Evolving Superpowers

Wouldn't it be cool to have super-powers?

That's the premise for a huge number of TV shows, movies, books, and of course comics. Apparently wondering what it would be like to be able to fly, read minds, teleport, or stop time is a pretty universal past-time.

And as every fan of superhero stories knows, one of the most important elements is the origin story--how the hero gets their powers. They could be from an alien planet, or be vested with an alien artifact. They could be an ordinary person with access to specialized technology. Radiation could be involved. Or it could be that humanity is evolving to its next state, and that state involves super-powers.

This last one is among the most popular. It's the basis for X-men, one of the biggest superhero franchises out there, as well as the TV show Heroes, and numerous other series. And it's the basis for the new TV series (which is a re-boot of the old TV series) The Tomorrow People.

I've watched the first couple of episodes of The Tomorrow People, and I liked it. I'm hopeful that, by focussing on just three powers, the show will be able to look at their implications with a little more depth than normal and avoid painting themselves into a corner (as in, "wait, doesn't Peter Patrelli have, like, every power? Why are there any world-threatening problems he can't solve?"). I also like the whole double-agent angle, and I hope the show has the courage to explore some murky waters and moral ambiguity around whether those with super-powers should be policed, and if so, how.

But what I want to talk about now is the science.

Yes, I'm sure you can already predict where this is going. "Evolution doesn't work like that, there would be many harmful mutations for every beneficial one, evolution can't 'look ahead', how could a single gene cause people to teleport..." Well, I'm not going to complain about those (mostly). I'm willing to cut a TV show some slack in its superhero origin stories; it's primarily entertainment after all. If I wasn't willing to suspend disbelief I wouldn't enjoy much media.

I do want to point out two things, though. First, the leader of the bad-guys is supposed to be an expert genetics researcher. At one point, when threatened by one of the super-mutants, he discusses how the tomorrow people can't kill anyone--they freeze up if they ever try to. Bad-guy-leader talks about how this will eventually be a beneficial mutation, but sadly right now it's a liability.

This is exactly the kind of mutation that can't evolve. Evolution has no "look-ahead"; genes proliferate because they're beneficial right now, not many generations from now. Having the scientist character basically rub the audience's face in bad science took me out of my suspension of disbelief for a moment. It's always better to leave some things unsaid and let viewer's imaginations fill in the details than to over-explain and blunder.

The more important issue is the show repeatedly referring to "the gene" that causes these superpowers. It also refers to the tomorrow people as being a new species, not entirely human--it's something they stress on multiple occasions in the first two episodes. The clear implication here is that a change in one gene can move you from "human" to "not-quite-human". And this, to me, is a problem.

In any species there is a fair bit of genetic variation--humans are no exception. You have different genes from the person standing next to you (unless you're standing next to your identical twin). A large part of that variation comes from sexual mixing--because you get half your genes from each parent (and because there's a lot of genes to pick each half from) you end up with a unique mix of genes.

And of course there are also mutations. Humans have an estimated average mutation rate of 175 mutations per generation--meaning the average person has 175 new mutations they didn't get from their parents. Since each person also inherits the 175 mutations that their parents had, and the 175 their grand-parents had, etc, etc, we're all walking around with thousands and thousands of mutations. (Sadly, after extensive testing, I can report that none of my mutations have led to latent super-powers.)

None of this variation makes any of us not human; it just means we're all unique. Humans simply aren't a mono-culture.

Why am I picking on this particular point? Because in our non-fictional world, people have used a small locus of genes to argue that certain other people weren't fully human. Genes like the ones controlling skin pigmentation, or hair texture, or even nose width. We have a long, sad history of classify some people as subhuman, and even today there's still some hold-outs to that view.

This may be part of the point in some superhero stories. Certainly in a number of the X-men stories the parallels between the mutants and oppressed minorities in the real world were intentional. I worry, though, that the emphasis The Tomorrow People puts on a single gene leading to a new species will lead audiences to internalize the message, "different genes always mean different (sub)species". This would be a disservice, regardless of what else the story might say about tolerance.

It would be nice to hear, just once, in a story about mutants with super-powers, someone point out that mutations aren't rare, and that genetic variation doesn't make some people not human.

Can we work on that, TV writers?

Headlines in Science: Higgs Nobel Prize Edition

It's time to award the prize for best headline about the awarded of the prize for best physics by the Nobel committee. And by "best", I mean in the can't-look-away-from-the-train-wreck sense.

Background: as you may have heard, the Nobel Prize for Physics was announced, and surprising no one, it honoured the discovery of the Higgs boson (just the theorists though--no love for the experimentalists who, you know, actually found the thing).

Anyway, there were obviously lots of headlines on this issue, but I hearby award the following one from The Register, a British technology news website, for the honour of best headline, (by which I mean worst headline):

"Brit boson boffin Higgs bags Nobel with eponymous deiton"

I don't even know where to begin.

Scratch that, I'll begin with the words. "Boffin" seems to be some sort of British word for expert. That's fine, but the headline implies that Higgs is an expert on "bosons". Bosons, for those who don't know, are one class of particles; the other class is Fermions. Every single particle or collection of particles (which includes, well, everything) can be classed as either a boson or a fermion. Higgs isn't really a boson specialist, though--the category is so wide it's hard to know what that would even mean. Rather he used quantum field theory to predict a new particle, which happened to be a boson.

