Tag: bio

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Great Success = Some Talent + A Lot of Luck

Spotted this wonderful, and very accurate, ‘equation’ by Daniel Kahneman:

The Secret of Regression to Mediocrity

Success = Some Talent + Luck
Great Success = Some Talent + A Lot of Luck

The term ‘regression to mediocrity’ (also known as ‘regression to the mean’) was first coined by Francis Galton in 1886. Galton showed that, on average, the children of tall parents tended to be shorter than their parents, and that the children of short parents tended to be taller than their parents.

Say what?

The point is that height is partly determined by your genes, and partly by the environment you grow up in (e.g. food, healthcare, etc). A confluence of good genes and a good environment might produce a very tall person. If that tall person has a child with another tall person, sure, the child will have good genes – but they certainly aren’t guaranteed to have a good environment. In fact, they’re probably just going to have an average environment. That means that the child, on average, just isn’t going to be as tall as their parents.

This applies for all sorts of different things wherever luck, or random chance, is involved. Take gambling. Imagine I win the World Series of Poker this year. Now, if this happened, you would agree that I must be a pretty excellent poker player; perhaps even the best poker player in the entire world. Would you expect me to win next year? Even 50% odds? Probably not. But why? Continue reading “Great Success = Some Talent + A Lot of Luck”

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Food Miles

Sometimes, when I come across a particularly interesting article, I try to find the research paper that it’s based on. I don’t always read the entire paper (in fact, I normally skip over huge chunks) but it’s always instructive to see the results and analysis as the original author wrote them; it’s not rare for reporters misinterpret results or selectively quote from papers, for a variety of innocent and nefarious reasons. But even if the article is excellent, I get a buzz from reading the actual research. Maybe that’s just because I’m weird, or because I occasionally hanker for my neuroscience days, but I do feel that reading papers puts you as close as you’re going to get to the scientific process.

This post and the next are both about papers I read recently. I was going to put them in a single post, but it ended up being too long, so you’ll just have to wait until tomorrow for the second one.

Food Miles

The New York Times ran an op/ed piece called Food That Travels Well about the use of ‘food miles’ when it comes to labelling and buying food. The idea is simple – you find out how far each piece of food has travelled to reach a supermarket, you print that on the packaging, and let consumers decide whether they want to buy it. The unspoken but obvious assumption here is that the more miles food has travelled, the more carbon dioxide has been released, and the worse it is for the environment. Thus, you should favour local produce over foreign produce, even if it costs more, because it’s better for the environment.

When I first heard about food miles, I immediately thought there was something fishy about it. Apart from smacking of protectionism, it ignored a whole host of factors, such as the means of transport. If you’re (say) loading ten thousand tonnes of potatoes on a ship from America to the UK, will that release more carbon dioxide, per potato, than driving five tonnes of potatoes on a truck from one end of a county to another? The answer is, I have no idea. But it’s clear that some forms of transport are more polluting than others, and just looking at the physical distance covered is a poor way of measuring environmental impact.

The op/ed piece was about research conducted by Lincoln University in New Zealand, which went way beyond my transport concerns by doing a life cycle analysis on the transport and production of food. In other words, they looked at:

…Water use, harvesting techniques, fertilizer outlays, renewable energy applications, means of transportation (and the kind of fuel used), the amount of carbon dioxide absorbed during photosynthesis, disposal of packaging, storage procedures and dozens of other cultivation inputs.

What did they find?

…Lamb raised on New Zealand’s clover-choked pastures and shipped 11,000 miles by boat to Britain produced 1,520 pounds of carbon dioxide emissions per ton while British lamb produced 6,280 pounds of carbon dioxide per ton, in part because poorer British pastures force farmers to use feed. In other words, it is four times more energy-efficient for Londoners to buy lamb imported from the other side of the world than to buy it from a producer in their backyard. Similar figures were found for dairy products and fruit.

How similar? Referring to the original paper, Food Miles – Comparative Energy/Emissions Performance of New Zealand’s Agriculture Industry (PDF) by Saunders, Barber and Taylor:

The UK uses twice as much energy per tonne of milk solids produced than NZ, even including the energy associated with transport from NZ to the UK This reflects the less intensive production system in NZ than the UK, with lower inputs including energy…

NZ is also more energy efficient in producing and delivering apples to the UK market than the UK is. NZ energy costs for production are a third of those in the UK. Even when transport is added NZ energy costs are approximately 60 per cent of those in the UK. Consequentially the CO2 emissions per tonne of apples produced are also higher in the UK than in NZ, reflecting the higher energy use but also the lower emissions from NZ electricity generation.

This shouldn’t be surprising. Most foods grow better in some parts of the world than others; considerably better. Looking at the raw data, the UK uses vastly greater quantities of nitrogen fertiliser than NZ, partly due to those clover fields mentioned earlier. When it comes to dairy production, the UK has to bring in comparatively huge amounts of cereals and concentrates to feed animals, whereas in NZ, animals can graze outside all year round. All of this releases more carbon dioxide and pollution.

