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New gene discovered for misinterpreting genetic evidence!

September 13, 2010

There’s a fantastic article in The Guardian debunking some commonly held myths about genetically acquired traits:

People’s understanding of genetic effects is heavily influenced by the way genetics is taught in schools. Mendel and his wrinkly and smooth peas make a nice introduction to genetic transmission, but the downside is that we go away with the idea that genes have an all-or-nothing effect on a binary trait. Some characteristics are inherited this way (more or less), and they tend to be the ones that textbooks focus on: for example eye colour, colour-blindness, Huntington’s disease. But most genetic effects are far more subtle and complex than this[…]

What are the implications of all this for the stories we hear in the media about new genetic discoveries? The main message is that we need to be aware of the small effect of most individual genes on human traits. The idea that we can test for a single gene that causes musical talent, optimism or intelligence is just plain wrong.

It’s great reading, and includes an explanation of the way scientists evaluate genetic determinism in humans (in mice it’s much easier, we can just delete a gene and see what it does), and why it’s hard to evaluate definitively.

[h/t Mindhacks]

Splitting the Difference

September 13, 2010

It’s no secret I love science, but sometimes the conclusions arrived at by science go against the grain of personal experience and conventional wisdom. When it does, many people are unwilling to believe the science, and dismiss it as intentionally misleading or biased. Case in point: Glenn Beck’s Rally a couple weeks ago.

How many people are in the crowd?

On August 28th, from the steps of the Lincoln Memorial, Glenn Beck tweaked the press as he surveyed the crowd attending his “Restoring Honor” rally because he knew the truth. As he said later, “We’ll have aerial photography here shortly on the numbers, but I can tell you that it was in the hundreds of thousands. Let’s be on the low end, 300,000, and maybe as high as 650,000.”

But Minnesota Republican Michele Bachmann at her own post-Beck rally disagreed. “We’re not going to let anybody get away with telling us there were fewer than a million people ’cause we were here. We are witnesses!” Crowd estimates flew overhead like the geese over the rally. ABC News went with 100,000 plus, NBC News with some 300,000, and NPR with tens of thousands. Meanwhile, CBS News actually paid for some research and arrived at a figure between 80 and 90,000. Stephen Doig helped calculate it by using aerial photos.

A bunch of media outlets went with rough estimates. People supporting Beck’s positions went with higher numbers, detractors went with lower numbers. But one news organization actually decided to use some science, and arrived at somewhere between 80 and 90,000. Plenty of people weren’t happy with this number. Steven Doig, who used statistical methods to make an estimate of the crowd size was attacked:

Well, obviously I must be a liberal dupe who was paid to underestimate it and, of course, others on the other side of the ideological stream said, oh, yes, you know, obviously you’re doing very scientific methods and clearly that’s very good.

That really amuses me because 18 months or 20 months ago I did the Obama estimate. I came up with a number of around 800,000 being there on the mall for the inauguration. That number was lower than the pre-event predictions, some of which were laughably high, like five million. So my prediction then became embraced by those who didn’t really want to see Obama draw a big crowd and was sort of ignored by supporters.

So, exactly the same methods predicted exactly the opposite reaction from the different ends of the political stream.

The folks at On The Media have been doing a bunch of great reporting lately on myths and fabrications in the media, both current and historic, and it’s well worth listening. What gets me most about this Glenn beck rally thing is how the main stream media dealt with it. It’s understandable that political operatives would try to spin the results – they have a particular ax to grind. But other media outlets just split the difference. When OTM interviewed Dan Keating of the Washington Post how they dealt with it, he basically said they just threw all the estimates into the air, and let them fall on readers minds where the would:

DAN KEATING: I believe we’ve made reference to Glenn Beck’s number. I believe we’ve made reference to Michele Bachmann’s million number, and I believe we may have made reference to the number that CBS derived.

BROOKE GLADSTONE: But if they just gave each of those three numbers equal weight, that’s a problem. Wouldn’t the normal reader see one as the low estimate, one as the high estimate and maybe wind up with Glenn Beck’s number as the right one? And isn’t that, given that there was no science behind Glenn Beck’s number, foisting a misrepresentation upon the public in order to appear fair?

