Comments on: Lowering the Ivory Tower with Molecular Evolution http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/ Writing about biology and other sweet things Mon, 09 Nov 2009 17:44:06 +0000 http://wordpress.com/ hourly 1 By: Paras Chopra http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-47 Paras Chopra Sun, 26 Nov 2006 08:51:12 +0000 http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-47 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. :) 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. :)

]]> By: Sandra Porter http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-46 Sandra Porter Fri, 11 Aug 2006 00:47:08 +0000 http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-46 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. 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.

]]> By: Jacob http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-45 Jacob Sun, 23 Jul 2006 18:20:08 +0000 http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-45 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; <a href="http://oregonstate.edu/~tennessj/funwithsequences.htm#Seriously" rel="nofollow">the page on my website</a> 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? 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?

]]> By: Doug http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-44 Doug Sun, 23 Jul 2006 11:06:45 +0000 http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-44 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 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

]]> By: Evolgen http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-48 Evolgen Tue, 18 Jul 2006 14:31:08 +0000 http://salamandercandy.wordpress.com/2006/07/17/lowering-the-ivory-tower-with-molecular-evolution/#comment-48 <strong>Molecular Evolution for the Masses</strong> 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... 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…

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