive knowledge and fired-up curiosity about cone snails, gulper eels, triggerfish, several species of whale and of shark, various crustaceans, the Amazon River, and deep-ocean topographic features like trenches, hydrothermal vents etc. It does make their teachers a little bit crazy with their level of smartypants marine science knowledge.

One thing about this TV show has made me very uneasy for some time. I suspect all the domestic work on the Octopod is done by slaves.

Octonauts as Slave Owners

  • I put it to you that the Vegimals (see that little yellow-headed fellow to the bottom left of that first picture, just above the Octonauts logo?) are the quintissential slave race. As explained in the episode 'A Very Vegimal Christmas' (which you don't have to watch unless curious about brine lakes and marine mucelage):
  •     The Vegimals were brought into the Octopod in infancy, separated from their previous environment, and taught to serve the Octonauts.
  •     They perform menial and service jobs, and are not paid for their labour (well, to be fair, financial renumeration of any kind is never discussed)
  •     They are all but invisible the bulk of the time, they are not acknowledged by any plot device in any episode until roughly the end of the 2nd season, and this episode at the end of the 3rd season is the very first one in which they feature significantly.
  •     Their leader - Tunip - is almost afforded the lowest-raking crew position, but not quite. This is a classic slave control tactic. He is Malcolm X's House Negro
  •     Many of them have no names. A Wiki I found has a list of 16 vegimals but only 8 are in the episode. Some - like Wallabaga, Charchard, and Salapeno have never ever been named or even seen on the series (and I have watched the whole series). They might be field negros.
  •     And the Vegimals are critical to the success of the Octopod's missions. Without someone else performing all the daily thankless tasks, Captain Barnacles, Kwazii, Peso and the others wouldn't be able to go on all their fabulous missions. In the words of Octonaut Chief Scientist Shellington: "I don't know what we'd do without the Vegimals". 
  •     They sing as they work.
  The Octonauts got me thinking...

Slavery and Exploration - are they a natural partnership?

Exploration - the act of going far outside your territory to simply see what is out there - requires a (relative) large amount of resources. Risks to the explorers are high - the new environment often pushes the limits of survival. Resources - food, equipment, fuel - are taken from the community to support the explorers, and everything must be taken into the unknown, because it may not be available when you get there. The probability of the mission returning anything useful to the community is small, but when exploration pays off, it pays off megaloads. And glory shall be bestowed on the magnificent and triumphant explorer, or at least whichever explorer got the credit to stick to him.

I shall explore this with examples and stop when my indignation gets too hot.

 Mount Chomolungma

I remember reading about Sir Edmund Hillary reaching the top of Everest. There was a photo. In class, I wondered how he got a tripod up to the summit. My fat-headed yr 9 history teacher said "Oh, he probably balanced the camera on a rock or something, and used the auto-timer."
It was some years before I found out that Tenzing Norgay was actually the one in the photo, and that Hillary was the cameraman.
 
What I failed to appreciate until relatively recently is that although they each carried their own loads up the mountain, Tenzing and the other sherpas spent - and their descendants continue to spend - vast energy and time in the preceeding weeks hauling equipment and supplies for "explorers" for very little financial reward (this page suggests $5000/climb) and virtually no recognition.

Tenzing Norgay and Sir Edmund Hillary

Sir Edmund Hillary did understand this massive inequity, and he devoted a large part of the rest of his life and fortune to the sherpa community. the Sir Edmund Hilary Foundation runs a hospital and secondary schools and supports reforestation and sustainable adventure sport in Nepal.

Polar Exploration

Job ad for Shackleton’s 1914 South Pole ExpeditionYou might think that polar exploration didn't have the same shameless exploitation of the native population as Everest. This is indisputably true. But all the polar expeditions were resourced by, and built on, colonial imperialism, and economic growth.

I found this paper which talks about the funding of Arctic expeditions, eg looking for the North West Passage, and mentions the South Polar expeditions in passing. They were a mixture of publicly and privately funded, but aside from a few oddball explorers like Amusden, they were heavily nationalistic and driven by imperial expansion or competitive advantage in trade. Empires - whether national or corporate - are prepared to finance risky exploration on the possibility of a rare but massive payoff. Also see my future blog post on imperialism, slavery triangular trade, and economic growth.

