Monday, 23 September 2013

What's Political and What Shouldn't Be: Science in Canada

Last week protesters gathered in a number of Canadian cities to draw attention to the science policies of the current government. Their concerns are, according to the press, that the government is keeping scientists from communicating to the public, and also that it's defunding important scientific projects.

Here's my problem with this: the media reports are making two things on very different scales of problematic seem equivalent.

First, the money issue. If you read the second article linked to above, it's the main reason for the protests. Scientists aren't happy with the funding for science under the Harper government, particularly with regard to basic research. This is a legitimate complaint for scientists to make; they want to see Canada reap the benefits that come from having a strong research community and they see these cuts as threatening that.

We do live in a democracy, though, and the people of this country elected the Conservatives on a platform to cut government spending. So while it makes sense to argue that the cuts are ultimately going to hurt the country (an argument I am on board with, as it turns out), it's also important to realize that in this regard the government is, in fact, doing what they said they would do during the election campaign.

The muzzling issue (which is the main reason for the protests according to the first article linked to above) is an order of magnitude more serious. This isn't about saving government money. Public money was spent on research, then once the results were in the government demanded that they and they alone see the them, before deciding what to pass on to the public after suitable editing.

Selectively releasing results is a form of dishonesty; it's no different than when pharmaceutical companies release studies that show their products in a good light and bury ones that point to potential risks. When certain research outcomes are suppressed the government is, as a whole, giving the public a misleading picture.

This is an issue that should transcend political affiliation. Whether you believe in big government or small, decision makers need the clearest picture they can get from the people the public is paying to investigate some of the most pressing issues facing the country.

It's no secret that the Conservative government and the science community have been at odds. By both occupation and political leaning I am on the side of the science community, but this is a bigger issue than just some professional researchers wanting job security. Ultimately the question is this: Is the government is interested in getting the best answer to the questions that matter to policy, whether or not those answers line up with political ideology? The alternative is a government which cares about protecting their image, even if it means wilfully distorting the research the public paid for.

I'm not saying that cutting the funds to science is a good thing, or that scientists are wrong to go out and engage the public in the need for science funding. That is how you build democratic support for your position. But by conflating the funding and the muzzling, these latest protests and the media reporting them have watered down an important message about the way this government treats public research like the property of the Conservative Party. That's unacceptable, and it should have been the focus last week.

Wednesday, 11 September 2013

More on individuals and averages

I seem to keep hitting on this idea: the individual may not be well described by the average. In fact, it's possible for no individual to be well described by an average. It's an important point because it really strikes at the heart of where a lot of science reporting goes wrong.

I'm not the only one saying this: Jamil Zaki, a psychologist at Stanford, has a great post on a Scientific American blog going into detail about exactly this idea. His point is that psychology deals with averages, and sometimes there's a lot of variation around those averages that isn't often reported.

Zaki only discusses psychology in his article, but of course the idea extends beyond that. Any science that deals with populations and tries to extract generalized information from them carries the same caveat. "Populations" as I'm using it don't even have to be people; they could be animals or even stars, or events, or days. In other words, most of science, including all of economics and medicine, is covered here.

So the weather in one season in one part of the world may not be well described by a global average temperature (It was minus 20 here yesterday! What happened to global warming, eh?) Your risk of cardiac disease may not be well described by the average for other people with similar habits and backgrounds to you. It's even true that, if you smoke, the decrease in your lifespan may not be well described by the average decrease in life expectancy for smokers.

The average is simply one measure of a population. It might be a good way of describing things; it might not be. As an example, I could take the average height of my family. Adding myself, my spouse, and our toddler, and dividing by three gives me something around four and a half feet. That's not anywhere near any of our heights; in this case the average is simply an irrelevant measure.

More commonly, the average isn't a bad measure per se, it's just incomplete. What you usually need is the average, plus some indication of how spread out the population is around that average. The standard deviation is one such measure.

Any reputable scientific paper will have calculated many measures for the population it's looking at. Here's a list of, among other things, various measures that can be applied to a population. It's a little bewildering, which is likely why most media reports focus on one number and strip away the complicating details.

What to make of all this? Well, don't start smoking. Even if there is a certain amount of variance in the data, it's foolish to assume that you'll be an outlier. For well-established health issues, the average is, more often then not, a good guide.

Moving outside of that, if the study is new it's always worth asking, what's the variation around the average they're reporting? We looked at a study a while back in which the a connection between autism and induced labour was reported; the actual research paper showed that the variance around their average results was so large that it threatened to undermine the conclusions.

Knowing when an average is a bad measure is a little harder. Often when this happens the person reporting the average is deliberately using a poor measure to make themselves look better. Economic data is a prime example. Whenever you see the GDP per person, unadjusted for inflation, you can safely discount that number as worthless. The average simply isn't a good measure for the typical person's income. Politicians report it, though, because it's a quantity that governments can reliably increase through monetary policy, even if life for the typical person hasn't changed.

The key point here is that populations are complex. Any time you see them reduced to a single number, it's worth asking, "What am I missing here?" And, as Zaki points out, it is not always about you.