DAN KEATING: Well, I think it’s hard to completely ignore what people say. We put it in the best possible context we can. We’ll go to a lot of effort to put some science behind a number, and then it kind of goes up into the media atmosphere and gets sucked up in with every other number that people just whip off the top of their head.

And I wish there was an easy way of saying, you know, hey, my number’s better than all your numbers. But the number that we worked really hard to put a lot of facts behind sometimes loses its weight as compared to all the other numbers bandied about.

There IS a way to say one number is better: by saying it’s better, and giving the reason why. Why is that so hard?

Bacterial charity – the bad kind

September 3, 2010

Antibiotics are awesome. They can be credited with saving more human life than any other invention and have been one of the best advancements in public health second only (maybe) to sanitation. But, as with all things pathogen related, the microbes are fighting back. Antibiotic resistance is on the rise, and diseases like MRSA (Methicillin-resistant Staphylococcus aureus) have been making the rounds in hospitals and causing a significant number of deaths.

Antibiotic resistance arises due to random mutation and natural selection. If there are a few hundred billion bugs in an infection, and even one has a slight growth advantage in the presence of an antibiotic, that bug will divide, pass on it’s beneficial mutation to its offspring while the less fortunate die off, and open the door for even more mutations and increased resistance down the road. At least, that’s what we thought.

But a new paper in the journal Nature shows that the resistant strains can actually cooperate with each other to increase the resistance of the whole population:

This work establishes a population-based resistance mechanism constituting a form of kin selection whereby a small number of resistant mutants can, at some cost to themselves, provide protection to other, more vulnerable, cells, enhancing the survival capacity of the overall population in stressful environments.

These researchers took a strain of bacteria that was sensitive to the antibiotic norfloxacin. They gave the population a sub-lethal does of the antibiotic (it slowed them down, but didn’t kill them entirely), and watched resistance develop. After a few days, the bugs were able to grow at a normal rate. So they upped the concentration of antibiotic, and and watched as the bugs devised new ways of fighting it.

The little green dotted lines show the concentration of the antibiotic as the stepped it up over the course of a couple weeks. The red line shows the resistance of the total population, and it increases with a slight lag behind when the dose is increased. That part isn’t all that surprising – we know bacteria can evolve pretty quick. The interesting part is that they took individual bacteria out of these cultures and assessed how good they were at resisting norfloxacin. If the model I talked about in the beginning were true, you would expect only the most resistant individuals to survive, and the rest to fall by the wayside. And you’d expect each individual to have the same resistance as the total group. But that’s not what they found.

Look at the grey bars in that graph – those represent the resistance levels of individual bacteria pulled from the main culture. Each individual isolate they pulled had a far lower resistance than the population as a whole. This means that the bacteria must be cooperating with each other in order to survive. Cooperation amongst bacteria isn’t a new idea, but this is the first time that it’s been directly shown with respect to antibiotic resistance. I’m not sure this research necessarily helps us design better antibiotics or prevent resistance, but it’s an important reminder that the bugs are pretty smart – we need to be smarter to defeat them.

246 Trillion people

September 3, 2010

According to CNN’s homepage, that’s how many people shared this article about Stephen Hawking’s new book.

246 trillion people? Really?

Just a brief snippet of The Grand Design was released to generate buzz and considering that the number of people apparently sharing this article is 6 orders of magnitude larger than the number of people on earth, I’d say it worked.

The comment thread is also pretty entertaining – people (probably with no more astrophysics knowledge than your average 5th grader) claiming that his data is misleading, his reasoning flawed, his conclusions erroneous, and he’s probably a bad person to boot. And they conclude all of this based on a report about 2 pages of a book that isn’t even released yet. This post sums it up pretty nicely.

Science in the News Fall lecture series

September 2, 2010

I’m a member of a graduate student group called “Science in the News.” Every fall, we do a lecture series of fun and interesting science topics, and present them to a general audience. I’ll be talking more about it later, but the schedule is up.