"Deiton" appears to be a new word coined by the good people at the Register. No explanation is given but it would seem to refer to the fact that the Higgs boson has sometimes been called the "God particle".

"Eponymous" seems like a strange choice for a context in which clarity is presumably important, especially when paired with the made-up "deiton".

Beyond the actual words, though, there's a bigger issue here, and it's conceptual. The issue is whether a headline exists to inform, to set context, and to draw in interested viewers; or to show off the cleverness of the headline writer. It seems like the Register opts for the latter.

So, an open letter to the Register (because they totally read this blog...):

Dear Register,

Please be aware that a truly clever headline is one that sets up the reader for what is to come in an accurate, concise, and clear way.

Also, as a rule of thumb, headlines should probably not contain words you just made up. Just saying.

Sincerely,
Everyone who cares about science communication

Quick Hits

I've been pretty busy the last week and a bit, which has kept me from writing anything substantial here, but here's a few quick thoughts about some science stories that have struck me:

• So the Nobel Prize in Physiology or Medicine was awarded today to three scientists for their work on how vesicles move various molecules and substances around cells. The science here is very cool. I will note, without taking anything away from the work done by the recipients, that the prize went to three white men; two born in the US, one is Western Europe. Since its inception more than a hundred years ago, ten women have one the Nobel Prize in Physiology or Medicine (out of 204 winners), four women have won the Nobel Prize in Chemistry (out of 162 winners), and two women have won the Nobel Prize in Physics (out of 193 winners). No Nobel Prize in the sciences has ever been awarded to a black man or woman. We still have a long way to go.
• If it wasn't enough that industrial fishing has killed off 80% of the biomass of the oceans, the effects of warming and CO2 absorption (which changes the ocean's acidity) are causing the world's largest ecosystem to decline faster than previously thought.
• This is a great post on Malcolm Gladwell and the danger of oversimplifying science--a perennial concern here.
• Finally, this is terrible.

Hopefully I'll find a little more time for writing this week. Well, maybe next week. Okay, it's going to be a while.

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.

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.

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.

Simple

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.

Deterministic

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.

Lie-to-children

I admit, the first time I saw this phrase in print, I was a little put off. Lie-to-children? That sounds like the kind of thing that gets you a lot of extra time in purgatory.

Then I learned more about it and decided that perhaps it wasn't so bad after all. Well, maybe. It still could be bad.

I should explain all that. The first thing I thought when I saw the phrase "Lie-to-children" was that people were talking about the kind of thing that you tell kids because it's convenient, even if in the long run it doesn't help them at all. That's not what it actually is.

What lie-to-children refers to is the type of simplification that happens when you are teaching someone (anyone, it turns out: doesn't have to be a child) about physics, or math, or chess, or any field of human endeavour with a deep and complicated body of knowledge. The idea is that throwing the full force of, say, quantum electrodynamics at a beginner will only turn them off the field all together, so you teach them simplified forms (in this case, simplified electricity and magnetism) that you know aren't entirely correct. Since it wouldn't really be good teaching practice to emphasis their incorrectness at each turn, you're sort of lying. Hence, lie-to-children.

In this sense the concept has some merit. I've come to realize, though, that there's two different types of simplification. One is a type that, while simplified, gives students the right intuition about how the more complicated process works. The other type does the opposite: it is a subject simplified in such a way that students either don't make any progress towards understanding the fuller ideas.

Here's an example of the good type. In high school and early undergraduate physics, we teach students a theory of friction. In this theory, friction forces depend on the materials rubbing past each other (eg rubber on concrete or skin on carpet) and the force pushing them together (gravity in most cases)--and the dependence of friction on the force pushing the two objects together is linear (double the one force, double the other). There's no dependence on the size or shape of the contact area, or any other factors.

Clearly this can't be the complete theory of friction. If it was, then all cars with the same material in their tires would have the same stopping distance, and sports cars wouldn't need fat tires or good suspension for good handling--skinny tires would work just as well. But it works as a lie-to-children because it lets students figure out things like force, energy, and work in ways that serve them well as they move on to more complete forces. (As an aside, the wikipedia article about friction is terrible. Please don't read it unless you want to be seriously confused and misled).

An example of the bad type of lie-to-children is how we teach uncertainty estimates. The most common way of introducing students to measurement uncertainty in high-school and first year labs is to tell them to look at the four or five data points we've told them to collect, and subtract the largest from the smallest to get a range of uncertainty.

Why is this so terrible? For starters, it gives students the idea that a range of uncertainty on a reported value means that the true value cannot possibly be outside of that range. That's an unfortunate idea, though one that even professional scientists sometimes seem to have. It's not the worst of it, though. The worst part of calculating uncertainty this way is that the uncertainty goes up the more measurements you take. Taking more measurements gives you a higher chance of having a particularly large or particularly small one, which makes an uncertainty based on max minus min get larger. This is bad; we want students to get an intuitive feel for uncertainty as a measure of the confidence in a set of data, then we give them a way of calculating it that implies that the more data you have, the less confident you are in it.

I'm not going to go into how I think uncertainty should be introduced in high school. All I want to do here is point out that we need to shift the question from "how can we simplify this body of knowledge?" to "does this simplified version build students' (or readers', depending on context) intuition in the right direction?" If we can do that, the lie-to-children will be a little less of a lie.