At risk of setting my bra on fire and waving it about, I would love to mention in passing the misogyny of exploration - and polar exploration in particular. I heard a radio interview with Jesse Blackadder, author of a historical novel about the first women in Antarctica, and she was quite scathing about the ongoing attitude that Antarctica is no place for women, she even called it something like ' the last refuge of machismo'. The first women there - and many women since - have had to fight hard and pull sneaky tricks to make it there to visit, let alone winter. A relative of mine who wintered there in the 1960's described to me that women weren't allowed to winter over, notuntil the mid 1980's. The reunions have an extremely small number of women at them. I also found interviews with Sara Wheeler, author of an account of her own winter in Antarctica on the American base, who made reference to the ingrained sexism, for example that the survival manual suggests that if bare skin contacts cold metal and sticks to it, the best way to remove the skin is to urinate on it. And my final piece of evidence, while the ashes of my bra swirl away in the breeze, is the very educational "Culture" page of the US Antarctic Program, complete with Shakespearean cross-dressing in the theatrical productions.
Depending on where you go and who is in your team, the summer gender ratio varies from 2:1 to 5:1, and the winter ratio from 8:1 to 80:1.
Special thanks to Messrs Bellingshausen, Scott, Shackleton, Amusden, Shackleton again, Amusden again, Byrd, and Hillary & Fuchs for taking government money, never acknowledging their wives, peeing on their own skin, eating their dogs, and dying or not dying as the during polar exploration.

The Age of Sail

No. Don't even get me started on the crimes against humanity from the five hundred years of European ocean exploration and colonisation. I sometimes get vivid nightmares about the trails of scurvy corpses from abducted sailors that would be left behind those ships, the spread of smallpox and panic and violence across continent after continent, and the magnitude and horror of the enslavement of native populations. There's a whole indignant post coming on the Triangular Trade. It is still in draft because I get so very angry while writing it.

The Moon

The Space Race was driven by Cold War imperialism and military aggressiveness. Not strictly slavery - although some of the Russian engineers may have had cause to dispute the line between coercion and enslavement - but on balance, I think the lunar and space programs have been the best of our human exploration endeavours. 

My brother has an autograph from an Australian astronaut, Andy Thomas. We found it in a box of old papers the other day. It's awesome.


I am running out of juice, even though I would also like to talk about mineral resource exploration, the history of aviation, and modern ocean exploration (both surface and deep). 

So I will stop yakking and ask you guys - all three of my readers - 


What do you think? Is exploration inextricably tied to slavery?

Wednesday, 5 March 2014

Writing and not writing and a vegetarian lunch menu at the bottom

I have not written very much this summer.
I had wanted to make excuses; I am now working two jobs; our youngest has turned into a very strong-willed little person and is making family life both rich and complicated; the beach was so very much more compelling than this laptop; I have been ill and it's not likely to improve; we demolished one very mouldy bathroom and we are not really agreeing on the replacement design and I would rather spend my evenings painting watercolors of tile layouts involving giant squid and Fibonacci sequences than writing a blog....
... but each of these, all of these would be surmountable if I got my hiking boots on and started climbing (where 'climbing' happens wrapped in a blanket on a couch, between 10PM and 1AM, and sometimes just after dawn)
Why am I not climbing?

It kindof goes like this.

