Gas station without pumps

2012 January 15

Individual work in collaborations

Filed under: Uncategorized — gasstationwithoutpumps @ 12:09
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I have protested in this blog before about the excessive use of inappropriate group work in schools, though recognizing that there are projects that are big enough or varied enough that groups are the appropriate way to tackle them.

A much more eloquent article on the subject by Susan Cain was just published in the NY Times: The Rise of the New Groupthink.

There are nice sound bites like

But decades of research show that individuals almost always perform better than groups in both quality and quantity, and group performance gets worse as group size increases.

She does suggest that on-line brainstorming may work better than in-person brainstorming, quoting Proust’s description of reading as a “miracle of communication in the midst of solitude”.  Her prescription for effective teamwork seems reasonable to me:

To harness the energy that fuels both these drives, we need to move beyond the New Groupthink and embrace a more nuanced approach to creativity and learning. Our offices should encourage casual, cafe-style interactions, but allow people to disappear into personalized, private spaces when they want to be alone. Our schools should teach children to work with others, but also to work on their own for sustained periods of time. And we must recognize that introverts like Steve Wozniak need extra quiet and privacy to do their best work.

I certainly have found that my best collaborative work has come out of fairly incidental contacts (meeting someone from another department in a hallway, chatting after a research seminar, talking with a student in someone else’s research group), followed by days or weeks of intensive work on the problem.

My sabbatical this year has been going through fertile and dead periods.  The dead periods have been times when I was not getting any contact with students and colleagues, and was not getting anything done.  The fertile periods were intense bursts of activity by myself after a chance contact with someone sparked an interest in a particular problem.

Most recently, I’ve been working on putting together a bioinformatics protocol that will let us reconstruct the cagY genes from hundreds of strains of Helicobacter pylori using PacBio sequencing.  Most of the sequencing technologies are not suitable for this gene, as it has long blocks of many repeats that vary from strain to strain.  Because the tandem replication is very recent (divergence between the strains may be only a few generations earlier) and there is selective pressure to maintain the open reading frame, the different repeats are often identical for long stretches, making short-read data nearly impossible to assemble. Even Sanger sequencing to confirm the gene assembly is difficult, as it is hard to find unique primer locations.

I started this project as a result of a short discussion with a couple of H. pylori researchers, but I spent weeks writing programs and Makefiles, testing them, twiddling parameters to see if they were robust, and so on.  I could not have done the work without the collaboration (I needed someone who had a difficult, interesting problem and the data to work on), but I could not have done the work if someone had kept interrupting me or making suggestions either.  The project would probably have died halfway through if I had had to do it with my usual teaching load, as I was spending 12–16 hours a day on it for weeks.

I need to alternate between working alone and contact with others. Sometimes talking through a problem with someone who understands and can ask good questions helps me clarify my thinking, after which I need hours or days to work out the details, after which I want to share again.

2011 May 23

H. pylori may trigger Parkinson’s

Filed under: Uncategorized — gasstationwithoutpumps @ 22:18
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I collaborate with someone who works extensively with Helicobacter pylori, and so I was very interested to see H. pylori in the news (in Science News, to be precise): Suspect Bacterium May Trigger Parkinson’s.

I knew that mice could be infected with H. pylori (indeed, I helped assemble the genome of a mouse-infecting strain, which we are trying to finish up to publish), though the mice don’t usually get stomach cancer from the infections (they tend to die of old age first, though a few long-lived mice get cancer).  I was surprised to hear that the mice get other illnesses from the infections. One thing surprised me a lot:

The bacteria didn’t have to be alive to cause the problem. Feeding mice killed H. pylori produced the same effect, suggesting that some biochemical component of the bacterium is responsible.

I wish I had access to the original article, and not just the reporter’s interpretation of it.  I’d like to know what the real evidence is for the link to Parkinson’s and how well tested the hypothesis is that a sugar-modified cholesterol  is the responsible chemical agent.

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