Everyday Scientist

TARDIS

One of my labmates attended Comic-Con last week in San Diego and decided to dress up as a TARDIS (a sort of time-machine from Dr. Who) in what can only be described as an epically awesome costume.

While there is a side-on photo of her with writer/director Joss Whedon (Firefly, Serenity, Buffy the Vampire Slayer, the Avengers, etc.) that’s been circulating on Twitter, below is an EXCLUSIVE photo from her own camera.

In addition to attracting the attention of the famous and powerful, she also managed to attract the very sketchy. Link

how do you read PDFs?

I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)

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Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.

Man, I need to test-drive these devices for a month!

Other options?

even JACS is excited about the new Tron movie

I thought this TOC looked pretty awesome.

academic genealogy

Jeremy over at Chemistryblog posted a few sites with info on academic lineage of many chemists. That inspired me to finish researching my academic genealogy. Kallie’s page at UT’s site was a nice confirmation of the lineage I had independently found. But I actually found links further back (through Rowland to Helmholtz, and eventually back to Leibniz’s dad); I’m not exactly sure why the UT page stops at Mendenhall.

I also explored my lineages from my undergrad and postdoc advisors. Interestingly, those two lines meet up in the mid-1800s (Liebig).

Anyway, below is the entire tree.

(I know this is a little self-indulgent. But whatever.)

Sam’s Academic Genealogy (via PhD advisor)

Samuel Joseph Lord
Postdoctoral research 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

William Esco Moerner (Stanford)
PhD Cornell 1982 (under A.J. Sievers)
BS Washington University 1975

Albert John Sievers III (Cornell)
PhD Berkeley 1962 (under Michael Tinkham)
BA Berkeley 1958

Michael Tinkham (Berkeley, later Harvard)
PhD MIT 1954 (under M. W. P. Strandberg)
BA Ripon College

Malcom Woodrow Pershing Strandberg (MIT)
PhD MIT 1948 (under A.G. Hill)
BS Harvard 1941

Albert Gordon Hill (MIT)
PhD Rochester 1937 (under Lee Alvin DuBridge)

Lee Alvin DuBridge (Rochester)
PhD University of Wisconsin–Madison 1926 (under Charles Elwood Mendenhall)

Charles Elwood Mendenhall (Wisconsin)
PhD Johns Hopkins 1898 (under Henry Rowland)

Henry Augustus Rowland (Johns Hopkins)
Civil Engineering degree Rensselaer Polytechnic Institute 1870
later studied under Helmholtz in Berlin

Hermann von Helmholtz (Berlin)
PhD Royal Friedrich-Wilhelm Institute (under Johannes Peter Müller)

Johannes Peter Müller
Bonn University (under Philipp Franz von Walther & Karl Rudolphi)

Karl Rudolphi … Friedrich Leibniz (1597-1652) [Gottfried Wilhelm Leibniz’s father]
Philipp Franz von Walther … Gerard van Swieten (1700-1772)

Sam’s Academic Genealogy (via postdoc advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Jay T. Groves (Berkeley)
PhD Stanford 1998 (under Steve Boxer)
BS Tufts 1992

Steven G. Boxer (Stanford)
PhD Chicago 1976 (under Gerhard L. Closs)
BS Tufts 1969

Gerhard L. Closs
PhD Tübingen 1955 (under Georg Friedrich Karl Wittig)

Georg Friedrich Karl Wittig
PhD Marburg 1923 (under Karl Friedrich von Auwers)

Karl Friedrich von Auwers
Berlin, 1885

August W. von Hofmann
Giessen, 1841

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

Sam’s Academic Genealogy (via undergraduate advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Sergei S. Sheiko (UNC)
Habilitation University of Ulm 2000 (under Martin Möller)
PhD Institute of Chemical Physics of the Russian Academy of Sciences 1990
MS Moscow Physico-Technical Institute 1986

Martin Möller (Ulm)
Postdoctoral research University of Massachusetts (under Robert W. Lenz)
PhD University of Freiburg 1981 (under Hans-Joachim Cantow)

Hans-Joachim Cantow (Freiburg)
PhD University of Mainz 1950 (under G.V. Schulz)

Gunter Victor Schulz (Mainz)
PhD Kaiser Wilhelm Institute of Physical Chemistry and Electrochemistry 1932 (under Herbert Freundlich)

Herbert Freundlich (Kaiser Wilhelm Institute)
PhD University Leipzig 1903 (under Wilhelm Ostwald)

Wilhelm Ostwald (Leipzig)
PhD 1878 Dorpat University (under Carl Schmidt)

Carl Schmidt (Dorpat)
PhD University of Giessen 1844 (under Justus von Liebig)

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

what the heck is permanent press?

OK, what the heck is the “permanent press” cycle on my washer? On the dryer, I think it just adds a cool tumble to the end to avoid wrinkles. But what about for the washer?