The point is, no matter what your priorities are, you can’t make a sensible decision on food purchases based solely on the distance food has travelled to get to your plate. There are good reasons for why someone might want to favour local produce over foreign produce. The environment is not necessarily one of them.

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The Name of the Gene

While studying biology and genetics at Cambridge, we learned the names of a lot of genes. One of these was Sonic Hedgehog, a rather important gene involved in development of many organisms. Our lecturers always seemed inordinately pleased to tell us this gene’s name, perhaps hoping that the ‘cool’ name would rub off on the subject and themselves. Let me tell you this: there is nothing cool about calling a gene ‘Sonic Hedgehog’.

The New York Times has found a few people who agree, in their article ‘Sonic Hedgehog’ Sounded Funny, at First (at first? I don’t know if it ever sounded funny). There are many other genes with similarly foolish names, although none quite as silly as ‘Sonic Hedgehog’. I think even our lecturers got tired of it and after a while we just called it ‘Shh’.

At the moment, people can call genes pretty much whatever they want, and so it’s no surprise that you get a lot of crap; let’s face it, people aren’t scientists because of their sense of humour or literary skills. The whole thing still depresses me though; it suggests to the world that geneticists are just a bunch of jokers who can’t take things seriously, or at the very least, make a good joke.

There is no equivalent body in biology to the International Astronomical Union, which officially names all stars, planets, asteroids, and pretty much everything else in space, and there probably never will be. Biology moves faster than astronomy, and there are an awful lot of organisms and genes out there, and far more biologists than astronomers. The prospect of being able to name your very own gene is no small incentive for biologists, and most people take the privilege quite seriously. As usual though, there are a few people who spoil the fun for everyone.

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The cause of Type 2 diabetes

Why a fatty diet leads to diabetes – type 2 diabetes, specifically. This article at the Times is a surprisingly detailed report of how researchers at UCSD determined that hyperglycaemia suppresses the GnT-4a enzyme, which is basically a blood glucose sensor for the cells that produce insulin. Too much suppression results in pancreatic cell failure, and then type 2 diabetes.

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Lab: The Show

During the England game yesterday we came up with an idea for a new reality show. There are already shows centred around pop stars, hospitals, pirates and all sorts, but what about scientists?

Introducing LAB: The Show. 12 graduate and postdoc students in biology are placed in a lab for ten weeks in order to produce a proper research paper. Every week, one student is voted out of the lab, and then in the last week, the final three students compete to become first author. The show will be livened up with surprise visits by star scientists, and the various challenges the students will face include deciding what to spend their money on (e.g. food, or more Gilson Pipettes?) and designing posters for conference.

Naturally, the students will not be allowed outside of the compound, with includes living quarters, a kitchen and a dining room. Controversially, there will be only two computers with Internet connections, so watch out for heated arguments over who gets to use them, and if they should be used for work or play!

No doubt Fox will be the first in line to purchase this stunning concept from me…

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Some Things Are Better Left Unsaid

Olivia Judson, an evolutionary biologist at Imperial College, has written a piece in the New York Times yesterday called Some Things Are Better Left on Mars, where she argues that the risk of infection by Martian lifeforms far outweighs any scientific gain from bringing back rock and soil samples. Given that we know organisms on Earth can survive in extremely harsh conditions, and the terrible lessons we’ve learnt from history of the first encounter between human populations without resistance to novel pathogens (e.g. the Americas and influenza), why should we risk it?

I’ll tell you why: her two main reasons are totally worthless. Firstly, organisms adapt to survive within a narrow range of conditions; while humans can live almost anywhere on the surface of the planet, we cannot live underwater, nor can we live underground at high pressures or temperatures above 50C or below -50C (and this is a generous estimate). We can’t live in an atmosphere that doesn’t have a particular pressure of oxygen, and there are plenty of chemicals that would be harmful or even fatal to us. Similarly, there are organisms that can live above 50C, or at high pressures or in different atmospheric mixes – but those organisms would drop dead, or at the very least become totally inert in any environment other than that which they are adapted to.

Mars has an atmosphere that is 100 times thinner than ours, mostly carbon dioxide, with a completely different chemical environment, much less water and much colder and dimmer. The planet is exposed to different radiation, different winds and different weather cycles. There is no environment on Mars, even underground, that remotely resembles Earth or more importantly, the human body. There may well be extant life on Mars in the form of extremely hardy micro-organisms adapted for low temperatures, low pressures, carbon dioxide atmosphere and low nutrients. They probably have a very slow metabolism due to a lack of energy inputs. If you put any of those organisms in the mostly water, 37C environment, high pressure and alien chemical environment of a human body, they would die.

And this ties into the argument that we should be afraid of novel organisms because of the influenza plague. Sure, we’d have every reason to be wary if there happened to be humans (or even remotely mammal-like organisms) on Mars, since they’d have provided an environment for pathogens to evolve that’s similar to our bodies. But there aren’t.