I am always having ideas, globular amorphous things that drift out of some deep thought process, float up past my awareness, and I go "Hey that's cool? and sometimes note them down. My current list has no particular order:
  • Specific Gnostic texts firing up my feminist indignation with Christianity (I knew I shouldn't have hit the theology)
  • Bees and food security vs. suburban anxiety about insects
  • 21st century slavery and the new Triangular Trade
  • Super tasty vegetarian lunch
  • Social virtue is now measured in learning and eating habits rather than good manners and religion
  • 5 steps for how a husband can stop a fight quickly without losing
  • The slogan of an empire probably encapsulates the seed of its destruction
  • The appropriate demographics to be In Charge of Stuff (not necessarily 50YO Caucasian men)
  • Peoples' minds are much more diverse than our similar bodies might encourage us to assume
  • Developing a too-late crush on Christopher Hitchens and George Eliot
  • That shark cull in WA
See? Ideas. All over the shop. In Terry Pratchett's Discworld, I might have been caught in a meteor-like shower of incident beams of inspiration. In Elizabeth Gilbert's genius paradigm, I might be compelled by a possessing force or chasing an external genius (genie) to identify and chip out these ideas. But you can see that they are still stuck in rock (or maybe spongecake - I am possibly more like Martha Stewart than Michelangelo), and I have only traced the outline on the surface and am not digging in.
I am not digging in.
I am not brave enough - which is strange because I am not normally one who suffers from fear.
  1. Writing has an effect on me and my family. Carving out the texture of an idea, the fine grained detail, cross-referencing and finding credible sources to back it up with some evidence is both time-consuming and absorbing. I get small strange obsessions, like the life cycle of an octopus and the CO2 sequestration potential of different eucalypt species. My colleagues have started to ask me how to fix a toilet, what's the deal with the Ukraine, and what to plant which will trail nicely and cool their verandah - and I mostly have answers. Ideas lead to more ideas, I stay up later, I write a bit of blog, a bit for a magazine, and then go read up about plankton identification. I freak out about fisheries management, talk to my family and before I know it my 7YO tells me that he wants to crew on the Steve Irwin to stop the shark cull in Western Australia, and my 4YO is explaining the Fukushima nuclear disaster to his kinder group. With everything else in our busy life, I don't need to be chasing these trails. I figured it might be easier for us all to be happily ill-informed and quiet, and leave those ideas in the rock/spongecake.
  2. I risk my idea being wrong in the first place. I'm getting a reputation for being right (within the broad definition of right = not wrong). What if I'm wrong?
  3. Worse, I risk discovering that it is actually a really good idea and someone else wrote about it before I got there. (Recently; Niesche, Battlestar Galactica scriptwriters, and some bird contributing to Melbourne's Child magazine have all got there before me)
  4. Worse still, I risk not being good enough to write about a good idea. I am worried that I am a bit like a duck who got struck by the wrong incident idea, and is struggling to communicate the solution to the world's energy crisis by ruffling her feathers and going quack.
  5. Worst of all, I risk pointlessness. Even if it's good, what if it's a waste? I risk being the person who patents a superior typewriter during the rise of IBM. I wonder about Isaac Newton spending his best thinking years trying to find numerical patterns in the Bible.  
  6. And I have recently been really enjoying knitting. I can't knit and write at the same time.
 OK I'm done, and shall get on with writing.

Super tasty vegetarian lunch menu, for my best friend from school and her Danish Sikh husband when they come to visit next month.
Flat mushrooms sprinkled with olive oil, oregano and breadcrumbs, grilled for 10mins
Home-grown potato gratin; slice and pre-microwave the potatoes, make a dairy free Bechamel sauce substituting soy for milk and olive oil for butter, bake for 20mins
Corn, bean and chick pea fritters, bound with egg and flour, flavoured with fresh coriander and probably a dash of worcestershire sauce, served with habanero chilli sauce for the grownups and sour cream for the kids
A basic green salad with added mango and mint for variety
Honey-baked quince for dessert

Now the list of ideas is one shorter.  I am off to sleep.

Friday, 28 February 2014

At the school pickup - no we're not at all like a pack of colobus monkeys, honestly.

It's a delicate political situation, the early primary school pickup pack. The only thing I have in common with the drop-off and pick-up parents is the common choice of school. But there is such a powerful social pecking system established and maintained with bodylanguage and non-verbal cues. I can't take it seriously - but I sortof do, because of the way, last term, that the social skirmish between H's mum and B's mum played itself out in a literal and quite brutal punch-up between the kids around the side of the play equipment. Nobody wants to be labelled a weird mum in case their little prince or princess ends up the weird, teased, terrified kid by association, and ends up stuck with it for their whole childhood.

Going into the pickup pack presents certain basic challenges.

