Monthly Archives: May 2011

Not dead, just sick.

I’m not a blogger of huge volume to begin with, but recent silence has been due to a rather epic battle with the stomach flu over the past few days. We will return to your regularly scheduled programming when the author can see straight again.

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The heroes you don’t know.

A couple of days ago, a friend posted that ridiculous “article” that had popped up about DCA and the “cure for cancer that no-one wants you to know about” on Facebook and asked if it was true.  I actually applaud this action;  my friend has no background in science, and when presented with something that seemed incredible, solicited advice on whether it was true.  I had to tell her that it wasn’t, but I still raise a glass to the spirit of inquiry.

But ever since I read that piece of tripe masquerading as an attempt at journalism, the whole story has been crawling under my skin, and I only figured out why today, when I was reading this great post from Steve Novella (linked to from an equally awesome summary of the whole DCA affair by Maggie Koerth-Baker at Boing Boing) about why there’s no hidden cure for cancer.  Novella writes:

Finally, there is the human element. A hidden cure would require individual people to know that a cure for cancer is available but to deny this cure to dying patients in order to protect their or someone else’s profit. There may be people in the world who are that callous and evil, but think of all the people who would have to be that evil, over years or decades, to maintain a hidden cure. These are people who also have loved-ones who are likely to get cancer at some point in their lives, and who themselves are at risk for cancer. I would not casually assume that the medical establishment is full with such cartoonish maniacal villains.

It’s actually this last statement which summarized the problem for me, which is that conspiracy theorists (and even people on the street) treat researchers and doctors involved in searching for cures to these diseases as the enemy.  And this bugs me.  Because I believe that the opposite is true:  they are much more heroes than villains.  These are people who will labor, day in and day out, sometimes for their entirety of their lives on a problem which has no clear solution and no timeline for discovery.  They will dedicate their energy and effort to this problem, despite demonization by ignorant members of the public, chronic underfunding, life and family stress that comes from long hours and often terrible pay, and the very real prospect that their work will never be recognized or understood by anyone outside of their own peer group.  These people aren’t firefighters or soldiers or any of the other groups that we traditionally hold up as paragons of virtue, but I’m making the claim here and now that they deserve this recognition.  Novella wrote:

Conspiracy theorists also tend to ignore the huge incentive to find a cure. For the researchers involved, it would mean fame, fortune, Nobel prizes and an enduring legacy within the halls of medicine. It is safe to say that it is every cancer researcher’s dream to be part of the team that finds the cure for cancer (or at least as big a breakthrough as is plausible).

And this is true.  But even if this were the biggest draw for researchers, it’s an incentive with pathetically long odds:  there are thousands of cancer researchers around the planet, at hundreds of institutions.  And when that one team makes a huge breakthrough or “cures all cancer”, they will be standing on the backs of a thousand of the unsung whose name you will never know.

I don’t wish to claim that the simple state of being a cancer researcher makes you a good person, any more than being a firefighter automatically makes you immune from sin.  But in the same way that we ascribe nobility to those classes of people who obviously deserve it (like firefighters), we should do the same for the people who are trying to save our lives with test tubes instead of guns or hoses.  So I say to you:  hug a cancer researcher today.  Or a researcher working on heart disease.  Or MS.  Or HIV.  Or indeed any of dizzying array of illnesses that people from every nation are fighting the good fight against in relative silence. And sparing a grateful thought for the doctors, the nurses, the technicians, the administrators who are all involved in this fight would probably not go amiss, either.

They’re working for you, and they deserve our thanks.

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P.S. Here’s a representative example of what people really think, taken from a comment by “justanotherday” at the original article:

Couple of things one must consider. If there was an indisputable natural cure for all cancers, we would never hear about it. So, although this may be promising, if it every turns out to be a cure then it will be discredited and/or ban from the US or impose sever penalties if used for cancer. Cancer is annually a multi-billion dollar industry with hundreds of millions toward research. No one benefiting from that is interested in stopping that flow of money and it all would stop. Once you realize the economics of cancer you find that it is not just big pharm or insurance companies, but also government. There is population issues, SSI, medicare/medicaid and healthcare facilities. With that said, a cure could be a matter of National Security. I digress. In short, the US economics is partially based on and requires that people strategically be undereducated; work for someone else for the most of their life; get sick periodically and die before or shortly after they start collecting social security. Heart disease and Cancer followed by the unofficial third leading cause of death medical errors offers an alternative to mandatory human euthanization. There is a much much bigger picture. If this article angers you, then you don’t know the half of it.

The crazy, the stupid, the ignorance, it burns.

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The creationist is still in charge…

Stephen Harper, Canadian politician

This guy isn't helping. Image via Wikipedia

In the cabinet shuffle being reported by CBC today, it seems that Harper declined to make a change in the minister responsible for science, Gary Goodyear.  You may remember Goodyear as the guy who “won’t confirm his belief in evolution” (as if it matters what he believes on the topic);  David Ng has a great piece at Discovery about how the Harper government – with Goodyear at the tiller – is kicking the beejezus out of science in Canada.