Even supposing that we did bring back harmful micro-organisms from Mars, the safety measures proposed for any sample return mission are nothing short of gargantuan. The samples would be returned to the highest class of biohazard facility, at or above the level required for highly infectious lethal human pathogens such as ebola; namely, sterilised, pressurised, air-tight facilities with multiple layers of redundancy and safety. There would certainly be a purpose-built facility for any sample return missions. I’ve also heard proposed for sterilising the returning spacecraft with a rocket exhaust while in orbit.

I find it totally puzzling why the New York Times would run such a badly-informed article as this, and I’m also confused as to why Judson would wish to make herself into a fool by writing it. Perhaps she does have a good reason for opposing a Mars sample return mission; unfortunately for all of us, it isn’t in her article.

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Genetic Enhancement

The Atlantic ran an anti-genetic enhancement article this month called The Case Against Perfection. Written by Michael J. Sandel, a member of the notorious President’s Council on Bioethics, the article is cogent and well-argued.

Essentially Sandel believes that embryonic or hereditary genetic enhancements would remove the ‘giftedness’ of every child – in other words, the fact that the traits of a child would no longer be left to ‘chance’ would cause a number of ethical and societal problems. These could include a deterioration in parenting, as parents might expect their children to succeed in particular areas instead of accepting their unique characters, and also the explicit creation of a new class of humans which could damage the solidarity among all humans, and more conventionally, in insurance markets (of course this could happen with genetic screening as well). The fact that this new eugenics would come without coercion does not, in his opinion, remove the potential danger to parents and children.

While reading the article, I unusually found myself agreeing with Sandel, as I’m normally a proponent of genetic enhancement. Most of the arguments I’ve heard against it are of the ‘who needs bigger muscles/taller children’ variety, which I actually agree with – I’m not sure I see the point of these things. However, I hadn’t heard the ‘giftedness’ argument before, which was initially appealing to me but has left me a little uncomfortable.

My problem with genetic enhancement supposedly removing the giftedness of children is mainly in the way that it abstracts the issue entirely. Surely we should be looking at the concrete benefits that genetic enhancement might give children, not just the fact that parents will know about them? How would improved vision and a better heart change the attitudes of parents towards their child? Sandel uses the examples of height and muscle improvement when he talks about the problems of genetic enhancement, which are understandably fraught with complications – but these shouldn’t extend to all variations of genetic enhancement.

Also, Sandel is noticeably quiet about the potential use of genetic engineering to correct diseases such as Parkinson’s. I find it difficult to believe that he would argue against genetic ‘corrections’ unless he believes that such debilitating diseases are also a part of the giftedness of a child, thus if we do use genetic engineering to correct diseases but we don’t use it to ‘enhance’ people, exactly where do we draw the line? What’s the extent that people are prepared to accept in the name of “our appreciation that life is a gift”? (his words).

I understand that my position is pretty vulnerable, given that if we allow genetic enhancements, people will use it to design taller and stronger children whether I like it or not. My only answer (and a weak one it is) would be to raise the bar on genetic enhancements extremely high and only allow those that would not predispose the child to any particular path; hence, improved eyesight and increased memory is useful for anything a person might care to do, but stronger legs clearly suggests that you are at least implicitly expected to make good use of them in some physical activity. I do agree that there are serious issues concerning genetic enhancement and that we should move very slowly with it, but I just don’t see that its removing the ‘giftedness’ of children is a strong argument against banning the whole thing.

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Snapshot

The feeling of total, horrified incredulity is not one that I get to enjoy very often, but this afternoon I had a stiff dose of it. For the past week or so I’ve been working on some tissue samples that have probably seen close to a dozen hours of solid work going into them. Today, I was engaging in the most difficult and skilled job that biologists are trained in – the time honoured art of moving the tissue samples from one container of liquid to another every five minutes for an hour while listening to the radio.

It is the sort of job that, you would think, would be very difficult to screw up. Yet when I placed the first carefully labelled and ordered rack of samples into a jar of alcohol, and stared on in horror as their ink labels mockingly drifted away from the glass slides to form diffuse, unreadable clouds, I reflected upon the utility of an education in chemistry; unsurprisingly, 70% ethanol is strong enough to clean pretty much anything from a glass slide.

In fact, it turns out that there is basically no way of labelling glass slides to survive dipping in strong alcohol. The only solution is to label the racks themselves. Thankfully, this story has a happy ending because I remembered the order of the slides and their racks and can still reconstruct their labels.

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The Sunny State

After a week of dismal weather and tiring winds that sap all of the enjoyment out of cycling, not to mention dozens of niggling problems at the lab and a whole host of other things, things have finally started to improve here in Oxford. Yesterday I found out that I’ll be going to a vision science conference in Florida at the end of April, fully paid by the Wellcome Trust, bless their generous souls, and today I received a bunch of books and CDs from Amazon, including The Amazing Adventures of Kavalier and Clay and Perdido Street Station. This weekend is looking gratifyingly relaxing and I have managed to sort out a lot of background irritations as well.