Sunday, December 30, 2012

Reading assignments, vol. 5

Despite the widely celebrated secular/pagan holiday this week, science-related journalism trudged on. Some interesting posts below related to the fiscal cliff, science education (creationism is sneaking back), scientific imagery and creativity, and some science- (and pseudoscience)-related awards.

Science and politics

  • New Statesman guest editors Brian Cox and Robin Ince have written a pointed commentary on the role of science in policymaking. They highlight that non-scientific political issues have invaded public interpretation of science; this risks damaging society's confidence in scientific truth. It's a good read. A couple of responses quickly followed, including two weakly critical responses from Rebekah Higgitt (The Guardian), Jack Stilgoe (also The Guardian), and a favorable reply from Jon Butterworth (still at The Guardian). I commented on this earlier this week here.
  • Discover Magazine blogger Keith Kloor (Collide-a-Scape) comments on the above article and also on the current toxic environment of the science-vs-religion fights. He argues against the "Puritanical" zero-tolerance policy of Richard Dawkins and like-minded skeptics.
  • Bill Nye has written a sort of open letter to the federal legislature regarding the impending fiscal cliff; he urges (like most of us do) a combination of spending cuts and tax increases, but makes the case that legislators avoid cuts in science. His argument is that science drives innovation which drives American economic superiority. Is science going to be immune from the cuts? I doubt it, unfortunately.
  • Antibiotic use (also discussed last week) in livestock is a major contributor to widespread drug resistance. Laura Rogers reports on recent issues and developments in laws and regulations regarding antibiotic use, including increased oversight of how and where the drugs are used, an end to non-prescription antibiotic use for animals, and stopping the practice of using antibiotics when they're not needed.

Bad science and bad journalism

  • Under the "bad journalism" theme comes a Fox News (!!!) science section piece titled "Duh! 12 obvious science findings of 2012". I have a problem with pieces that pander to readers by highlighting "obvious" research (especially since many things previously considered "obvious" are now known not to be true). To be fair to Fox News, this same piece appeared at Huffington Post.
  • Complementary to bad journalism is bad science. Christopher Wanjek writes on HuffingtonPost about  the top five science retractions of 2012. The first one (the scientist who made up his own peer reviewers and clued editors in by responding too favorably and too quickly) is the best. This, too, is cross-posted to Fox News. Although the retractions highlighted are certainly disturbing, the tone of the article's introduction sets an atmosphere of general mistrust of scientists and science. Of course, scientific misconduct is serious (and increasingly we are being made aware of it) but the author seems to de-emphasize the role of kneejerk journalism in public disappointment.
  • Disgraced doctor Andrew Wakefield (the guy who had that fraudulent study linking autism and vaccines) has been given the Golden Duck award for 'lifetime achievement in quackery'. The award is part of an effort by scientists and science advocates to spread awareness of bad science and pseudoscience. However, some, such as Frank Swain of SciencePunk, feel the award is counterproductive: things like this come across as smug and contemptuous, and the group giving out the Golden Duck isn't influential enough to matter.
  • To the long list of "people at The Ohio State University who have gotten caught committing research fraud" we can add pharmacologist Terry S. Elton, who apparently manipulated over two dozen figures in papers and grant applications. (For other examples see pharmacy professor Robert J. Lee and, most familiar to chemists, Leo Paquette).

Science education

Imagery in science

  • Imagery and aesthetics are usually the last thing on scientists' minds, but they can be instrumental in promotion of science. See not only this post by Alex Wild asking readers to submit the year's best science imagery, but also this fascinating blog where a chemist uses large quantities of materials and takes beautiful high-resolution -- and artistic -- photos of labware and reactions.
  • Wired features a gallery of what they describe as the best scientific figures of 2012 (i.e. figures in journals, not "figures" as in people/scientists). I like "The Essence of Tomato" -- it's the one that looks like a DNA microchip heat map and it describes relative abundance of various flavor compounds in varietals of tomatoes. There's also an image of a lonely yttrium atom.
  • On a related tangent, there's a piece by Virginia Hughes on Only Human over at National Geographic regarding perception of science and the importance of creativity. It's short and well-written and highlights important issues in how children at impressionable ages are losing interest because they don't see creativity in it. The piece also addresses strategies for combating this notion.