1) What do you wear? Designer labels? A professional outfit - suit and jacket, fluted skirt and crisp tailored shirt? Gym clothes? (Pristine or sweaty? Or designer gym clothes?) Beige slacks and camel pumps and some floaty layered top system?
On Wednesday I miscalculated. I only just managed to extract the younger kids from the park and prise the scooters from their indignant claws, I hoisted and clipped them into the car seats, and raced up to the hill, arriving at pickup just in time - and then I realised I was still wearing my very best potting-mix-decorated gardening clothes, embellished with a giant dried-snot smear from one of the kids still encrusting my shoulder. Oh, the disapproval! This is a good school in a good suburb - one really ought not arrive in tracky-dacks and festy t-shirt! The social ladies really gave me the look-down, look-up, turn-away, sneer-over-shoulder. It was 'lucky' for me that I did the drop-off the next day wearing a nice black dress with pearl drop earrings to reestablish my status. Another aberration may not be tolerated.

2) Who do you walk over to stand with? This part is worse than Year 9 girls were, because now we identify each other by our cars, our husbands' professions, and whether our outfits are properly styled and coordinated. The real-estate magnate's wife won't sit with the tree lopper's wife, and there are a few who who won't sit with you if your shoes aren't right. And while we do know we shouldn't get too stuck in our ways or caught in cliques, we do fall into the same friendship groups as our kids, maybe hoping that our children have chosen their friendships based on some kind of instinctive, inherent compatibility, which extends to the families too. Or maybe it's just pragmatism: we'll have to sit through all the closest friends' birthday parties sometime so we ought to get a little bit social now.

I actually do like a few of the other mums. I want to have the families over for a barbie and a proper conversation, but have been working too hard to get organised. Hey I can barely catch up with my own friends! And the women most like me and who I like most, are, like me, working - with grandparents to pick up the kids, or using after-care, and so we only get these few short grabs of socialising.
S is a doctor, she is smart and nice and dresses a bit like me. (Too bad that our sons have recently been trying to shove each other off the play equipment - she and I hang out anyway.) A has just started her own business and doesn't at all mind me in gardening clothing. K is a civil engineer with very similar battle stories to mine. We all have a lot in common, up to the point where we really fundamentally don't - funnily enough, it's just like that between our kids.

3) What do you talk about? What is new to talk about with the same other mums who have met every school morning and every afternoon for the last two years - and probably for coffee and tennis in between? (The men doing pickup don't talk; they just stand under the tree, arms folded, like emperor penguins with their backs to the wind waiting for their chicks to waddle out of the snowstorm.)
Conversations must also be timed carefully so they can be broken off as soon as the bell rings, and so much of the interrelational subtlety is in postural inclusion and exclusion rather than content. Having said that, if you have some particularly juicy topic, you become the centre of the pack for that crucial 3 to 8 minutes.
Two of the mums have a clear advantage in the socially-agreed-interesting topics discussions.
  • M works in costume, hair and makeup for a TV station, and so she has an endless supply of dirt and inside information on the stars she dresses. When the talk turns to daytime TV (which can be the most talk-worthy thing that happens between drop-off and pick-up), M can step in with "Oh my god ... he is hopeless, he stuffed up the camera angles... they had to do, like, three takes of the kiss, and it was so awkward, because her husband was there, giving advice.... ." One on one, M is very down to earth, but she can really turn it up for the pickup pack.
  • S, aforementioned, has a doctor's collection of wacky, gross and outrageous medical stories. I asked her what's new and she said "Oh have I got a story for you.... and then the surgeon said... it came out in pieces!... the smell... and then the charge nurse came and....  " Just make sure you're not eating any smallgoods while she's talking.
4) How Good are you as a Parent? There are norms, and stepping to either side of a norm is the path to ostracism. It is the pick-up pack, after all.
  • Are you on time? Early means you're obsessive. Late means you're neglectful or sloppy.
  • How do you groom the younger siblings for the school pickup?Are they snotty? Do they stink? (Are they in designer clothes?) Acceptable paramaters vary according to the clique.
  • Have you been seen to yell, threaten, or lose the plot with your children in the playground?
  • Are there any stories about your parental neglectfulness? eg. did someone once see you in tears in the local shopping centre before the nice policeman returned your lost toddler?
  • Do your children eat bad food - so therefore you are neglectful? Do they live on perfectly nutritious things - so you must be a killjoy parent?
  • Do your children exhibit appropriate abilities in sport and music - or are you either turning them into worthless couch-potatoes, or pressure-cooking your children to achieve? 
  • etc.

