Fetus, Eat Your Soy!

March 30, 2006 at 4:29 pm | | news

A recent study from Duke University Medical Center suggests that a pregnant woman’s consumption of soy “reduces an embyro’s risk of becoming obese later in life.” Scientists fed genistein, an active ingredient in soy, to some mice. Their babies were slimmer than the babies of the mice who didn’t get the soy. Soy might also help make sense of the lower rates of cancer among Asian populations. But I’d like to know how Americanized Asians fare against their Asian counterparts. You know, to see if they are superhuman or something. Source

Raving with Acrylic teef?

March 29, 2006 at 2:28 pm | | cool results, nerd


The consequences of snowboarding continue. As shown in Figure 1, it looks like acrylic behaves more like water than delicious tonic water under UV light. It’s too bad. I prefer homogenous teef.


Figure 1. Inhomogenous teef.

I am practicing several dance moves enriched with head shaking to minimize teef exposure, as shown in Figure 2.


Figure 2. The Cobra: a popular dance routine.

I just measured Fopt for my ‘scope

March 28, 2006 at 5:14 pm | | everyday science, hardware, tutorial

So here’s the deal: the detection efficiency for the stream of photons coming from one single fluorophore is kinda crappy (~10%). But that’s the state of the art; it’s part of the reason single-molecule measurements are so tough … and fun!

The detection efficiency D is:

D = nQFcollFoptFfilter

where nQ is the camera quantum efficiency, Fcoll is the percetage of light collected from the objective, Fopt is the efficiency through all the optics in the microscope, and Ffilter is the transmission through the various filters. Today, I measured Fopt to be 50% at 488 nm. Here’s a page from my notebook that shows my setup:


orbecular candy?

March 27, 2006 at 2:35 pm | | cool results, everyday science, software

Doesn’t this look like some kind of molecular lolly-pop material candy?
So I don’t really get any interesting info from this result, but Gaussian can really make some pretty pictures … that take a long time to make.

This is DCDHF-2V optimized using BLYP/6-31G(d). I’m displaying the HOMO orbitals.

french college chemistry explosion

March 24, 2006 at 10:21 pm | | lab safety, news

BBC NEWS | Europe | Huge blast rocks French college
Not very much information, yet, but at least one person died. Hard to tell whether this is chemistry-related or terrorism…


March 24, 2006 at 6:05 pm | | everyday science, literature

I just found that SciSearch v2.4 has a cool feature that you can plot the number of citations of someone’s papers. Here’s an example of W.E.’s plot of number of citations versus publication year:


Cool, eh? Go play with it and try your favorite scientist.

h value

March 24, 2006 at 2:39 am | | everyday science, journal club, literature, nerd

I presented a paper at my Chemical Physics Journal Club a while back. Here’s a citation: Hirsch, J. E. An index to quantify an individual’s scientific research output. Proc. Nat. Acad. Sci. 2005, 102(46), 16569–16572.

The basic idea is that h measures your (career) scientific output, the higher the value, the greater the output (convolved with impact). h is the number of papers that you have authored, each with h or more citations. In other words, if you have 50 papers, but only 30 of them have been cited 30 or more times, your h = 30. This method tries to avoid giving a lot of credit to people who write oft-cited review articles or people who write millions of papers that no one ever reads.

It’s mostly sorta bullshit, but I enjoyed calculating the “h value” (or “h index” or “h number” or “Hirsch number” or…) of several of the profs at Stanford:

PI h
Pande 28
Moerner 43
Andersen 48
Fayer 51
Boxer 52
Zare 94

But there are some things that are unfair: Pande is a younger scientist, so he hasn’t had as much time to publish or have his works cited as, say, Zare or Fayer. So we can normalize to the number of years since earning PhD (where m = h/#years):

PI m
Andersen 1.2
Fayer 1.6
Boxer 1.7
Moerner 1.9
Zare 2.2
Pande 2.5

Comparing m values is probably a little more fair. But now there are some more problems. Pande is in his steep period, which will presumably level off like this:


So you get your PhD, then you die. The value of m also doesn’t take into account that Andersen is a theorist or that W.E. spent until the mid-90s in industry, where people normally don’t publish as much. Oh well, it’s still pretty fun.

By the way, hsam = 1

UPDATE: Check out my new measure, the Lord h-bar index.

freeze pics

March 23, 2006 at 7:14 pm | | cool results

I’m happy with these results because they are pretty. Here’s our favorite environmentally sensative fluorophores in liquid (left) and frozen (right) toluene:


And we have red dyes, too! Here’s a nice red one in ethanol:


They get so much brighter! There’re even cooler looking in real life: the digital camera doesn’t capture the colors as well. For instance, as the red solution thawed, there were beautiful purple veins of liquid solution throughout the “ice.”

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