Posted by: salamandercandy | July 17, 2006

Lowering the Ivory Tower with Molecular Evolution

Can molecular evolution help bridge the gap between professional scientists and everyone else? At first this might sound ridiculous, since molecular evolution is a highly technical scientific field, requiring intimate knowledge of biochemistry, statistics, and a great deal of theory. When I try to discuss my research with non-scientists, I struggle to explain basic concepts like the neutral theory, cladistics, or correcting for multiple substitutions. On the other hand, every scientific field is hard to understand, but curious amateurs frequently tackle complex ideas even without formal education. Because of the vast amount of bioinformatic data freely available on the web, it’s possible to do cutting-edge research in molecular evolution at essentially no cost, if you know what you’re doing. Promoting molecular evolution as a geeky hobby could be good for both scientific progress and public awareness of it.


As I have explained elsewhere, every DNA sequence used in a peer-reviewed publication is deposited in an online database, GenBank. Using a variety of free software, you can analyze these sequences and see how they’re related to each other, what kinds of evolutionary forces have caused them to diverge, and what sorts of functions uncharacterized genes are likely to have. For the most part, this hasn’t already been done; a gene is usually sequenced for a particular reason, and all the other interesting questions you could ask about that sequence are ignored. Who knows what truths might be quietly sitting on the web, waiting to be discovered by someone who puts the pieces together?

Skeptics might groan that sitting at a computer analyzing molecular data sounds far too boring for anyone but the academic elite to ever attempt it. Sure, lots of people are interested in science, argue the skeptics, but they dream about its more romantic, exciting aspects: trekking through the rainforest searching for a cure for cancer, traveling to outer space, tracking a herd of wildebeest by helicopter, creating and testing new explosives, and so on. Most science-based pastimes try to mimic those thrills with hands-on, outdoor activities: model rockets, butterfly collections, chemistry sets, and so on. But… humans display incredible variety in their passions. Many people already spend hours of their free time in front of a monitor, just surfing the web or playing video games. When I was a teenager, if I had had access to a fast computer, millions of DNA sequences, the right analysis software, and a good academic library, I might have spent days playing around with the data. Granted, I was much nerdier than most teenagers, but other folks like me are out there. And it would have two advantages over most science-based hobbies. First, it costs essentially nothing if you already have a computer with an internet connection anyway, and second, if you know what you’re doing you have a good chance of generating publishable results for a real peer-reviewed scientific journal. Not everyone will know what they’re doing, of course, but the possibility of figuring out something really novel is a good motivator, and anyone who tried would certainly learn a lot, even without getting a paper out of the experience.

Fields like astronomy and paleontology have benefited from the contributions of amateurs for years. The more non-professionals we have doing science, the better, because not only does more science get accomplished, but laypersons don’t feel so distanced from the world of academic researchers with all the letters after their names and their government grants. It’s clear that public understanding of science, especially evolutionary biology, is much poorer than it ought to be. Even mistrust and fear of scientists is disturbingly widespread. So next time, instead of World of Warcraft, consider exploring the NCBI site. Show your fundamentalist relatives a phylogeny you’ve reconstructed with neutral sequence data, and ask them to explain why it matches a morphology-based tree. High school teachers should think about giving that bright student an independent project looking for the signature of positive selection on genes, instead of the rote science assignment the rest of the class is working on. I know this isn’t for everybody. But I think there are a few folks out there who would be interested if they only knew about it.

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Responses

  1. Molecular Evolution for the Masses

    Jacob at Salamander Candy has written the post that I have been meaning to write. With so much freely available sequence data in GenBank and loads of free software with which to analyze it, we should encourage the general public…

  2. The reason your proposal is unlikely to work is contained in your post; “…I struggle to explain basic concepts…”.

    If you can’t bring it down the the level of the person you’re talking to, the battle is lost. You MUST find ways to communicate these concepts to non-science types. Hell, I’m a clinical chemist and I can’t follow this stuff. Free software? You mean the stuff the user has to compile? Free db? The one that makes no sense at all? The one written totally for the evolutionary biologist?
    How can you possibly compete with ‘god says and I believe it’ if you can’t make this stuff sensible?
    What we need is a Gerry Springer for science – vocal, abrasive, pedantic, opinionated, and able to play to the hind part of the brain.

    Education is the way, but with school boards under seige by Intelligent Design advocates and teachers who don’t know the basics (much less evolutionary biology), it’s a LONG road.

    Sorry for the rant. Please understand I think you’re pointing in the correct direction.

    Now, off to see if I can make any more sense of your links (here’s a concept – EB for Dummies FAQ).

    Doug

  3. I know this is not the secret to getting everyone excited about science, just a step, as you said, in the correct direction. And this post is certainly not supposed to be a “how-to” manual for the novice evolutionary geneticist; the page on my website comes closer, but even that is not sufficient. User-friendly software and detailed instructions would be ideal, and perhaps a lot of that can come from the research community if we emphasize the importance of making this stuff accessible to non-professionals. Still, I never took a class that told me how to used these programs, I had to sit down and figure it out myself. Granted, I have taken lots of classes in molecular biology and evolution, and as a grad student it’s easy to go ask another researcher if the software confuses me. But there’s no reason why a committed beginner couldn’t teach him/herself, the same way s/he might learn to play the guitar, fix a car engine, or identify local edible plants.

    But a Jerry Springer of science would make a bigger impact. Anyone want to step up?

  4. This is a fun article. I think the idea is very reasonable, so reasonable in fact, I spend a fair amount of time trying to do it.

  5. Can you cite any example of amateur research in bioinformatics which has been published in a peer-reviewed journal?

    I, myself, can act as an example. Earlier this year, I got my hands dirty in doing protein secondary structure prediction. I downloaded loads of data from the net and tried many different methods (ANN, Decision Trees, etc.) to do the prediction. At last, I got it with a technique known as cellular automata. Although the accuracy of my method was quite low – only 58% – but the method was simple. I wrote a paper and have now submitted it to a journal. I hope it gets accepted. :)


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