I spoke to my Master’s advisor the other day, and in the conversation he mentioned that he has to renew his grant this year and that he’s concerned about it.  Truthfully, reading these articles, I am too.  Thankfully, I’m moving to Australia where they seem to have money for science right now;  I’ll come back when (if?) Canadians elect a government that gives a damn about basic research.

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Odd happenings at Psychology today: did Kanazawa go too far?

I noticed – in my RSS feeds a day or two ago – an article entitled “Why are Black Women Less Physically Attractive Than Other Women”?  by Satoshi Kanazawa over at The Scientific Fundamentalist blog at Psychology Today.  Kanazawa is the guy behind the “why beautiful women have more daughters” idea that Andrew Gelman took apart on statistical grounds in that talk I linked to before, and he’s no stranger to provocative headlines in general.  Given the nature of the title and the often dubious nature of his evolutionary psychology claims, I left it unread in Google Reader to come back to.  However, when I clicked through today, I immediately got a 503 error, and a 404 (page not found) when I clicked through from Google, as in the screenshot.  The article is also nowhere to be found on the front page of the blog.  And so I wonder:  what happened?  It’s considered bad form to pull down articles with no explanation once they’ve gone up on the web, so barring some sort of easy-to-explain technical problem (somebody poured coffee on the server … that only publishes that page, since the rest of his blog is accessible?) I can only assume that Kanazawa or somebody higher up the chain pulled the plug.  There’s a good chance that no-one will notice this, but I’ll say it anyways:  this needs an explanation.  Wherefore art thou, oddball article?  I was so hoping to take a swipe at you…

Update: If you’d like to read the actual article, some enterprising soul has put it up on Scribd.  I’ll take a look at it later when I have a few minutes…

Update 2: PZ Myers at Pharyngula is unimpressed with the post.  I don’t think I need to add much here.

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My Ph.D. in plain English…

I guess that this meme has been going around on Twitter for a bit – I picked it up over at Carly Tetley’s blog Wildlife Research and Training – but I thought that since I had submitted my thesis to the department for review (avant de la défense), it was a good time to write about my Ph.D. work in plain English.

My Ph.D. research has been about the evolutionary foundations of social foraging behaviour in animals.  What does that mean?  Well, social foraging is the study of foraging decisions that animals make when they’re in groups, and when the decisions that they make depend on what the other members of the group are going to do.  This is an inherently game theoretical problem.  Now, that won’t mean much to you unless you know what game theory is, so here’s an illustrative example:  imagine that you’re at a party, and you get snackish.  You look over and see the snack table loaded with all sorts of goodies, from cookies to cakes and everything in between.  Individual (a.k.a. optimal) foraging research would study your decision of what snack to take based only on what snack you prefer.  Social foraging research would consider your decision-making process when you and your two best friends head to the snack table at the same time.  If all three of you like cookies, and there’s only two cookies left on the table, then it might be a smart decision for you to switch to cake – even though you prefer cookies over cake – rather than engaging in a bare-knuckle brawl over the last piece of chocolate chip heaven.  We can apply the same logic to the study of animals foraging and interacting in groups.  (If you’re paying attention, you might notice that there’s a third possibility where individuals forage in groups but make decisions independently;  this scenario corresponds to the outcome where everyone at the party has their own plate of goodies to choose from.  You forage together, but your decisions don’t affect each other).

Birds foraging socially...

A slide from my Ph.D. seminar: birds foraging socially.

We know that a lot of species across many taxa forage socially; for instance, it has been observed in birds, fish, mammals, and there’s even evidence for insects and possibly bacteria.  In these foraging species, the most common social foraging game observed is what’s known as the “Producer-Scrounger game”.  This is a game in which individuals take one of two roles, as the name suggests:  producers or scroungers.  Producers spend their time searching for food resources, while scroungers wait for a producer to find a food resource and then they join in the discovery.  Extending the party metaphor above, if you were producing you would be searching through the room to find a table with food on it;  a scrounger would be that lazy friend who waits for you to do the work of finding the goodies before strolling over to take advantage of your effort and help themselves to whatever’s on the table.   In foraging systems, there will be an mix of these two tactics where the “fitness” (usually measured by proxy as food intake, i.e. the number of cookies you scarf) of the two are equal.  This is what’s known as an ESS, or evolutionarily stable strategy.  I don’t want to delve too deeply into evolutionary game theory here, but you can think of the ESS as the best mix of producing and scrounging for you to play given the mix that everyone else is playing.

That’s the back-story to my Ph.D.  My research has focused on the theory of these social foraging games, and how to extend them to match real foraging situations more effectively.  For instance, most of the work done on the producer-scrounger game to date has been very agnostic when it comes to representing the world spatially.  This is deeply weird to me, because if you spend more than a few seconds looking at animals foraging in the wild it becomes obvious that spatial relationships – both between foragers and between foragers and their environment – have a significant impact.  Close foragers will interact more heavily; a patchy, broken landscape will be different to forage on than a regular grid with patches spaced evenly;  and so on.  Adding these spatial components into the theory of social foraging has been a major focus for me.