Sept 22 Evidence-based Medicine: A Case Study of Vaccines and Autism
Sept 29 Bots That Mimic Bugs: Flying, Crawling, and Squishy Robots
Oct 6 You Are What Your Mother Ate: The New Science of Epigenetics
Oct 13 Beyond Agribusiness: New and Old Ways to Grow Food
Oct 20 The Laser Turns 50: A Brief History and New Frontiers
Oct 27 Forget-Me-Not: How Memories Are Formed and Lost
Nov 3 Our Microbial Organ: The Good and Bad Bugs of the Human Gut
Nov 10 The Science of Dogs: History, Psychology, and Genetics of Man’s Best Friend
Nov 17 Star Power: New Ways to Harvest Energy from our Sun

I’m doing the one on commensal microbes November 3rd (surprised?). If you’re in the Boston area during any of these lectures, you should definitely stop by, they’re always a lot of fun.

This year, we’re also filming the lectures, and I’ll mention when/where they are posted.

Algal blooms as seen from space

August 30, 2010

There’s a great article over at Wired showing pictures of enormous algal blooms in the oceans, along with descriptions of what caused them.

The images are absolutely stunning, and they kinda remind me of the paintings of my friend Paul

Woo, cancer, and human Fallacy.

August 25, 2010

I have a friend that has ovarian cancer. She was diagnosed a little over 2 years ago, but the doctors hadn’t been looking for it. She was only 23, with no family history of cancer, and then it showed up on a CT scan the doctors did when she had abdominal pain. After two and a half years of chemo, surgeries to remove first one ovary, then the other, then finally her entire uterus, the cancer won’t go away. It’s aggressive, and she has tumors everywhere, including two now in her esophagus that make it hard for her to breathe. A few weeks ago, she finished her last round of chemotherapy, a last ditch effort to poison her to the brink of death, in hopes that the cancer would die before she did. There’s nothing more the doctors can do, she’s gone to the limit of what science-based medicine can do.

So she looked for alternatives, and found Dr. Forsythe. At his clinic, he purports to treat cancer with dietary changes, supplements, and all manner of “wholistic techniques:”

Dr. Forsythe’s style in conquering cancer focuses on respect for the natural healing mechanism of the body and its stressors. We discover your unique environmental challenges brought about by poor life style choices including; dietary indiscretions, lack of sleep, excessive stress, decreased exercise, environmental toxins, lack of supplementation and detoxification, insufficient enzymes, and hormonal imbalances.  Integrative medical therapies that are aiding the immune system to give the body an opportunity to restore itself back to optimal health.

This all sounds pretty great, but does it actually work? If you listen to the testimonials on the site, youtube videos of people who are thrilled with their treatments, you might be compelled to say that it does. These people feel better, they are happy. My friend, after being there for two weeks and getting “detoxed” from all the chemotherapeutics, feels great. She feels stronger than she has in years.

But if we look at these patients six months or a year after their treatment, what are their survival rates? It’s no surprise that chemotherapy makes you feel like shit. It’s poison. But it’s poison chosen for a purpose, and we know it works. Getting those chemicals out of your system are undoubtably going to make you feel better, but improving emotional well-being is not the same thing as treating a disease. Diet changes, exercise regimens, and everything down to the soothing voices used by the people running the clinic and the positive attitudes of the people around you are going to make you feel better.

But what about the cancer they’re trying to treat? Six months out, how are the people at this clinic doing relative to people who don’t go? The truth is, we have no way of knowing. One thing I know for sure is that if my friend survives, this clinic will get the credit. Never mind the hours of surgeries and month after month of science-based medicine. That made her feel like crap, and she still has cancer. She probably would have died a year ago without those interventions, but it’s hard to argue that the year was worth it considering the pain she was in. The statistics on survival rates don’t mean much if you’re on the losing end.