I'm not getting paranoid. Honest.

Monday, 20 January 2014

A Crisis on Free WIll Most Recently Triggered by Epigenetics Research

"Some people think that science takes the wonder out of the world."
"Nonsense. [It] absolutely baffles me about how anyone can think that how learning more about something can take the wonder out of it. I mean, you look at the stars and they are [just] pretty points of light in the sky... and once you know about it, once you learn some more about the physics and that just blows your mind!"

- Elise Andrew, founder and maintainer of Facebook page and very nifty blog "I Fucking Love Science", responding to Natasha Mitchell on ABC Radio National a couple of weeks ago.

..."OK I'm here... I read your last post on epigenetics. We made it through all that sciency stuff. Where's your free will crisis? Isn't a deeper scientific understanding clearly more marvellous?"


I am just getting worried that there isn't very much of 'me' in this brain and body. Nor of any other human in theirs. That our 21st century Western cultural conception of self, of freedom of action, and of mastery of our own destiny, is (broadly speaking) totally false. Just about all the time, we are reactive, contextually adaptive, neural systems with only a very tiny capacity for self-control or self-change, and what we perceive as self-change is actually the consequential shifts in habits following a series of standard epigenetically driven life-stage transitions, awakening latent multi-generational adaptations at the key trigger points of time (eg. puberty) or contextual stresses (eg. a tricky work situation or a new best friend). 

Any human being is a complex system. But complex systems can be modelled, if you know the parameters. Here is the history of that modelling of 'self', in super-fast-forward and in diagrams. (These are mine, not ganked, If you're pinching them, have the courtesy to drop me a message & say hi.)

Enlightenment (1650-1709) philosophy provided the following simple and happy framework based around clever well-to-do gentlemen:
Displaying Enlightenment Self.jpg


In 1921, Sigmund Freud published a revolutionary and highly controversial idea that everyone had a 'subconscious', which made a person do things without their conscious awareness and shaped their perceptions, and that this was worth exploring in conversation. These days it seems obvious but at the time it was very difficult for the medical and philosophical communities to swallow. This might be because Freud instantly halved a person's capability to control their actions (although this had been coming; the law had invented "criminally insane" as a defence some time before....)
Here is a diagram of that revolutionary idea.

Displaying Freudian self.jpg

Come with me to the year 1985. Through the 'science' of marketing, the modelling of human behaviour was no longer a purely intellectual pursuit - large amounts of money were being made. The models of human behaviour had been divided into sub-populations, mostly for the purpose of predicting and manipulating buying habits. Based on age, gender, socio-economic origins, current profession, income, and geographic location, a good marketing database can predict purchasing habits quite precisely. The spooky thing is that what works very well for aggregated humans also works quite well for each individual in that demographic. Any 6 yr old girl is very likely to covet a set of pink butterfly hair clips. Any reasonably affluent, urban young man is extremely likely to have an interest in car audio. Any mid-50's male is likely to be totally unwilling to change his political stance. Thus, our model of 'self' now includes an age, gender, and socio-economic context component - all embedded deep in Freud's subconscious.
Displaying Marketing self.jpg



Psychological research in the 20th century included a number of fragments, which, when pieced together in the 1990s, give a picture of how this 'subconscious' might work. Kahneman's "Thinking Fast & Slow" (...have you read it yet? It's a very good book. Just sayin.....) assembles a number of these fragments to provide a construct of two different systems of thinking, 2 different bosses job-sharing the task of being in charge of your decisions. 'System 1' works quickly, automatically, without conscious effort, and uses short-cuts like emotional preference and whatever is stored in your short-term memory to make its decisions. It is very good at answering questions of preference (eg. Do you like apples?). Its counterpart, 'System 2', finds mental effort a bit painful, and works much more slowly, but is better at weighing up alternatives (Do you like apples more or less than you like peaches?) and providing answers to non-intuitive problems (148 x 51 = ?). But System 1 almost always interferes with the result that System 2 gives.
Kahneman and Tversky's 2-system model leads me to draw up a model of 'self' a bit like this:
Displaying kahneman self.jpg

See how that conscious part, where "I" have conscious control, is shrinking. Every time the model gets richer, the conscious part gets smaller.