Wiki says that some machines might spray a little water during the spin, but I’m fairly sure that my cheap washer does not have that feature. From what I can tell, the perm press wash cycle is 2 min shorter than the “normal” setting, and the second rinse is a “cool down” rinse. However, my washer make the second rinse cold anyway, so I don’t think this makes perm press special. I wonder if the agitation is weaker (or stronger) for perm press compared to normal, but I sorta doubt it.

So, in conclusion, I have no idea what the “permanent press” settings on my washer are for. Maybe they just had extra space on the settings knob, so they added some fictional settings?

UPDATE: I called GE to ask them this question about their washer. The woman at the technical service said, “I have no idea.” And sorta laughed. No help there.

my world is crumbling!

What the what?!?

JACS will now consider Communications of any length up to 4 journal pages and will include the Abstract in the PDF and print versions, starting with Volume 132, issue 27 (July 14, 2010). Authors should refer to the online Information for Authors and use the Communications template when submitting Communications.

Four pages is not a letter. That’s an article, dammit. And abstracts for letters. WTF? No no no. This is all wrong.

What’s the best part of JACS Comms? That they’re short and sweet. You can actually read the damn things, instead of just reading the abstract and looking at the pretty pictures (like we all do with full articles). No longer. Now JACS Comms will be long and complex. Boo.

Instead of destroying the sanctity of the blessed JACS Comm, ACS should have added an intermediate category between Comms and Full Papers.

This is almost as bad as when ACS defaced the elegant JACS by adding images!

(Unlike FSP, I really am a curmudgeon.)

Creatine, a popular sports supplement

Creatine, a small-molecule found naturally in red meat (and biosynthesized in our bodies), is a popular supplement for weight lifters. To understand how it works, one needs to know that ATP (adenosine triphosphate) is the body’s energy molecule.  It gives muscles the energy they need to function, but in the process, it loses a phosphate group and is converted to ADP (adenosine diphosphate).

Creatine monophosphate has the ability to convert this low-energy ADP molecule back into the super-charged ATP molecule that muscles crave.

Creatine monophosphate

As a consequence, lifters that supplement with creatine can do more reps, which can lead to better results in the gym on a shorter timescale.  Creatine supplementation also has the effect of increasing water volume in the muscles, causing them to swell and look bigger; this effect subsides quickly once creatine supplementation is stopped.

It is well known that consumption of simple sugars with creatine increases creatine absorption.  When you consume sugar, your blood-sugar level increases, and your body releases insulin in response (assuming you don’t have type 1 diabetes).  Insulin instructs the cells to take up sugar from the bloodstream.  Insulin also has the nice effect of stimulating creatine transporters, which transport creatine from the blood into cells.

Now that the background is finished…

I was at GNC yesterday buying some creatine.  I looked at the ingredients on the GNC-brand creatine and gasped.  Creatine and sucralose!?!?!?!  Sucralose???  OK- a little more background.  Sucralose is a zero-carbohydrate, synthetic, sugar mimic.  As you can see below, it looks a lot like sucrose, only it has some chlorine groups that basically make it unrecognizable by the body’s enzymes.  So your tongue recognizes it, but your waistline doesn’t because it’s not metabolized.

“Sucralose”

Sucrose

Now to the remarkable part.  Sucralose has no effect on the blood sugar level. So this GNC-brand product that I bought containing 17% sucralose/83% creatine is ridiculous.  Uninformed weightlifters don’t want “sugar” calories so the industry introduces 1 g calorie-free sucralose per 5 g creatine, which has no effect on creatine uptake and actually tastes quite disgusting (sucralose is 600x sweeter than sucrose, which is regular sugar).

So who is the bigger idiot?

man, i’ve been really slack lately

Sorry I haven’t posted anything for such a long time. I’ve been on vacation before my postdoc starts. I’ve been out of the loop, mainly because I don’t have access to journal articles until July. The break has been nice, but I am sorta looking forward to doing some science soon!

That’s all.

Inappropriate Labware

We have these Al bases floating all over the place.  I guess when Stanford sanitized their mascot, we never got around to PCing our opto-mechanics.

seminal (hehe)

This has got be be a joke, right? The letter to the editor suggests that the term seminal is “sexist” because it refers to semen (figuratively meaning full of potential).

No way this is serious.

P.S. The letter writer describes the word as “distasteful.” Hehe.

naturally depressed

The documentary video “Naturally Obsessed” follows some graduate students at Columbia through their trials and tribulations in science. Personally, I found parts quite depressing. However, it is an interesting video and I wish they would film other labs to round out the picture.

Or watch here: http://www.thirteen.org/naturally-obsessed/

Here are some of my thoughts (spoiler alert!):

The nature of their research, protein crystallization, is especially depressing: because the results are all-or-nothing, the students work very hard and may see zero reward. In other bench sciences, this can also be true. However, it is often the case that there are many small discoveries and accomplishments along the way. Protein crystallization work, on the other hand, means that if you find the structure, you publish; if the protein doesn’t crystallize well enough to get a structure, you don’t publish. Ouch.

