The Notebook

Lab notebooks are important; as far as paper goes they're more important than your diploma and probably even your social security card (which you can get replaced, albeit painfully). If your lab notebook vanishes, you're in trouble. Big trouble. So naturally, we see a variety of lab notebook practices.

Gosling and McAdams express their
mutual enthusiasm for efficient , timely
laboratory recordkeeping.
Source: NewLine Cinema/Netflix.

I think notebooks of students at the beginning and end of their graduate school careers are most interesting. Beginners because they don't know what information is important or how much room they're need, so the things end up looking like a William Faulkner/James Joyce novel. Grizzled veteran students because they just don't care anymore and procedures end up super sparse, with four or five crammed on a page.

The following are, in my experience, the most common lab notebook styles:

Spiral notebook: Lazy grad student (read: cheap PI) doesn't need to buy a fancy notebook with actual gridlines or thick paper or sturdy binding. The last three quarters of that barely-used spiral notebook, from back when taking notes in spectroscopy seemed a good idea, will suffice.

• Advantages: Cheap and convenient. If your friends see the notebook, you can avoid looking like a dork who has a lab notebook and instead say something about "YOLO", thus retaining social status. 
• Disadvantages: If seen in lab, PI will think you are studying for class instead of running columns. Prepare for awkward talk on time management.

Hard-bound notebook: Your PI has money and/or wants to keep up appearances, so everyone's got the $300¹ leather Amazon-rainforest-paper hardbound notebooks.

• Advantages: Nerd cred. Ability to use notebook as blast shield in the event of a lab explosion. Also ability to build fort out of lab notebooks once enough labwork has been done (think of it as a reward).
• Disadvantages: If taken outdoors, this notebook will likely be stolen by humanities majors for use as a diary/composition book. And if the notebook is lost, it's obvious and your life is meaningless.

Hard-bound notebook with carbon copy paper: Your PI is old-school but realizes that backups are pertinent given the hundreds of liters of organic solvents and pyrophoric reagents dancing around the lab space. Unfortunately, the method of backup is the 1950s method of carbon copies of your notebook, so it's a lot like being in undergrad lab again.

• Advantages: Shouldn't lose your work.
• Disadvantages: Will probably lose your work anyway because you leave the carbon copies in a pile next to the original notebook.

Electronic lab notebook: No fear of technology in your group. Everyone's lab notebook is on "the cloud", and that's not even the cloud of weird thiol fumes coming from that one guy's bay. Instant sharing, instant backup.

• Advantages: Everyone (read: PI) knows what everyone else is doing and has done (or is this a disadvantage?)
• Disadvantages: Put on gloves. Measure out alcohol. Take off gloves. Type amount of alcohol. Put on gloves. Measure out triphenyl phosphine. Take off gloves. Type amount of triphenyl phosphine. Put on gloves. Measure out carboxylic acid. Take off gloves. Type amount of carboxylic acid. Put on gloves. Dispense dry THF and precise volume of DEAD. Take off gloves. Type amount of THF and DEAD.

Kimwipes and Sharpie: It's written on the hood. Take a picture. That's good enough for SI, right?

• Advantages: Frees up bench space for unwashed glassware.
• Disadvantages: What do you mean, you cleaned my hood sash?? That was 3 months of work!

The miiiiiiind: Oh yeah, that experiment happened... totally ran that reaction, no, I wasn't playing Angry Birds instead, why do you ask. The yield was... uh, yeah, it was 87%... The NMR? Oh don't worry, it's already characterized in the literature.

• Advantages: Chemistry works however you want it to.
• Disadvantages: None.

On a serious note, why do people still use hard-bound notebooks without any sort of backup? That seems like risky business. (N.B. apparently there are companies that will digitize all your lab's records. Interesting.)

¹ $300±300. I don't pay attention to these things.

Reading assignments, vol. 2

Here go some interesting reads from this week:

Research policy:

• Check out this commentary by AAAS CEO Alan I. Leshner over at the Chronicle of Higher Education. He and Steven J. Fluharty bemoan the increasing cost in money and time of administrative burdens on research labs.
• Also at the Chronicle, Peter Suber (Harvard Open Access Project) and Darius Cuplinskas make the case for open access to research in order to benefit the public and spur innovation.
• At Scientific American, James M. Gentile writes about the persistent gender bias in the sciences. Most troubling is the double-blind study showing that male and female faculty members both rate female job applicants lower than male regardless of content.