And now here is my crisis of self.
The book "The Epigenetics Revolution" describes in some detail the intercellular mechanism that allows trees, mice, bees etc. and certain human bad-behaviour and disease populations to be shaped, and triggered at key times, sometimes for multiple generations, providing extraordinary degrees of flexibility for the organism to adapt to its environment. And the book keeps mentioning how 'tagged' (in long words: multigenerationally persistent epigenetically modified) sections of chromosome are more active in human brain cells, to up-regulate and down-regulate neurotransmitters and hormones, sure, but also possibly to store memory, control synapse growth and activity, and in short, shape the structure that holds our 'self'. But that's only speculation because we don't know yet. Genes and proteins are very very small, and it's unethical to set up experiments on live human brains (which wasn't a problem for those the enlightenment-era gentlemen, by the way!)
So, my epigenome drives how my experiences alter the structure and function of my brain (and body), and the brain holds 'me', and the structure keeps adapting itself at the neurochemical level to all the immediate situations and changes in life, refining how I react moment-by-moment. All of my actions are reactions by my epigenome and my physical soma to my life up until then. I cannot control anything in the moment. The consciousness is an observer, running a commentary on the things the mammal body and brain does. In the moment, nothing is a choice.
A little pathetically, this is the model that I am left with.

Displaying Epigenetic self.jpg


So here I am, a human, with a genome almost identical to every other human, plus a bunch of unique epigenetic marks. What is 'me', as opposed to my genetic, epigenetic, demographic, and somatic reactions to my environment? How much control do I really have over what I choose? How much of my life is destined by my epigenome - how long I live? My faith in a higher power? My physical abilities? The way I look? My intelligence? The way I will adapt to situations in my future, of which I have no idea yet?
  • Based on honeybee studies, the book thinks that memory is a function of DNA methylation.
  • Based on rat studies and backed up by psychological evidence, the quality of my relationships is linked to my emotional self-regulation and my ability to love. These are built on histone bonds in my hippocampus, which were mostly set when I was being held and cuddled and carried around by the people who loved me when I was an infant, and in early childhood, while my brain was growing neurons and laying down synapses in the hippocampus, amygdala, and related deep brain structures. Emotional intelligence is a combination of the epigenome and childhood circumstances.
  • Based on the outcomes of the "Terman" longevity study, as a vaccinated and urban 21st century woman, my life expectancy up to age 40 is more or less determined by my 'conscientiousness', ie my natural temperament and tendency to look after myself (and temperament is loosely linked to epigenetically-set neurochemical base levels, from environmental conditions during my mum's pregnancy with me). A component of my life expectancy includes my predisposition to early-onset disease, both genetic and epigenetic, eg. diabetes, asthma, breast cancer, schitzophrenia, alcoholism.
  • Based on the same longevity studies, my life expectancy past 40 is more or less determined by the quality of my physical and mental lifestyle up to age 40. These are somatic variations, or the way the human organism in question bounces off their environment and circumstances. If I smoke, drink, party hard, take performance-enhancing drugs or get psychologically traumatised, I could change my late life trajectory, in particular my predisposition to disease, and my socioeconomic status. But my highly conscientious temperament makes such somatic variations unlikely.
  • Various meditation frameworks including Tibetan Buddhism and Alcoholics Anonymous provide a suggeston on how to have some power over self. The first step is almost always to acknowledge that a person is powerless over their destructive actions. Then by submitting to faith in a higher power and by engaging in deliberate, difficult, persistent reflection, you can retrain your old habits, incrementally, painfully, day by day.
While I gaze in wonder at our species (and all mammal species) and consider our capacity to adapt to environments and situations, the science of self has indeed blown my mind. It has also, inadvertantly, blown 'me' into a very insignificant and powerless little spot on the periphery of what I used to think of as my mind. I feel very very small.
I might stop reading neuroscience and go study some theology for a bit.

Sunday, 12 January 2014

Epigenetics - leading to a personal crisis about free will (coming soon)




(....tackling the small issues today, hey Lexskigator....)