The other major theme of my thesis has been information use.  In behavioural ecology, “information” has a specific meaning that relates to how animals use observations of the world around them, especially other animals, to make decisions.  In foraging terms, this often works out to “Hey, how is Bob getting along at that patch over there?  Oh, he hit the jackpot!  Let’s go get some of that!”  Anthropomorphism aside, we can ask sensible questions about how animals collect and use public and private information.  Glossing over some nuances, we can think of private information as information gathered by the animals itself and not accessible to any other observer, like information about the richness of a patch gathered by sticking your head into it.  You can see what’s in there, but no-one else can.  Public information, on the other hand, is information that is accessible to anyone who’s paying attention.  If I’m a producer who has found a food table at a party, this becomes obvious to anyone tracking my movements when I begin stuffing cookies into my mouth as fast as I can.  Scroungers rely on public information to scrounge, otherwise the game would break down;  this means that information use is central to the study of social foraging.

For historical reasons, though, behavioural ecologists haven’t spent much time thinking about the mechanisms by which animals use this information.  They’ve vaguely assumed that natural selection will have worked this out, but haven’t done much to figure out what that product will be.  In social foraging, it has always been assumed that natural selection will bring animals to the producer-scrounger ESS (the optimal foraging strategy) on its own.  But we see animals adjusting their use of the producer and scrounger tactics over their lifetime, and often on a very short time scale (seconds, not generations) as they respond to rapidly changing environments. So how do they do this?  I’ve spent a fair bit of time looking at mechanisms that will allow an animal to learn an ESS, and how natural selection might act on those mechanisms instead of fixing an ESS right off the bat.

Answering these questions, both about space and learning, has required the use of computer simulations to augment the mathematical models that currently exist;  unfortunately, creating new formal models of these processes is an extremely difficult task and I prefer to let the computer do that work for me.  Therefore, I’ve spent a lot of time creating individual-based models and genetic algorithms to study these questions;  in the interest of keeping this post to a reasonable length, I’ll refer the interested reader to the Wikipedia pages for those topics, and I would be happy to answer any questions in the comments.

And I could talk about this for hours, but I think I’ll cut off the level of detail there so that I don’t drown innocent readers in progressive elaborations.  In any case, that’s a high-level view of the type of research that I have been involved in for the past four years.  Please feel free to ask questions in the comments!

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Andrew Gelman is giving a talk..

Truthfully, I don’t even know where Hunter College is, but the statistician Andrew Gelman will be giving a talk there on Thursday, and he has helpfully posted his slides in advance.  Aside from some really smart advice on dealing with the problem of estimating small effects, the slides contain a fairly powerful demolishing of that study by Satoshi Kanazawa suggesting that beautiful people have more daughters.  It’s worth a read if for no other reason that that.

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ClipGlue: A utility to join video files for OS X.

FFmpeg

Image via Wikipedia

I’ve found myself needing to splice together some bird videos that I had laying around on the hard drive, because when I got them they were segmented into multiple pieces. The task is extremely frustrating on OS X, because it involves a bunch of command line work using a tool like ffmpeg, using a heavy-weight tool like iMovie, or paying a bunch of money for a one-use utility. So, I decided to write up a quick wrapper for ffmpeg that would make the process easier, and I’m releasing it into the wild as ClipGlue.

Warning: this is a program I whipped up in a day, and it’s not fully baked. It’s ugly as hell, for one thing, and I haven’t done a bunch of testing on it;  I decided to release it because I thought it might be of use to others, but it’s not production-quality code.  Use it at your own risk, because I’m not taking any responsibility for damage it does.

Usage is simple:  download the program from Github (look for the “Downloads” button on the right;  this is also where you can also get the source code for the project) and unzip it.  When you open the program, it presents a target onto which you can drag the video files that you want joined;  press the “Glue” button and go get a coffee.

Problems you are likely to face:

  • The program is only built for Snow Leopard (OS X 10.6), because Xcode 4 doesn’t come with the 10.5 SDK.  If someone out there downloads and builds it for Leopard or earlier, let me know and I’ll post the binary.
  • If you try to glue together files which are of different sizes (or bit rates, etc), ffmpeg is going to die a nasty death.  This is meant for files which are basically a whole video cut up into pieces, not for more serious editing work.
  • Similarly, I haven’t tested it with multiple encodings in the sources files (mixing .avi with .mov, for example), but that may throw a wrench in.
  • There may be a couple of UI bugs I haven’t caught yet.

Like I said, I hope it’s useful to people, but please don’t complain to me that it doesn’t do x, y, or z.  If you have a simple feature request I’ll entertain it, but I’m not turning this into much more than it is now.

And with the “rowr, rowr, rowr, I’m a meanie!” out of the way, enjoy the program!

UPDATE: If you’re looking for a low-cost but more professional alternative, SplitFuse looks like a likely candidate.  I haven’t tried it myself, though, so your mileage may vary.

Also, I’ve been using the program today and I’ve noticed that for many files, especially .avi, the file size after gluing is significantly larger than the combined file size of the parts.  For some reason, the conversion back and forth balloons the file size;  I’ll look into the problem and see if I can find a combination of ffmpeg flags that will handle the issue without degrading quality.

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