Apr
28
2010
1

Managing by Being Absent

Last night I was filling in for the scoutmaster at my son’s troop. Because time is flying, we held the patrol leaders council (PLC) anyway, so I got to see how it works. And, as usual, probably created a little bit of an (apparent) innovation. I say apparent only because what I did was to follow the scoutmaster’s handbook.

In the beginning I passed on a few things that needed to be done, and then wandered off. When I returned one of the older scouts had joined the group, and there was a question of why he could be there as he wasn’t a patrol leader. So I pointed out that this was the senior patrol leaders party and if he wanted someone to be there they could be. I added that I was a guest as well, and if asked, would leave.

So they asked me to go!

Great! While I watched from a fair distance away, talking with other adults, they got down to business. When they were done, they called me over and we reviewed what had been decided. Exactly the way it should happen.

Written by Rob in: scouting |
Apr
10
2010
1

On controls in science

There was a bit in the Atlanta fish-wrapper this morning by one of the local “child rearing advisors” (can’t call her/him/it a psychologist in good faith).  To skirt the laws of libel I’m not identifying him/her/it any further, but let’s just say it/him/her is of the “smack’em hard, lock’em up” school of parental advise. (it might be more charitable to say the ‘children should be neither seen nor heard school – which makes great foot soldiers and poor Americans)  The article was about fish oil or dietary supplements for ADHD and ended with

“Although these parent reports are dismissed as non-scientific by what I term as the ADHD establishment, the issue boils down to one fundamental question: Why would these parents say their kid’s behavior improves if it didn’t?”

Can you spell placebo?

More seriously there is an expectation effect in science.  People, and scientists are people, see the results they want to see.  That’s why we do control experiments.  It’s also why magicians wear slightly outlandish clothes and use pater. One of the difficulties in a complex experiment, and children are complex, is that this expectation effect is very pronounced.  Simply doing anything will have an effect.  I could develop a “theory of re-ionized water” complete with some impressive apparatus – say a UV steripen or one of the miox water purification devices, a pinch of some magic and harmless chemical – say potassium chloride, and a ritual for their application, and show that it worked.  It would really work, not by addressing the biological basis of the problem, but by cynically manipulating the experimental subjects.  The more complex and disturbing (or expensive) I make the apparatus and its associated spell the more effective it will be.

It’s a pity that there is this little thing called scientific ethics in the way.

Written by Rob in: engineering,laboratory practice,science |
Apr
08
2010
1

Partitioning Matters!

Yesterday I had a couple of “ah ha” moments, which allowed me to improve or solve a couple of long standing hard problems. Since these will eventually be published, I’m going to dance around the details, but hopefully still say something useful.

  1. (near)Optimal Networks of Distance Restraints in Models.  We’ve been exploring how to merge data from many different protein models in a deterministic fashion (this is different from the state of the art which is somewhat randomized).  Turns out if you get the partitioning right – which specific distances – then you get significant improvements in model quality.
  2. Partitioned Model Building. One of the tricks of the trade in polymer Monte Carlo algorithms is to remove a segment of the model and rebuild it.   This avoids many of the local minimum problems.  AMMP can now do that and it seems to be very helpful.  Initial tests show that it can readily optimize a more or less random structure to meet all NMR distance restraints.
  3. Differential Evolution over Ambiguous Degrees of Freedom. Fully automatic, phase-free, direct solution of crystal structures is a computationally difficult problem.  (this is different from conventional direct methods where phase probabilities are estimated and the structure ‘bootstrapped’ from a poor initial image or the use of a reference phase via heavy atoms or anomalous scattering.  We’re trying to “just solve” the simultaneous transcendental equations that relate scattering to structure.)   Differential evolution methods are a class of function-only methods that are highly convergent.  On ‘normally hard’ problems, they tend to beat the competition by several orders of magnitude in speed and effectiveness.  (slight exaggeration, but only a slight one).  So I thought they’d make a neat quick Acta Cryst. paper eight months ago.    It was pretty simple to make them work on my favorite easy structure.   But no others.  ARGGH!    I’d had similar results with other powerful methods like particle swarm optimization.   (and there isn’t an error in the crystallographic part of the code).  Turns out there is a N! partition problem over N ambiguous degrees of freedom.   So any method that tries to compare  labeled degrees of freedom, where the labels are just arbitrary with some other random partition of labeled degrees of freedom can run into “mixing axes” and get completely screwed up.  Explicitly searching for a close partition allows the system to evolve into one partition and then handily be solved.
Written by Rob in: science |

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