I'm reading a book on epigenetics. Some reviewers of this book think it's a bit technical for a non-bioscience audience, but I find it absolutely enthralling. It's a summary of the exploding research field, where science is gradually getting a grip on the magnitude of the complexity of interaction between genes, junk DNA regulating gene operation, epigenetic 'tags' regulating gene operation, and a person's physiology, behaviour, habits and life trajectory. And bioscience is starting to realise that if they mess with any of it, the downstream effects are multiple, complex, and not really predictable.... although drug companies don't usually let that do more than slow them down a little bit.


My summary of epigenetics from this book follows - from the very beginning, as fast as I can!

For all earth lifeforms with cells which have nucleii and reproduce sexually:


  • Every nucleus in an organism has the same DNA. The DNA of cells in identical twins is also the same. DNA is a double helix: a dual-chain linear chemical base-4 code, notated in A, C, G and T.  Each letter denotes a chemical in the chain, and they always pair up to the same partners. A (adenine) always connects to T (thyamine). C (cytosine) always connects to G (guanine).
  • The bulk of our DNA sequence is contained in the chromosomes, which are twisted-up little squiggles in the nucleus of each cell of our body. Each chromosome is a big long string with two ends. The ends are called 'telomeres' and they have repeating sequences which get shorter as you get older.
  • Chromosomes look like this under an electron microscope:
  • You can see that chromosomes come in pairs, joined like four sausages twisted at the middle. Most people know that half of your DNA comes from your mum, half from your dad. More specifically, one out of each chromosome pair comes from your mum, and the other one from your dad. This is common to every organism that reproduces sexually, including flowering plants.
  • The only exception to chromosomes in identical pairs is the non-identical X and Y chromosome "pair". Your mum has two X chromosomes and she gave you one of them. Your dad has an X and a Y chromosome and he either gave you his X - making you female - or his Y chromosome - making you male. Only one X chromosome functions in any cell at any given time. So this means that in every cell of a female organism, one of the X chromosomes is switched off (it is apparently 'gaffa taped' up in methylation, hangon a sec I'll get there...)
  • As cells do their daily work, sections of the DNA chromosomal strands are constantly being unzipped, being copied by mRNA, and zipping up again. One protein unzips the strand. A special little DNA-copier called messenger RNA (mRNA) walks along the strand matching up the base pairs to their partners, and producing the matching half of the strand. Sometimes this is for the production of a new piece of mRNA. Sometimes for the production of proteins. Sometimes this is to exactly replicate the entire chromosome for cell division. Sometimes this is for we-don't-know-exactly-why-yet. 
  • There are also tiny fragments of DNA outside the nucleus of each cell, which are called mitochondrial DNA. Unless you are a honeybee or a mussel, you would have got them from your mum.
  • DNA are too small to see directly with anything except an electron microscope or a particle accelerator. We can't see them in action at all. X-ray crystallography has been used to image DNA for decades but you have to know what you are looking at to see it. The people who work on the how and why of the zipping and unzipping are extremely clever.
  • Within the chromosome, specific sections are identified as genes, meaning that they produce proteins. We know where they are because they are all a similar length, have a known starting sequence (intron), and a known stopping sequence (extron). 

 For humans specifically:

  • We are genetically remarkably like a bunch of other species. In the 1990s, we expected to have more genes than, say, mice, because our chromosomes are bigger and have many more base pairs (Human: 3.08x10^9 vs Mouse: 2.64x10^9). But we have just about exactly the same number of genes (20,000), just bigger non-coding sections of DNA in between them.
  • There are long sections of chromosome which are called non-coding DNA but they used to be called junk DNA, back when geneticists didn't know what they did. Now, some sections are called regulatory DNA because the mRNA copiers tend to look there before they go make a protein from a gene. The rest is still a puzzle.
  • Anthropologists can trace ancestry along the male line using the Y chromosome, and mitochondrial DNA along the female line. Both mutate very slowly. The idea was clever, but the results were fabulous. Here is the genetic tree up to the Roman Empire. I might get to mention other stories later.

Epigenetics is:

1) A chemical explanation of why, if every cell has identical DNA, how does it know to be a skin cell and not a liver cell - ie, why don't we grow liver on our skin?