The person I felt the worst for was the blond kid, Kil. He was so positive at the beginning of the film—almost to a fault. Near the middle, he begins complaining about the strains being a graduate student has on his life and relationship with his fianceé. At the end, we learn that Kil and his fianceé broke up (at least partially because of grad school), and he has no interest in academic science. The viewer is at least relieved to discover that Kil gets a good job after graduation!

The ending of the film reminded me of the end of The Graduate: it was bitter, but maybe only intended it to be sweet? Rob, earns his PhD, has a baby, is happy, and becomes a postdoc. But I feel bad for him trying to raise a child on a postdoc’s salary (his wife is also a graduate student). Not to mention the fact that he is already over 30 years old and has several years of a postdoc ahead of him. I’m just not sure it’s the happy ending the film-makers intended. On the other hand, Rob seems really motivated and wants to become a professor, so maybe he’s on his way!

My overall opinion is that the film is interesting, and fairly accurate. However, I think a couple more episodes could really strengthen the documentary. This episodes follows a graduate student as he “succeeds” by toiling away for years, getting a chance success, and then publishing in Science. Instead, I would like to see the day-to-day, week-to-week, year-to-year successes of graduate work: positive interactions and collaborations with fellow students and postdocs, brainstorming in meetings, little “ah-ha!” moments while sitting over a sample, and publishing in J. Phys. Chem. B. In the end, I think this little documentary does a good job of portraying the ups and downs of grad school. However, I think another few episodes in different types of labs would reveal a more realistic overview. Moreover, I think it would be healthy to show students accomplishing smaller steps along the way to their PhD or best paper, instead of the view that students must toil away for 6 years with no rewards until the end.

(via BiteSizeBio)

cleaning-chemicals industry takes on the final frontier…

…invisible stains. Finally, there are cleaners on the market that can clean up stains that are undetectable by any of the human senses.

Have you seen that commercial for a toilet-bowl cleaner? They say, “Bleach only hides stains.” Then they pour some purple stuff on the ceramic to reveal the hidden “stains.”

Um, what? Isn’t hiding a stain mean you get rid of the stain? By definition? I think it’s nuts that the cleaning-chemicals industry is inventing the problem of invisible stains. I have a solution to this problem: don’t pour that purple stuff in your toilet!

And then there are those “chemical residues” that watch you shower. The invisible, undetectable residues. How do we know that invisible residues are there at all? The TV tells us that they are there, of course. But wait, how do we know that the alternative cleaner doesn’t leave an invisible residue?

All this reminds me of the Emperor’s New Clothes. Or, more aptly, that old joke about the elephant repellant (“You don’t see any elephants around here do you? It must be working, then!”) People need to ignore these silly commercials and relax a little bit about cleaning. Just scrub the toilet bowl every week or two with a brush, then wipe the seat etc. with diluted bleach and be done with it! Jeez!

McNASA and whale oil

This is the strangest paragraph I’ve read in a while:

“But during the 1980s, [NASA] lost much of its old high-quality data. Its early tracking stations recorded satellite data on high-resolution master tapes that used whale oil to bind iron particles to the acetate. The whale oil made the tapes far more durable, but when commercial whaling was phased out in the mid-1980s, NASA couldn’t get such long-lasting tapes. So it reused old ones. NASA engineers taped over some 200,000 previously recorded master tapes, including high-resolution records from spacecraft as diverse as early Landsat satellites and Apollo 11, and preserved only low-resolution copies.” (source)

I checked to make sure it wasn’t the April 1st issue of Science. The entire article is weird, including the fact that researchers are working out of an abandoned McDonald’s.

Just another reason to start hunting those smug whales again.

lost my library proxy

Stanford already took away my off-campus access to journal articles. I thought I’d have a couple months of access after I graduated, but I guess not. So keeping up with the literature means going to campus and sitting in the library like an undergrad.

I suppose I could rent articles, but I’m too spoiled by free access! Ah well, I’ll catch up reading my PDFs, then keep up better once I start my postdoc in a couple months.

obscure paper

I was recently looking for a prep for p-bromophenylphosphine, and I found exactly 1 reference for it’s synthetic prep that’s cited by every paper that uses it.

It happens to be in (possibly) the most obscure journal in the world – “Phosphorus and the Related Group V Elements.”  It had all of 6 volumes in the 70′s before it merged with the “International Journal of Sulfur Chemistry” to form “Phosphorous and Sulfur and the Related Elements.”

I finally found TWO places in the world that had hard copies – the North Carolina State University library, and, of course, the National Library of Australia.

I’m beginning to think what I want must be some obvious synthesis, and that I’m just an idiot.  However, I did fail organic chemistry and am now working in a synthesis lab, so the “idiot” part is probably appropriate…