And if she doesn’t get better, will the clinic get the blame? I doubt it. They’ll probably say she waited too long, or had too much chemo, or make some other excuse for why the treatment didn’t work for her. The thing that struck me about all the testimonials I watched (which wasn’t many, I admit), was that all of them already had traditional medical interventions. The guy in the very first video had a tumor the size of a golfball removed from his brain by a surgeon, then had months of chemo and radiation therapy. According to him, he’s cancer free now because of the supplements and meds given to him by Dr. Forsythe after all of that. Post hoc ergo propter hoc. If the strategies used at this clinic were truly effective – by which I mean actually treating cancer as opposed to just making patients feel good – I’m sure that oncologists world-wide would be clamoring to use his methods. You might argue it’s because scientists haven’t actually looked at the results. I’d love to see a meta-analysis looking out outcomes of people from his clinic vs those that received only traditional medicine, but I’m not holding my breath.

As a scientist, I find this type of place incredibly troubling, but I can’t say any of this to my friend. She’s beyond the help of traditional medicine now, and nothing I say will change that. Even if this clinic does nothing but make her feel better, I think it’s money well spent. And if she gets better, as I hope she will, I won’t really care who gets the credit.

Radiolab – Words

August 20, 2010
by

The most recent episode of the always fabulous Radiolab is about Words – how we interact with language and how it shapes our perception of the world around us. And this accompanying video had a smile plastered on my face for nearly its entire duration

See what they did there?

I love video games

August 19, 2010

I’ve played video games most of my life. Starting with Tom Sawyer’s Island and Matterhorn Screamer (both released in 1988), the early Final Fantasies and Secret of Mana  on Super Nintendo in middleschool, games like Starcraft and Half-life (Counter-Strike, Day of Defeat etc) in high school, and Halo in college. Grad school finally ended my 3 year love affair with World of Warcraft. I’ve always played for fun, but two papers in last week’s Nature show how video games can be put to even better use (both are behind pay-walls unfortunately).

The first is a perspective about the new uses of video games as educational tools, especially about science subjects.

Over the past decade, evidence has grown that computer-based play can support learning in schools. Pedagogical studies and evaluations, summarized in a 2006 joint report titled ‘Unlimited Learning’, by the UK government’s education department and a software publishers’ association, found that students whose lessons included interactive games were more engaged in curriculum content and demonstrated deeper understanding of concepts than those who did not use games. Better exam scores and teacher ratings resulted when computer games, both commercial and bespoke, were used as support materials. A plethora of organizations have sprung up to explore computer-based learning; in the United Kingdom, these include Futurelab in Bristol and the Serious Games Institute at Coventry University.

This is not, strictly speaking, a new idea – using games for learning has been steadily increasing in popularity for over a decade. There are even plans to develop a charter highschool centered entirely around gaming (the segment starts around minute 28). But I think it’s great to continue bringing attention to this idea. And this article is more about the idea of educating the general public about important scientific topics of general concern (like global warming).

The other article though, that one totally blew my mind.

Read more…

Immune response from start to finish: Part 2

August 17, 2010

[I’ve been hooked on the immune system since I was a kid and my dad showed me electron micrographs of macrophages eating bacteria in Scientific American. Now that I’m in graduate school studying immunology, and macrophages in particular, my dad asked if I could give a play-by-play of an immune response. Here you go Dad:]

Part 2: T-cells, B-cells and adaptive immunity

If you’ve ever had the flu (and I mean for real influenza, not some sissy man-flu), you know how much it sucks. But don’t blame the virus. Many of the most unpleasant symptoms – extreme fatigue, snot-filled sinuses, and high fever – are all a result of your immune system trying to kill that nasty infection (ok, I guess you can blame the virus). In part 1, I described how the innate immune system usually blocks bugs from getting in, or kills them quite rapidly. That fever is a result of all the cytokines released by the macrophages and other immune cells (higher body temperatures are thought to speed up the immune response or make the environment less hospitable to the pathogens). That snot is mostly comprised of mucous secreted by the inflamed tissues of the nose, and dead neutrophils that swarmed in kamikazi-style to gobble up whatever bacteria or virus they could find. That fatigue is an attempt to conserve energy that might be needed to fight the infection. Most of the time, the innate immune system does a pretty good job on its own. But if you get to the point where you can’t breathe through your nose, it’s a struggle just to sit up in bed and you could fry an egg on your stomach, your innate immune system just isn’t enough. That’s where the adaptive immune system comes in.

Read more…