Science and the public:

• I like cringe-worthy television science. See Arr Oh points some out over at Just Like Cooking
• Mark at Chemistry-Blog laments over the idiocy of chemophobia when tied with administration.

Science writing:

• Here's a Guardian/Observer column by Ian Tucker with Q&A with some prominent science writers about what makes good science writing. 
• A series of tips from Scientific American blogger Khalil A. Cassimally on how science writers can harness social media to gather information for writing purposes. 
• Matt Shipman encourages researchers to engage in public communication of science, and says funding agencies want them to as well.
• At ERV, some comments/advice on how not to be a horrible pop sci journalist. 

Other:

• On Chemistry Blog, a writeup of a K.C. Nicolaou essay just published online for Angewandte. It's a historical perspective on total synthesis. Although perhaps calling total synthesis the "flagship of chemistry" is an exaggeration.
• Chemjobber puts the fiscal cliff in perspective, and the prospects look poor (don't they always?) for grad students and postdocs.
• Drew, of webcomic Toothpaste for Dinner, issues an important and vital homonuclear warning. He also coauthors Married to the Sea which four years ago published this comic which is taped above my desk at all times. (For those still reading, Drew was previously a chemist and is also hilarious).
• At Just Like Cooking, See Arr Oh points out some scatologically unusual reaction conditions.

On the nature of ignorance and the futility of facts

Two or so weeks ago, Adam Laats (author of Fundamentalism and Education in the Scopes Era and historian at the Graduate School of Education at Binghamton University) posted the following perhaps obviously-titled commentary (To Teach Evolution, You Have to Understand Creationists) at the Chronicle of Higher Education. The Chronicle often has some interesting (often either pleasantly interesting or agonizingly irritating) commentaries, and I found this one worth comment.

Denialism is well-established phenomenon, and Laats writes on the nature of creationists. Specifically, and somewhat aggressively, he points out the ignorance of evolutionists in the ongoing clash, using Paul C. Broun's famous remarks as a starting point. From the article's introduction (bold emphasis mine):

"If you follow the news about culture wars, evolution, and creationism, you've probably seen it by now. Earlier this fall, U.S. Rep. Paul C. Broun Jr., Republican of Georgia who ran unopposed for re-election, said in a widely distributed video that evolution, embryology, and the Big Bang theory were "lies straight from the pit of hell."

I don't agree. But the ferocious response to Broun's remarks tells us more about the widespread ignorance among evolution supporters than it does about ignorance among creationists."

I guess it's good that Laats doesn't agree with a statement attacking the entire foundation of modern science and medicine, for which an inordinate amount of evidence has been amassed.

But what is this about ignorance among evolution supporters? Well, Laats insists, evolution supporters are ignorant in assuming creationists are ignorant. He points to Broun's formal credentials:

"I disagree with Broun's views on evolution—and on a host of other topics, for that matter. But if we hope to understand creationism, we need to abandon the trope that only the ignorant can oppose mainstream evolutionary science. It is a comfortable delusion, a head-in-the-sand approach to improving evolution education in the United States. In the end, it stems from a shocking ignorance among evolutionists about the nature of creationist beliefs. 

First of all, Broun is no ignoramus. He holds a bachelor's degree in chemistry and an M.D. He is the most recent in a long line of educated creationists. In the 1920s, William Jennings Bryan similarly defended his role as a man of science. In response to Clarence Darrow's accusation that only "bigots and ignoramuses" opposed evolution education, Bryan listed his many college degrees."

While I think many of us have taught enough pre-meds to know that a B.S. in chemistry and an M.D. are not assurances of wisdom, or even common sense, the fact that Broun is as educated (formally) as he is while still assuming a denialist stance is eye-opening. (It's also a little embarrassing). 

I would argue that Broun, having received his B.S. and M.D. degrees in 1967 and 1971, respectively, in the Deep South, may indeed be ignorant. His education took place in the heartland of fundamentalism in an era before the massive leaps in bioinformatics and genetic knowledge. How likely is it that, in his career as a politician and practicing physician, he has kept up with the literature? (N.B. I would think a physician should understand embryology and evolution, admittedly, given the seriousness of antibiotic resistance, drug development, and reproductive issues, but I don't know how broad or narrow his practice was).