Thursday, December 27, 2012

Opinions on opinions on science's influence on opinions' influence on science

A post at NewStatesman by guest editors Brian Cox (British particle physicist and science popularizer) and Robin Ince (comedian/writer) highlights the danger of political controversies in undermining public trust in science. It's been responded to several times (read this or this or this or this or this), but it's worth pointing out some key passages.

Cox and Ince begin by contrasting pre-Internet times to modern times, which illustrates an important difference in how the public perceives science (bold emphasis mine):
The story of the past hundred years is one of unparalleled human advances, medically, technologically and intellectually. The foundation for these changes is the scientific method. In every room in your house, there are innovations that in 1912 would have been considered on the cusp of magic. The problem with a hundred years of unabated progress, however, is that its continual nature has made us blasé. We expect immediate hot water, 200 channels of television 24 hours a day, and the ability to speak directly to anyone anywhere in the world any time via an orbiting network of spacecraft. Any less is tantamount to penury. Where once the arrival of a television in a street or the availability of international flight would have been greeted with excitement and awe, and the desire to understand how those innovations came into being, it is now expected that every three months you’ll be queuing outside the Apple store for a new wafer-thin slab of brushed metal, blithely unaware that watching a movie in the palm of your hand has been made possible only through improbable and hard-won leaps in the understanding of the quantum behaviour of electrons in silicon.
It's pointed and true. We have more technology now than ever before; scientists even within disciplines are unable to explain it to each others (how many organic chemists, for instance, have a grasp of how LCDs, which are built on small molecules, work?). There's more to know -- more availability of wonderment -- than ever before, but given how common electronic devices are, it's easier to use them than to try to understand them.

The authors describe nature as an "arbiter above opinion." They quote Feynman with the assertion that if an opinion or guess conflicts with the available evidence, it is wrong.
The assertion is surely uncontroversial, but implementing it can be prohibitively difficult, primarily because it demands that everything be subordinate to evidence. Accepting this is fraught with cultural difficulty, because authority in general rests with grandees, gods, or more usually some inseparable combination of the two. Even in a secular democracy, a fundamental tenet of the system is that politicians are elected to reflect and act upon the opinions of the people, or are at least given temporary authority by the people to act upon their own. Science is a framework with only one absolute: all opinions, theories and “laws” are open to revision in the face of evidence. It should not be seen or presented, therefore, as a body of inviolate knowledge against which policy should be judged; the effect of this would be to replace one priesthood with another. Rather, science is a process, a series of structures that allow us, in as unbiased a way as possible, to test our assertions against Nature.
Cox and Ince then offer up climate change denialism as an example. From their piece:
The loud criticism of climate science is motivated in the main not by technical objections, but by the difficult political choices with which it confronts us. This is important, because there must be a place where science stops and politics begins, and this border is an extremely complex and uncomfortable one. Science can’t tell us what to do about our changing climate. It can only inform us that it is changing (this is a statement based on data) and tell us the most probable reasons for this given the current state of our understanding. For a given policy response, it can also tell us how likely that response is to be effective, to the best of our understanding. The choice of policy response itself is not a purely scientific question, however, because it necessarily has moral, geopolitical and economic components.
The key passage, I think, is this one, which comes near the end of the article (bold emphasis mine):
Science is the framework within which we reach conclusions about the natural world. These conclusions are always preliminary, always open to revision, but they are the best we can do. It is not logical to challenge the findings of science unless there are specific, evidence-based reasons for doing so. Elected politicians are free to disregard its findings and recommendations. Indeed, there may be good reasons for doing so. But they must understand in detail what they are disregarding, and be prepared to explain with precision why they chose to do so. It is not acceptable to see science as one among many acceptable “views”. Science is the only way we have of exploring nature, and nature exists outside of human structures.