Wednesday, 4 September 2013

Due to genetics, or, simplicity and determinism

I typed "due to genetics" (complete with the quotation marks) into google news, and this is what I learned: 

Due to genetics, you might have a higher risk of heart attacks.

Due to genetics, you can get dark circles under your eyes.

"Happiness is 50% due to genetics"

Due to genetics, some athletes are simply better at doping without getting caught. (This article was amusing for all the pictures of athletes who did get caught doping, as if somehow this proves their point)

Your enlarged pores may be due to genetics.

Other articles that came up on this search discussed autism, breastfeeding, stretch marks, and Larry Summers' views on women in science (if you're not familiar with them and you just have too much good feeling for humanity, google it). Clearly a lot of our health, in every sense of the term, is presented as being "due to genetics".

Genetics is certainly important, and an understanding of it should be a priority for science educators. It's one of the areas of science that directly impacts people's understanding of themselves and their health. I worry, though, that the dominant perception of genetics is one that is far simpler and more deterministic than the reality. To quote the heart attack risk article linked to above, "When it comes to certain diseases, preventing the onset might be almost impossible. Due to genetics and other factors involved, certain people have a greater risk of developing certain health conditions." Genetics here is simple: genes=heart attack. It's also deterministic: preventing heart attack "might be almost impossible". Genetics, though, is neither simple nor deterministic.


First, simplicity: genetics is complicated. As genetics prof John H. McDonald points out, a large number of "canonical" examples from high school biology, from eye colour to earlobes to hitchhiker's thumbs are simply wrong. Two parents with blue eyes can, in fact, have a brown eyed child.

Why is genetics so complicated? It's a question that is still a subject of academic research. One answer, though, comes from looking at what DNA actually does in a cell. What DNA does is surprisingly simple: DNA codes for proteins. That's it. That's the only thing it does. Each three base pairs in your DNA code for one amino acid, and a string of amino acids forms a protein. Everything else that DNA is responsible for is the result of those proteins interacting with other parts of the cell, such as other proteins, lipids, DNA itself, etc.

In order to go from a relatively simple mechanism (DNA-->proteins) to extremely complicated outcomes (the huge variety of cells in your body, which work together to form your nervous system, your immune system, and you) requires a lot of feedback loops. What I mean by that is that DNA codes for proteins, which then interact with the DNA to affect the way it codes for other proteins.

The interaction between your DNA and your environment, in the broad sense, is composed of many, many of these feedback loops. DNA interacts with proteins inside a cell, which interact with proteins embedded in the cell wall, which interact with proteins outside the cell (and also with the lipids that make up the cell wall), which interact with proteins on other cell walls, in a chain of microscopic links that stretches from deep inside you to the surface of your lungs, skin, or eyes. Is it any wonder this chain of interactions is hard to understand in simple terms?

What these complicated interactions mean, among other things, is that you can't in general apply average results to an individual. So if gene X causes people on average to be 50% more likely to die of a heart attack than people without the gene, that won't hold true across all sub-groups. More concretely, a vegetarian who is also an avid jogger with gene X isn't necessarily 50% more likely to die of a heart attack than a vegetarian jogger who lacks gene X. It could be larger or smaller; the 50% on its own doesn't tell us. The complicated interactions of DNA with the environment--keeping in mind that what you eat and what you do are part of "the environment"--means average results may not apply to a particular group, or worse: they may not apply to any group, and only be relevant when everyone is added together. Still useful, perhaps, but not to you as an individual.


Genetics is also less deterministic than it's made out to be. Part of this is because it's complicated. Another part is because you inherit more than DNA from your parents.

I don't just mean that metaphorically; I'm not saying here that you also pick up a variety of behaviours and ideas from them, though that's obviously true as well. No, I mean that you inherit, in a biological sense, more than just the information encoded in the base pairs of your DNA.

People have known that this is technically true for a long time. The building block of a human isn't just a piece of DNA; it's a cell, with a cell wall and organelles and structural elements and an environment. This much has been known for a while. What's changing is our appreciation for how that early environment can actually reverberate through a child's development to affect their life as an adult. (The grammarians out there should note that a child's development also effects the life of an adult.)

The interactions DNA has with the cell environment not only change the way it behaves in the short term, they can also change the DNA in ways that are passed on to daughter cells. DNA methylation is one such way. Here a particular piece of a molecule called a methyl group is attached to part of the DNA. Not only does it change the way the DNA codes for proteins, it's a modification that gets passed on when the cell divides--even, potentially, when the cells in the reproductive system divide, combine, and go on to form a new organism.

What this means is that environmental factors can alter genes for several generations before dying out. Since both the alteration and the time it takes for it to go away depends on the environment, trying to describe a deterministic role to genes is mistaken at best.

The field that looks at stuff is epigenetics. It's the field that studies the way the environment influences genetic expression, and it's currently a buzzword in science reporting. In many ways it is still a controversial field. What's clear, though, is that the environment does influence expression, even if we're still not sure exactly how it all pans out.

The amount of data available about both individual and group genomes is huge, and only growing larger. Soon people will be asked to make health decisions not only on current diagnosis but also on what their genes say about likely future scenarios. We need to keep this in mind, though: Genetics is complicated. It's not deterministic. Pretending it is only undermines our understanding and our health.