Methylation is a process which explains how a fertilised egg (a 'totipotent' stem cell) splits into two parts, the 'pluripotent' embryonic mass and the placenta, and then over the pregancy, differentiates into all the various parts of a perfect little baby. In each stage of cell division, the cells become more specific. More genes are 'methylated': a methyl molecular fragment is stuck to the cytosine at the intron of the gene. This prevents that gene ever unzipping and being copied, and in practical terms 'switches it off' for that cell forever, and for all its descendent cells (except sperm and egg cells whose methyl bonds get mostly erased). If you look at any single cell in a mammal body, somewhere between 60% and 90% of the genes on that cell's chromosomes are methylated.... but any particular gene may be active on a different type of cell elsewhere in the body. So only the liver cells maintain active genes to produce bile, blood plasma etc. Skin cells have those genes permanently switched off.

I imagine the chain reaction in a fertilised egg cell to be a microscopic version of this, where triggers cascade to a single outcome and subsequently cannot really be set back up again within that cell. Nifty video, anyway.

Epigenetics is:

2) A chemical explanation of how parts of the body can change the extent to which they do certain kinds of things, over time or under certain environmental conditions - ie. How come my 13YO cousin grew 6cm last year as he hit puberty, or alternatively how did an uncle of mine develop pancreatic cancer at age 89 and not before?

Methylation is more or less permanent-ish. Other epigenetic tags come and go under different environmental circumstances. In particular the book describes in detail how histone bonds allow a partial activation/deactivation of certain genes to change the level of, for example, cortisol in a neglected baby mouse's bloodstream. Histone bonds also are involved in time-dependent activation/deactivation of particular genes, for example in puberty, aging, and developing age-related illnesses such as certain types of inherited cancer. Histone mechanisms are also implicated in obesity. And schitzophrenia, And violence and autism and depression and just about anything our bodies or minds do. Most of the data comes from first animal studies and then human twin studies. The nice thing is that these tendencies are not fixed, they can be "up regulated" or "down regulated" on a sliding scale, cell nucleus by cell nucleus, and rockstar geneticist Dr. Tim Spector said recently on the radio in a hand-wavy way that roughly 60% of most traits have these kinds of genetic/epigenetic origins and 40% is up to you to change.

Methylation and histone bonds are not simple up- and down-regulators either. A histone bond can cause higher expression of a gene. Or it can cause expression of a section of DNA which produces a tiny fragment of mRNA (a micro RNA, or miRNA) which blocks a protein from exiting the cell. Or it can cause expression of a section of DNA which then makes a methyl group attach elsewhere and deactivate something else. 
It's a complex system. Don't lose heart. I'm getting there. Honest. You can see how much the book captivated me.


Identical twin studies also provide a lot of rich data about epigenetics. Identical (monozygotic) twins grow from the same fertilised egg, in the same placenta, and are born and grow in very visually similar ways. But as they age, the differences between their epigenetics (histone and methyl bonds) increase, and their psychological and medical characteristics and their life paths diverge. The book "Identically Different: Why You Can Change Your Genes" is supposed to discuss this in more detail and it is on my reading wishlist.

Epigenetics is:

3) A chemical explanation of a multi-generational, non-genetic source of individual differences - ie. how come we look and act so differently to each other when 99.99% of our DNA is identical? How can I be affected by how my parents and grandparents lived?

In certain regions of the genome, methylation and histone bonds can be modified within a cell responding to the environment, and these changes can not be erased but they can persist for generations. The paper "Persistent epigenetic differences associated with prenatal exposure to famine in humans" links previously studied growth and weight gain habits following a famine with an identified epigenetic marker. In other words, sixty years after being born in the first year after a famine, a particular cohort of people were overweight and had always struggled to lose weight because of a periconception or in-utero methylation of a growth gene IGF2. The subsequent rat experiment of exposing a male rat to a high-sugar diet, which triggered methylation of this gene, showed that the expected BMI gain was actually passed down to 4 generations of descendents, and that the change was less pronounced each time.

So this is the technical background to my recent existential crisis. I will post on the actual existential crisis shortly.