Though several of the responses to the piece have been negative, with respondents misreading the piece as an insistence that science and politics be divorced of each other, Jon Butterworth at The Guardian agrees with Cox and Ince and attempts to clarify the argument:
My reading of Cox and Ince is that they argue that the boundary between these cases, tricky though it can be, should be kept as clear as possible. This is not a claim for the supremacy of science, nor complete separation between science and politics, but is an attempt to direct political debate to the areas where it can be fruitful.
I don't see any suggestion there that science is, or can be, separate from politics. Not only are scientific results important input to political debate - often setting the boundary conditions of what is known to be possible - but politics at all levels influences the science we do. Taking examples from my own experience - CERN was set up with political as well scientific goals, to raise the level of European cooperation in an important science area - "Bringing nations together through science". The European Space Agency is explicit about having the political and economic goal of supporting the European aerospace industry, yet enables enormous amounts of science. The decisions as to what experiments are done are often influenced by politics, ranging from office to inter-governmental level. Suppression of results and cherry picking, as discussed for example in Ben Goldacre's books, are explicitly political, moral and economic issues. The progress of science is also potentially warped by journals, by funding reviews and by appointment panels. But progress it does, nevertheless. The evidence is all around you.
Agreement all around. Head-in-the-sand denials that politics has (or should have) any influence on scientific practice, or that science has (or should have) any influence on public policy are misguided. As a society, we need to be able to recognize what is political ideology and what is scientific truth/fact so that we can harness science to best influence policy and the public welfare. Science can't, and shouldn't, be separated from politics, but politics shouldn't be the bird droppings on the Windshield of the Car of Science that make it hard to see while at the wheel.

One of my favorite comments comes from a user named TheBabelFish, who offered this response to Butterworth's piece:
We have made specialists of our politicians. The career path is inexorable. They spend their entire careers learning to play the game of politics, how to get elected, how to spin stories, events, even facts, to their own advantage. It's a system that is very good at turning out politicians, but very bad at turning out leaders. 
If scientific data, to pluck a random example wildly out of the air, requires a 'hard sell,' persuading the electorate to make a sacrifice, then they won't do it. They just won't. They've been trained, in their speciality of politics, never to give the public bad news if it can possibly be avoided.
It's a good point. A symptom of our political system; with a dearth of scientists in government (they're trained as specialists in something else, after all), I don't see an easy cure.

Wednesday, December 26, 2012

Chemists who do other things

At Just Like Cooking, See Arr Oh pointed out John Kuhn, an NFL player with a chemistry degree and some internships under his belt.

Dolph Lundgren in Rocky IV.
Source: Wikipedia.
What other prominent folks have had chemistry degrees?

Actor and martial artist Dolph Lundgren, of Rocky IV fame, has both a bachelor's and master's degree in chemical engineering. Frank Capra, director of "Mr. Smith Goes to Washington", had a chemical engineering degree as well. Ally Walker, who starred in the 1990s drama Profiler, originally intended to be a scientist or doctor and holds a biochemistry degree from the University of California, Santa Cruz. Iron Man co-star Terrence Howard at one point wanted to be a science teacher and was reportedly three credits short of a chemistry degree.

German Chancellor Angela Merkel.
Source: Wikipedia.
Several political leaders have chemistry degrees. Margaret Thatcher is one example, as she studied X-ray crystallography and worked briefly as a research chemist (however, she clashed with the Royal Society and is not remembered fondly by many British scientists). Germany's Chancellor is Angela Merkel, who has a doctorate in physical chemistry. In the United States, John M. Deutch is a physical chemist who held prominent political positions in the Clinton Administration, including being the Director of Central Intelligence. Israel's first president, Chaim Weizmann, developed the ABE (acetone-butanol-ethanol) process to produce the three chemicals by fermentation of starch. Additionally, Ignacy Mościcki was a physical chemistry professor who was a president of Poland.

Russian composer Borodin.
Source: Wikipedia.
And I'd be remiss if I didn't mention a couple musicians. Alexander Borodin, the famed Romantic composer, was also a surgeon and a professor of chemistry. Borodin worked for Erlenmeyer and discovered the aldol contemporaneously to Wurtz (n.b. the timing of this is disputed). Bill Lipscomb was a 1976 Nobel Laureate and an avid clarinetist who befriended jazz legend Dizzy Gillespie. And Edward Elgar, the English composer of Pomp and Circumstance and Enigma Variations, was an avid amateur chemist who invented an apparatus for production of hydrogen sulfide.