But as the case probably is, this may be an issue more of confirmation bias. Laats doesn't say this explicitly, but it's hinted at as he discusses the formal credentials of a large number of creationism supporters and creationist science educators:

"Yet even among those 52 percent of Americans who know that scientists support evolution, large majorities still want schools to teach creationism. And, among those teachers who teach young-earth creationism, a majority—like Broun—hold a bachelor's degree or higher in science and almost half have completed 40 or more college credits in biology. [...] 

Nor can we take solace in the delusion that these teachers are somehow rogue agents of a vast right-wing creationist conspiracy. As Berkman and Plutzer demonstrate, the creationist beliefs of teachers embody the creationist beliefs of Americans in general. The teachers are not ignorant of evolution, yet they choose to reject it."

This raises some important questions: what does it mean to be ignorant with respect to science issues? What Laats is saying is that teachers and many Americans do know the requisite facts, have added up all the pieces, and have come to the conclusion that evolutionary biology is bunk. And that's certainly true in many cases; confirmation bias is objective science's biggest enemy. Our pre-existing beliefs color how we categorize and interpret data. Because of selective memory and selective reasoning, important facts get put in the dust pile and other facts get exaggerated. 

But is a confirmation bias-driven rejection of the facts altogether different from ignorance? Or is it just another level: ignorance on an argument-scale, rather than a fact scale? I'd be careful before I concluded that ignorance wasn't a problem among creationists. (Of course, that doesn't mean that throwing facts at the problem will improve anything).

So if facts don't work (re: educated creationists), is there hope for science education at all for converting denialists over to the side of scientific truth? A sobering comment from Laats:

"David Long, an anthropologist and science educator now at George Mason University, conducted an in-depth ethnographic study of creationists in college, reported in his Evolution and Religion in American Education (Springer, 2011). Among his batch of creationist biology majors, only one abandoned her creationist beliefs. Most striking, this woman was not convinced by the scientific evidence in her biology classes; rather, her home life in high school, including an out-of-wedlock pregnancy, had turned her away from her conservative Protestant upbringing. Of the biology majors Long studied, none was convinced of the truth of evolutionary science by scientific coursework alone."

Only one abandonment of creationist beliefs, and not even due to scientific education built from a foundation of decades of peer-reviewed research. That's a yield in need of optimization.

Another point:

"This commitment to creationism by those who know the facts of evolutionary science makes no sense to mainstream scientists, many of whom have always been utterly flummoxed by the durability of creationism. And a snarky insistence that Broun does not have the qualifications to serve on the House science committee blunders into an uncomfortable truth: Broun's views may fairly represent those of his constituents. Do we really want to demand that an elected official not fight for the ideas in which his constituents believe?"

I myself am guilty of "a snarky insistence that Broun does not have the qualifications to serve on the House science committee". And I stand by that.

This is the "uncomfortable truth" that Laats points out, highlighted above: Broun may represent his constituents' views. Hence he is, Laats hinted, indeed qualified for the committee.

No, no he isn't. Science shouldn't be a democratic process; we don't vote on the laws of the universe or whether carbon or nitrogen has a weight of 12 amu. Whether or not 50% or 95% of Americans believe the creation myth, evolution is factual. That aspect of science has implications: bacteria evolve resistance to drugs; embryonic stem cell research is powerful; the climate will continue to change and we influence that. Science-based issues are increasingly common. These are issues the House Science Committee has power over, via control of funding agencies. And the problem is, science-based issues depend utterly on facts.  Leadership should reflect that; leaders should strive to eschew confirmation bias with respect to these issues.

Near the end of his essay, Laats echos a sentiment that's been increasingly shared among scientists trying to solve the denialism problem:

"As it stands, scientists' blundering hostility toward creationism actually encourages creationist belief. By offering a stark division between religious faith and scientific belief, evolutionary scientists have pushed creationists away from embracing evolutionary ideas. And, by assuming that only ignorance could explain creationist beliefs, scientists have unwittingly fostered bitter resentment among the creationists, the very people with whom they should be hoping to connect."

This is in contrast to the Dawkins school of thought, but it's a fair point. And a challenge for science educators.

Obsession with molecular structure

Check out the main picture from the Wikipedia article on Asperger's syndrome. Note the odd behavior of the boy, who as Wikipedia says, is obsessed with molecular structure (bonus points for identifying the molecule without cheating and visiting the Wikipedia page).

Caption: "People with Asperger syndrome often display
intense interests, such as this boy's fascination
with molecular structure." Source: Wikipedia.

