Sorry for the Inconvenience

Life, the Universe, Everything

Correlation and Causation

From xkcd:

Correlation does not imply causation, but it does waggle its eyebrows suggestively and gesture furtively while mouthing 'look over there'

I’m taking a micro course called “Scientist as Citizen,” which is basically a workshop for scientists who want to know about interacting with the public, specifically through journalism. It’s taught by Cornelia Dean, Science Editor at the New York Times, so she has a lot of experience dealing with scientists and trying to communicate science to the public. Unfortunately, a lot of scientists have this attitude towards science journalists:

I dont think science/medicine journalism will ever catch up with ‘clergy/ministry/missionary’ for the title of ‘most useless profession’, but man, some days theyre certainly giving the Godbots a run for their money…

So whats my point? Hmm. I guess that more scientists should open blogs and take a moment to write about cutting edge research, and the profession of pop-science/newspaper/magazine ‘science’ writer should either shape up, cut the fat from their ranks, or disappear.

I can’t get quite as worked up as this because I haven’t personally experienced bad science journalism about my research. Nevertheless, it is clear that a lot of scientists are wary of science journalists for similar reasons. It’s tough to explain your research in a way that other people will understand, a process made more difficult because of the different ways that scientists think as compared to the general populace (and that includes science journalists who are by and large NOT scientists themselves). In this class, Ms. Dean brought up several examples of  these differences, but there is one that I thought was especially insightful.

A lot of people tend to assume correlation = causation; cum hoc ergo propter hoc. My favorite illustration of this fallacy is in an open letter written to the Kansas City School Board regarding their fight to get Intelligent Design taught in schools

You may be interested to know that global warming, earthquakes, hurricanes, and other natural disasters are a direct effect of the shrinking numbers of Pirates since the 1800s. For your interest, I have included a graph of the approximate number of pirates versus the average global temperature over the last 200 years. As you can see, there is a statistically significant inverse relationship between pirates and global temperature.

Ms. Dean said something that I think bares repeating, “A correlation is not an answer, it’s an opportunity to ask a question.” Scientists generally know this when it applies to their research, but even scientists can be mislead by this fallacy in their day-to-day lives.

Ultimately, I think science journalism is important (though I agree with Abbie from ERV that more scientists should blog about their own research). Unfortunately, with news organizations everywhere slashing their science reporting budgets and taking reporters off of dedicated science beats, the trouble journalists have understanding what they are reporting on will only get worse. It will be up to us to the scientific community to communicate more effectively to make sure it’s done right.

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8 March, 2009 Posted by | Education, Science | , , , , , , | 1 Comment

Short update

I’m terrible at keeping this thing updated, I’m aware, but to be honest, not that much has happened recently.

I finally finished up my 1st rotation on micro-RNA’s. It went pretty well in terms of getting to know the lab and the environment, but my experiments weren’t particularly successful. Then again, the point of lab rotations really doesn’t seem to be getting stuff accomplished. I was supposed to start my next rotation today, but space isn’t going to open up until next week, so instead I’ll just give a brief explanation of what I’ll be studying: Toll-like receptors (TLR’s).

TLR’s are proteins on the surface of the cell that detect bad-guys and tell the immune system to react. These are different than the receptors on B-cells and T-cells, which can be randomly generated to recognize almost any molecular pattern (so when the flu and cold viruses mutate ever year, you can make a new response to them). Instead, TLR’s are hard-wired by evolution to detect things that the pathogens have a hard time changing, and are present on almost every cell type. That way, if you get infected by a bug that you’re B- and T-cells have never seen before, the TLR’s can still tell the rest of the boddy, “Hey, something’s not right here,” and mount up a preliminary response to give the B- and T-cells time to get in the act.

My project will be to work on the evolution of these receptors. The first one was discovered in fruit flies (and is simply called “Toll”), where it is important in the response to fungal infections. The immune system of insects is dramatically different from that of vertebrates, but nevertheless, the original Toll gene was clearly duplicated and mutated to recognize a variety of different signals (humans have at least 10, mice have 13). I don’t have details yet about what exactly I’ll be studying about the evolution of these TLR’s, but I’ll let you know when I do.

Beyond that, not much to report. Classes are going fine but there’s a lot of reading to get done. I’ve also been climbing a bunch (I knocked out my first 5.10b today). Hopefully when the weather gets warmer I’ll be up for some out-door stuff. Keep checking back, I’m really going to try to keep this current.

2 March, 2009 Posted by | Personal, Science | , , | Leave a comment

Herpes Cure?

Well, not exactly. But this is a great example of new approaches to preventing disease using the tools of modern biology. It’s even cooler because it comes out of the lab that I’m working in.

Judy Lieberman, professor of pediatrics and a senior investigator at the Immune Disease Institute, has overseen the development of the treatment that uses RNA interference, or RNAi, to disable key genes necessary for herpes virus transmission. That cripples the virus in a molecular two-punch knockout, simultaneously disabling its ability to replicate, as well as the host cell’s ability to take up the virus.

This isn’t my project, but RNAi is closely related to microRNAs (which is what my project is). Both involve double-stranded RNA in the cell that interferes with the expression of particular proteins in a specific way. The only difference is that microRNAs are endogenously encoded (the code for them exists on a cell’s own DNA) and RNAi uses RNA introduced from an outside source. Once the RNA is out in the cell though, they both use the same molecular mechanisms to block translation of their targets. Since it’s discovery, RNAi has been extremely useful in studying what particular genes do (the best way to learn about something is to break it and see what else goes wrong), but it’s potential for theraputic use has been elusive.

Many in the field think RNAi-based drugs may be the next important new class of drugs. By introducing tiny RNA molecules into cells, researchers can target a gene of interest and, in effect, throw a wrench into that gene’s ability to build protein molecules. For all intents and purposes, that gene is now disabled.

While RNAi has profoundly accelerated the ability of scientists to probe and interrogate cells in the petri dish, therapeutic breakthroughs have proved far more problematic. Researchers have had a difficult time delivering these tiny RNA molecules and ensuring that they actually penetrate the desired cells and tissues in a living organism.

Modifying a delivery technique that Lieberman developed in 2005, she and postdoctoral fellow Yichao Wu and junior researcher Deborah Palliser (who now heads her own laboratory at Albert Einstein College of Medicine) treated mice with strands of RNA that were fused to cholesterol molecules, which made it possible for the molecules to pass through the cell membranes.

This approach works well in mice, but now needs to be developed for humans. The other problem is that it’s prophylactic, meaning it’s just a preventative measure and would not be able to treat people that are already infected, but it could be the first step in generating preventative tools for any number of STDs.

27 January, 2009 Posted by | Science | , , , | Leave a comment

How Science Works

I really couldn’t put it any better than this.

Science is so much more than the simplified “observation ->hypothesis ->data ->conclusion” that we learn in highschool, yet most science classes focus merely on the details of past scientific discoveries, and spend almost no time on the actual process. Carl Zimmer says it better than me:

These questions may seem too abstract to bother with. We all know what science is, right? So why don’t we just cut to the chase, and learn about black holes and viruses and everything in between? Pondering the nature of science is important, though, because understanding how science works lets us get much richer, deeper feel for what we do–and don’t–know about the natural world.

It also might get the masses that buy into anti-science bullshit to appreciate that scientists are not out there trying to corrupt their poor Christian children with godless ideas, but are in fact searching for an understanding of the natural world.

Well, probably not, but it’s worth a try.

2 January, 2009 Posted by | Science | , , | Leave a comment