Lastly, Drew, the author of webcomics Married to the Sea and Toothpaste for Dinner, writer of the hilarious blog The Worst Things for Sale, musician behind Crudbump and Kompressor, and novelist behind Veins, is a former industrial chemist.

Saturday, December 22, 2012

Reading assignments, vol. 4

The following are some interesting topics and posts from the last week or so. A lot of links, but they're pretty good.

Online education (i.e. MOOCs)

  • At the Chronicle of Higher Education, George Washington University Dean Doug Guthrie criticizes Coursera, a for-profit company that partners with universities to offer massive online open courses (MOOCs). Guthrie insists that Coursera is a fad; "thoughtful interactions" do not occur; and educators are frequently creating a crowd, not a community. It's a valid point; online education has promise but very often falls short, even with the best of intentions. See also this other criticism/analysis of MOOCs.   While we're at it, if you really want to read more about MOOCs check out this year-in-review about MOOCs.
  • In the midst of the recent surge in MOOC popularity, the University of Illinois at Urbana-Champaign is running an online Intermediate Organic Chemistry course, taught by educational specialist Michael Evans and Dr. Jeff Moore.
  • Dayna Catropa and Margaret Andrews compare MOOCs to MOCCs (midsized online closed courses), predicting that MOCCs will replace MOOCs, as they provide an opportunity to monetize the online experience and deliver it to smaller groups.

Public health

Scientific communication

The F word (funding)

  • At the Chronicle of Higher Education, Indiana University president Michael A. McRobbie warns that the fiscal cliff may spell out serious damage to research universities. He makes the case that this would be perilous to the economy, as research drives innovation in engineering/manufacturing.
  • The United States is not the only place where scientists are feeling the squeeze of a scant funding environment. Nature gives an account of Spanish scientists who protested their government's reductions in science funding (39% drop since 2009).

Scientific philosophy

  • On HuffingtonPost, Dr. Rupert Sheldrake writes a commentary on the arrogance of modern science, criticizing materialism and insisting that dogmatic thinking is "crippling" modern science. I disagree with most of what he says; it's overly dramatic, simplistic, and feels like it's pandering to the pseudoscientist crowd (as well as an advertisement for the author's new book). But it's worth reading; is this a pervasive viewpoint?
  • For the philosophically inclined, read this. (tl;dr = is science tool-driven or idea-driven??).


Sunday, December 16, 2012

Reading assignments, vol. 3

Some reads from the internet are below. I should have some organic synthesis-oriented post(s) on here this coming week, so for anyone who likes organotrifluoroborates: stay tuned.

Three themes for this week, as discussed below.

Research in practice:

Science and the public:

  • Via Talk Nerdy to Me, a good video commenting on anti-science politicians, including the House Science Committee. One of my favorite topics, so watch it.
  • Karen Kashmanian (a dean at the WPI) recommends that science (and access to science via technology) be formally deemed a human right.
  • Rebecca Harrington comments on a UC Berkeley study on the dialogue surrounding environmentalism. The rhetoric used to promote environmental protection (i.e. the wording, not necessarily the factual arguments) is critical in shifting conservatives toward environmentalism. Should be of interest to those fighting denialism.
  • An excellent post on Slate about the public's perception of conservation and ecology. Turns out white tigers are inbred mutants, and their breeding causes harm to animals as well as depletion of valuable resources otherwise useful for conservation. It's an important read for any scientist or conservationist.

Graduate chemical education:

  • Chemjobber points out that now even the higher-ups in ACS are acknowledging that there are way too many chemistry PhDs. In a separate post, other surprising assertions by the ACS leadership are noted.
  • An opinion piece by Stacey Patton at the Chronicle of Higher Education (posted also to HuffingtonPost) discusses the combination of student debt and poor employment prospects in the context of graduate school (more geared toward humanities but this applies to science to a degree). She and others recommend that graduate programs warn prospective students and offer guidance.
  • A commentary by science writer and Earth science professor Scott K. Johnson makes the case for a different model of science education in order to better teach critical thinking to science and non-science students alike. He argues against the current (failed) paradigm that thinking abilities come as a byproduct (side product?) when you teach the basics. He's right.