This immediately suggests an opportunity for total synthesis groups to get grants: just repurpose the synthesis and NMR studies as a therapeutic exercise for the PI with Asperger's disorder. No FDA approval or expensive clinical studies required.

I have approximately zero expertise in the modern state of clinical or research psychology, but I do remember from Introduction to Psychology the stressed importance of the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM), a diagnostic manual widely accepted by psychologists and psychiatrists for the purpose of describing and classifying mental conditions. Compared to handbooks in other fields (the CRC Handbook of Chemistry and Physics, for instance, is in its 93rd edition), the DSM has undergone relatively few revisions, progressing from DSM-I (1952) to DSM-II (1968), DSM-III (1980), DSM-III-R (1987), DSM-IV (1994), and DSM-IV-TR (2000). After a 12 year lull, the DSM-V is coming out in 2013. 

There are (obviously) some changes going into place, which psychologists find important and you can read about if you like. The changes (and the manual itself) are not without controversy. Most prominently praised/criticized have been the elimination of two items: dyslexia and Asperger's syndrome. That's interesting, as it's my understanding that both are relatively common and I know people who self-identify with either disorder. I can't help but wonder how these things impact treatments and outcomes of individuals. 

Conjugate addition, aqueous edition

Organocopper chemistry is one of those fields that doesn't get the attention it deserves in advanced undergraduate and many graduate synthesis courses. Usually, we settle for writing "R₂CuLi" and being done with it, but cuprates do some pretty neat things that plain old Grignards and organolithiums just aren't as good at. Just like pretty much any organometallic species, though, their reactivity is dependent on additives, solvent, aggregation state, etc., which all ties in to the method of generation as well. (For a good review, if you get Organic Reactions, see Lipshutz).

There's a bunch of flavors (Gilman homocuprates, mixed Gilman cuprates, controversial "higher-order" cuprates, cyano-Gilman cuprates, etc.) that people have argued over (especially the alleged higher-order variety). Organocuprate reactions are, of course, moisture-sensitive, which means fun with cannula transfer and good Schlenk technique when you need to use them (this is annoying, by the way, when adding one needs to add solids at various points of the reaction). Additionally, additives can make a big difference:

Thus, this JACS article came as a surprise: "C–C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature." (Lipshutz, B. et al. JACS 2012, DOI: 10.1021/ja309409e). Note that it's from Bruce Lipshutz, who has been fairly influential in the cuprate field.

From the abstract (with Fig. 1 from the paper): (note typo from the abstract, red emphasis mine)

"Conjugate addition reactions to enones can now be done in water at room temperature with in situ generated organocopper reagents. Mixing an enone, zinc powder, TMEDA, and an alkyl halide in a micellar environemnt containing catalytic amounts of Cu(I), Ag(I), and Au(III) leads to 1,4-adducts in good isolated yields: no organometallic precursor need be formed."

Sounds pretty good, doesn't it? The development of aqueous conditions for organic reactions is challenging, of course, due to the sensitivity of many reagents to water as well as the utterly poor aqueous solubility of many (most?) substrates. Nevertheless, Lipshutz points out examples, including an aqueous conjugate addition by Luche that beat this paper by 26 years, and a more recent aqueous Negishi reaction by his own group.

The reaction:

Both the Negishi reaction and this new work are powered by "nanomicelles", tiny nonpolar environments formed by a catalytic amount of an expensive-looking detergent added to the reaction medium. The amphiphile is a vitamin E derivative (polyoxyethanyl-α-tocopheryl succinate; aka. TPGS-750-M), interestingly enough (other compounds were screened and didn't work). The authors include the structure in their paper (I've included the image from their manuscript rather than drawing it myself in order to point out a curiosity: is it weird to use "Me" and "CH₃" in the same structure?)

Of course, you can read for yourself the details. A variety of conditions/additives were screened, and the reaction was found to be generalizable to primary/secondary alkyl iodides/bromides. The best loadings and rates were found for what was described as the "coinage metal triad" (copper acetate, AgBF₄, and AuCl₃) along with zinc metal.

It's probably worth noting that all the enones presented were relatively uncrowded; this isn't exactly surprising, since usually TMSCl, borane, or some other additive is needed in the normal, water-sensitive route in order to effect conjugate addition to highly substituted enones. It's a bit trickier to find additives like that here.