  • Greg Laden points out the convergence of a fake study and a real study on the conclusion that Fox News viewers are, on average, unintelligent. 
  • Because See Arr Oh likes odd things in chemistry, there's a post on Just Like Cooking about the use of Sweet 'n Low in an Org. Lett. procedure. At least it found a use in chemistry, because it tastes gross.
  • A brief New Scientist interview with Tom Knight about synthetic biology. On a somewhat related note, see this Scientific American post about complexity in science/engineering.
  • Derek Lowe (In the Pipeline) points out a scientist angry to the point of legally claiming defamation over not being awarded the Nobel Prize.
  • Chemists generally know about the helium shortage (better learn to do NMR without magnets!). Here's a piece that talks about it on Starts With a Bang.

Thursday, December 13, 2012

Blind to colorblindness

Since venturing into the more biology-oriented side of organic chemistry, I've noticed something in chemical biology and biochemistry papers that really isn't a problem in synthetic journals. Color. Biologists/chemical biologists love using color. And that makes sense; the meaning of a figure can be more easily conveyed by dyanamic coloration. Consider the following micrograph from an ACS Chemical Biology article (DOI: 10.1021/cb300171p). The figure depicts measurement of zinc levels in mitochondria in different cell types. It's a nice looking figure, and reasonably clear.

But then you go to print the articles (some of us do that) on your black and white printer and the figures become incomprehensible.

Of course, the obvious question: so what? Why not use a color printer? Or simply view things on the computer or a tablet? Content is delivered overwhelmingly by the web now; isn't it natural that figures reflect the most common viewing medium?

Well, yes. But it's still a problem for a sizeable minority (not many women, but as many as 10% of men) of the population who experience colorblindness. "Colorblindness" is a blanket term to refer to any disorder resulting in loss of color perception. Completely grayscale colorblindness is very rare, but difficulty telling red and green apart is relatively common. Variability is seen in the degree of impairment; many people are simply "red-green weak", whereas others cannot tell the two apart.  Blue and yellow are also indistinguishable to some people, though this is less common.

The previously mentioned figure would look like this to someone with protanopia, a form of red-green colorblindness (note that colorblind images were simulated using Photoshop and the Vischeck plugin).

An important thing to note is that what appears illegible in grayscale is not necessarily illegible for colorblindness; a comparative example is shown below  Thus, it's possible to use colors effectively and still accommodate the colorblind population. Take this example from a Merck drug discovery paper (DOI: 10.1021/cb2003225). The quality of the original image (left) is not significantly damaged for a person with red-green colorblindness (center), even though the figure is indiscernable when rendered grayscale (right).

Web developers take colorblindness into account. It's an important topic in website design; professional web designers must ensure their content renders to readers who can't see, can't hear, can't see well, use Apple products, or other disabilities. As such, guidelines have been set up to ensure accessibility, including recommendations for color and contrast. The W3C standards, for example, "help make the Web accessible to people with disabilities including auditory, cognitive, neurological, physical, speech, and visual disabilities" (read more here if you're interested). Validation tools are commonly employed to ensure websites meet these standards.

So why haven't some journals gotten the message?

Consider the following examples, shown in the original form on the top/left with simulated protanopia beneath/right. Both of the example figures are from a 2008 JACS article (DOI: 10.1021/ja807872s). In this first example,  the graph is illustrating the fluorescence response of a bisboronic acid rhodamine derivative to various peptide substrates in order to demonstrate its selectivity. First off, this figure is difficult to read in the first place. But in the original full color image, peptides 1 and 10 are clearly the top symbols. In the colorblind-simulation image, it's tougher to tell. Is it 10 or 6 or 4? Is it 1 or 7? 9 kind of looks close, too. There's the little lines behind the markers, but those are confusing themselves. While the text clarifies this figure further, the figure label does not.

The next example is even worse. The results of labeling studies are shown. In their original color (left) they're quite striking. But the labels are red and green. Hence, under red-green colorblindness, the pictures are meaningless.

This should be unacceptable; all modern fluorescence imaging programs have the option of changing the display color of a particular fluorescent channel; hence, it is trivial to simply recolor the red or green channel to another color (i.e. blue). Take the following figure from a Nature Methods article (DOI: 10.1038/nmeth735) by Alice Ting. Here, the authors have false-colored the fluorescent dyes (Alexa-568 is in reality red and has been colored orange; CFP is cyan-fluorescent protein and is usually cyan anyway but has been adjusted). As shown from comparing the original figure (left) and the colorblind-simulated image (right), very little detail is lost and the figure is clear.

What do the publishers say about color accessibility? Not much. Consider ACS's policy from its Author Guidelines for JACS:
Color. The use of color to enhance the clarity of complex structures, figures, spectra, schemes, etc. is encouraged. Color reproduction of graphics will be provided at no cost to the author. Color graphics should be submitted in CYMK, not RGB, color mode. Graphics intended to appear in black and white or grayscale should not be submitted in color.
Okay. No mention of accessibility. And JACS is fairly broad, and most of its TOC images even contain color. Let's also briefly consider the color policies of a few other journals: ACS Chemical Biology, Cell, Nature Chemistry, Science, PNAS, and PLoS One. There's not much point in reproducing the individual journal guidelines here, but ACS Chem. Bio., Cell, Nature Chemistry, PNAS, and PLos One all say essentially the same thing as JACS, with no mention of handicap accessibility.

The figure preparation guidelines for Science condense colorblindness to one concise sentence:
Avoid using combinations of red and green together.
Some journals are aware; the author guidelines for Nature Chemical Biology, for instance, make some recommendations (interestingly, Nature's formatting guide doesn't mention them, nor does Nature Chemistry):
Authors are encouraged to consider the needs of colorblind readers (a substantial minority of the male population) when choosing colors for figures. Many colorblind readers cannot interpret visuals that rely on discrimination of green and red, for example. Thus, we ask authors to recolor green-and-red heatmaps, graphs and schematics for which colors are chosen arbitrarily. Recoloring primary data, such as fluorescence or rainbow pseudo-colored images, to color-safe combinations such as green and magenta, turquoise and red, yellow and blue or other accessible color palettes is strongly encouraged.
Granted, for some applications, color is unavoidable; take fluorescent microscopy for example. But the ease of making color figures/graphs/charts/schemes has outpaced some journals' awareness of accessibility standards.

In practice, I think the Nature publishing group does a pretty good job with this. And it's possible these things are perhaps checked in the review process even if not mentioned in the author submission guidelines. But I don't think it would hurt to provide this information upfront.

Monday, December 10, 2012

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.

Saturday, December 8, 2012

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:


Thursday, December 6, 2012

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.

Monday, December 3, 2012

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

Saturday, December 1, 2012

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".

Friday, November 30, 2012

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.

Thursday, November 29, 2012

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:
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:
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:

Tuesday, November 27, 2012

Book Review: Anthill (E.O. Wilson)

I have to take a break from Science-with-a-capital-S once in a while (don't tell my advisor), so occasionally I read books. Recently, I picked up a fiction book (don't tell my advisor) by E.O. Wilson. Yes, that E.O. Wilson, with the ants and the sociobiology and the world-famous-Harvard-ecologist, is also a novelist, having in 2011 published Anthill: A Novel. The book was prominently displayed on the Sale shelf (but not the Bargain table) at Barnes and Noble, so it must be doing alright, but I guess not super well (its Amazon Sales rank is #939,041, which puts it only 938,037 spots behind Ann Coulter's #1,004-ranked racist book Mugged, so hey, good job America on taste).