Still, this seems, at first read, to be pretty interesting. It's aqueous, it's catalytic, you can recycle the catalyst/medium, and you can buy all the reagents. Yields seem to be good (but that doesn't always mean anything). Most importantly, the reaction looks to be facile. Facile is nice. Though I would have called the nanomicelles "transient nanoroundbottoms".

Reading assignments, vol. 1

A very short list of some new and old links of note this week:

This week:

• Bonny Swoger at Scientific American discusses information skills we should incorporate into science education.
• Chemjobber notes the attrition rate in PhD programs. The comments below are discouraging, including a comparison of PhD vs MD lifetime earnings.
• Read these comments by scicurious about the relevance of getting a PhD to science writers.
• I found Derek Lowe's commentary on a PLoS One article about human factors in selection of compounds for biological screening interesting.
• On CENtral Science and NorthJersey (source), an account of a 29-year-old chemist poisoning a coworker.

Old links rediscovered:

• Webcomic artist/blogger Drew points out the idiocy of caffeinated soap at The Worst Things for Sale.

Mark Johnson - Wrong on climate change AND Sasquatch

As a former denizen of Northeast Ohio, I can say with certitude that the state has several unappealing features, including John Kasich, meth labs, unconstitutional school funding, the Cuyahoga River, and Mark Johnson.

Mark Johnson is WEWS-TV ABC News Channel 5's Chief Meteorologist, which means for better or for worse, he is heard and trusted by a good portion of the population. His science background is not extensive: his education includes a bachelor's degree in telecommunications and a 'meteorology certification'.

Of course, he nevertheless weighs in on science issues to a broad audience (Northeast Ohio boasts ca. 4.5 million people). Unfortunately, he's a climate change denialist. Earlier this year, Johnson voiced his dissenting view on climate change, writing a full piece about claiming the Earth hasn't warmed in 15 years:

"Last week, the UK Met released its latest global temperature data to the world. It shows that the Earth has not warmed in 15 years. The warming ceased after the great super El Nino of 1998."

It's little wonder denialism is prevalent when public figures who should be versed in the science make these statements.

But it turns out Johnson's scientific misinformation isn't limited to climate change. The recent Bigfoot likely-hoax has attracted a flurry of attention from the general public but has been treated with due caution by science bloggers, including Greg Laden, Steven Novella, and Eric Berger, who have pointed out issues with the claim.

Unfortunately, Johnson's at it again. Yesterday, he wrote an article titled "New DNA Study Proves Existence of Sasquatch." Proves? Proves???? Sigh. It's, as you might expect, a pretty one-sided article that paints Dr. Ketchum's story as an effort commensurate to the Human Genome Project. And given the CSI phenomenon on TV (side node: apparently CSI effect is a real term), the mere fact that 'DNA' is in the title will carry a lot of weight toward convincing the public of the story's truthfulness. From the article:

"Researchers’ extensive five-year DNA sequencing study suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species."

"The study was conducted by a team of experts in genetics, forensics, imaging and pathology, led by Dr. Melba S. Ketchum of Nacogdoches, Texas. In response to recent interest in the study, Dr. Ketchum can confirm that her team has sequenced three complete Sasquatch nuclear genomes and determined the species is a human hybrid."

The piece is all-hype, without a word of caution or a shred of doubt. Pretty bold, for a press release about a study that has no accompanying data and some dubious claims from a company, as Eric Berger points out, with the worst possible rating from the Better Business Bureau.

Researchers’ extensive five-year DNA sequencing study suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.

Read more: http://www.newsnet5.com/dpp/news/local_news/water_cooler/new-dna-study-proves-existence-of-sasquatch#ixzz2Da7dZUjj

Researchers’ extensive five-year DNA sequencing study suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.

Read more: http://www.newsnet5.com/dpp/news/local_news/water_cooler/new-dna-study-proves-existence-of-sasquatch#ixzz2Da7dZUjj

Read more: http://www.newsnet5.com/dpp/weather/weather_news/United-Kingdom-Meteorology-Office-declares-Earth-hasnt-warmed-in-15-years#ixzz2Da3bx7oq

Last week, the UK Met released its latest global temperature data to the world. It shows that the Earth has not warmed in 15 years. The warming ceased after the great super El Nino of 1998.

Read more: http://www.newsnet5.com/dpp/weather/weather_news/United-Kingdom-Meteorology-Office-declares-Earth-hasnt-warmed-in-15-years#ixzz2Da3bx7oq