E.O. Wilson. Source: Wikipedia. Image available via
Creative Commons license via PLoS.
For those who aren't ecologists and don't know who E.O. Wilson is, shame on you for not knowing who E.O. Wilson is. He's the world's leading ant expert, as well as the pioneer of sociobiology, an avid environmentalist, an ecologist, and a humanist. He also extended his work on ant social behavior to human evolution, which Richard Dawkins doesn't like very much. But either way, he's regarded within biology as one of the world's top scientists. He doesn't have the go-get-'em aggression of Dawkins or Tyson, but he's got a long history of environmental advocacy, support for secular humanism, and cooperation/outreach to the religious sectors (he doesn't have a Conservapedia entry, so the church folk must not hate him too bad).

And now he's a novelist. This is unusual, for sure. Scientists are often notoriously bad writers, and a scientist being caught reading a novel is embarassing ("It's not mine!" "I only read Crichton to correct the horrible science errors!"). But writing a novel? That takes time and can interfere with the long hours of drudgery scientific pursuit. If you tell your advisor you're writing a novel, he frowns at you, wondering if it was wise to give you Sundays off and how quickly the next round of first year students are going to arrive so he can give your project away. If your advisor tells you he's writing a novel, you probably chuckle nervously and calculate in your head how much it would delay your graduation if you transferred labs. But then again, E.O. Wilson retired from teaching in 1996 and has pretty much defined our understanding of social insect behavior, so hey, he can do what he wants in his free time. Note that scientist-authors are not unknown: Sir Arthur Conan Doyle of Sherlocke Holmes fame was a surgeon, but usually you end up with things like climate scientist Rajendra Pachauri's racy dimestore romance novel or Amy Bishop of the shooting-her-department-over-tenure fame penning hauntingly autobiographical novels.

In short: what would this scientist's novel be like? I found out.

Anthill isn't the next To Kill a Mockingbird. It's too detailed, too matter-of-fact with its story, not conversational enough or shrouded in mystery/symbolism to be considered Literature-with-a-capital-L--you know, the kind you study for 8 years so you can get a job as a barista. It feels more like an autobiography than an adventure. But it's an enjoyable book, and it's written in an accessible manner that is not  dry as you might expect a scientist to write (though the scientist voice comes through). It may be because the writing is drawn from childhood experience: Wilson himself is from Alabama and took an early interest (obviously) in entomology. There's a lot of naturalistic detail in this book. To a chemist whose birdwatching skills entail distinguishing crispy and original recipe chicken, I guiltily found the naturalistic listings of species upon species in each chapter/scene a little overwhelming. Maybe this will turn off non-scientists who try to read the book; maybe not. Importantly, though, E.O. Wilson's book carries a clear tone of love for science and enthusiasm for how science can improve lives. Not enough scientists or authors communicate this. 

My favorite feature of the book was right in the middle: a series of chapters titled The Anthill Chronicles. (This isn't a spoiler, incidentally). Wilson narrated the rise and fall of several ant colonies from an ant-colony perspective, a sort of myrmecological Gallic Wars. It was the most interesting part of the book, and making ecology interesting to a chemist is not always trivial. And darn it, he fooled me into learning some things about ants. That part of the book is probably worth its own read.

The human part of the story is alright, too, but I already know some things about humans. It feels at first like your Harper Lee/William Faulkner/(other author I used to know) Deep South novel, with its commentary on family, tradition, racism, and the like. Again, there's more human detail than you would usually expect from a scientist. It smacks of sociobiology and determinism, but that's kind of the point of the novel, I guess.

In the last part of the novel, we get a healthy dose of environmentalism/denialism. Again, I won't ruin the story, so read the book yourself. But I think Wilson does a great job tying ant behavior to human behavior (surprise!). His approach to denialism is not one of Richard Dawkins' persuasion; it's a change-from-within strategy. I wish the ending been longer. It wraps up more quickly than feels natural, and a lot of opportunity was missed to delve further into denialism (especially religiously-motivated) and the interface of scientists and anti-science or fundamentalists. But these things are in there, and the novel did prompt me to question my own philosophies on how we should engage the public.

Read the book yourself--it's by E.O. Wilson for crying out loud. And/or read this other tangentially related article in Trends in Microbiology if you don't want to spend $12.