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.

Saturday, November 24, 2012

How's the cure for AIDS coming?

Adam Ruben, contributor of the column Experimental Error for some little journal called Science as well as author of the book Surviving Your Stupid, Stupid Decision to Go to Grad School, has posted this column about triviality in research. It's worth reading, both because it's funny and also because the frustration of "why am I doing this?" is common. It's common at smaller graduate departments, for sure, but even at the Big Universities where they solve Big Problems, there's lots of boring work. And the triviality leads grad students and onlookers to question why we're doing what we are. From the column:
"We’re accused of wasting money, wasting time. Spending 15 years on compounds that no human will ever likely inject or ingest. Studying the dusty corners of the universe but neglecting the bigger picture. Bear DNA. Shrimp on treadmills. The mating habits of screwworms. Writing our obscure little papers in our obscure little journals, blind to the fact that our research will only elucidate the trivial, or, even worse, the obvious. 
Now that the question has been asked, I see this attitude everywhere. Comedians say things like: “This week, scientists at Johns Hopkins University published a study proving that straight men enjoy looking at breasts. Do we really need a study for that?” Or Jay Leno’s snarky reply to research he deems unimportant: “Scientists at UCLA announced they have developed a unicycle for squirrels. Hey guys—how’s that cure for AIDS coming?” 
And that’s where I feel conflicted. Because a part of me acknowledges, sensibly, that a squirrel unicycle is a waste of time and money (though probably darn cute). But another part gets mad, wanting to yell at the TV, “We’re not all working on cures for AIDS, dumbass!” 
Then the first part asks the second part, “Um … why aren’t you?” 
Our kneejerk reflex—and also the usual response of scientific authorities when confronted with a claim that some bit of research is trivial—is to counter that our accuser just doesn’t understand how science works. What if every scientist had been forced to justify his or her wacky-sounding research? 
Antonie van Leeuwenhoek: “Well, I’m looking through pieces of glass at thin slices of cork.” 
Antonie van Leeuwenhoek’s Backwards and Anachronistic Uncle Who Likes AM Talk Radio and Reruns of 7th Heaven: “Hey Antonie, how’s that cure for bodily humor imbalance in black bile coming?”"
The comments from Jay Leno types he points out remind me of Eric Cantor's YouCut Citizen Review (or as it might be better called, Eric Cantor's Intellectual Crime against Humanity). It's a definite problem in science--the idea that taxpayers, as the source of funding, are also the best ones to judge if research is worthwhile. Are they? (Spoiler: no, they aren't).

Anyhow, read the column. And read his other stuff. It's good.

Friday, November 23, 2012

Wheatgrass: "Creat" your own reality!

Wheatgrass juice being made. Credit: Wikipedia.
Image available via Creative Commons license.
I've found the idea of wheatgrass funny for a while now. Pseudo-health stores that dress up fruit/sugar concoctions as 'health drinks' by throwing in a spoonful of nutritional supplement dust have become popular recently, and they all seem to peddle the privilege of drinking shots of wheatgrass juice. For a fee ($2-$3), you can get a bunch of grass squeezed into juice by a machine (itself a few hundred dollars) and then drink it. Cows consume grass, too, but it's free for them and then we turn them into delicious beef.

Proponents of wheatgrass juice basically think it's a nutritional panacea. But a lot of the health claims (i.e. it contains lots of vitamin B12, which is an important vitamin that is found in meat and so vegans don't usually get enough) are dubious (i.e. turns out the B12 content is negligible). There's not a lot of scientific literature on the effects of wheatgrass (PubMed lists only 2 random controlled trials involving wheatgrass, for instance). But most evidence seems to suggest that wheatgrass is no better or worse than any green vegetable. It's just trendier.

Lack of evidence doesn't stop the marketing people. One of my favorite wheatgrass companies is Pure Intentions, who not only sell the stuff to local smoothie shops but also operate a School of Energy (a "diverse spectrum of holistic and energetic facilitators and teachers for all ages and levels"). Their website contains all sorts of cringe-worthy pseudoscience/bad-science goodies.

Let's take a look at what Pure Intentions says about their product (red comments are mine)
"What is Wheatgrass?
Wheatgrass is the young grass of wheat grown from the red winter wheatberry seed. The fresh-squeezed juice of the grass produces high concentrations of chlorophyll, active enzymes, vitamins, minerals, and amino acids. It is true that 1oz. of wheatgrass juice has the nutritional equivalent of 2-1/2 lbs. of green, leafy vegetables. [no--it doesn't--Dole, for instance, points out that spinach is much richer in nutrients. and pressing it into juice to concentrate it is kind of cheating] It is one of the richest natural sources of vitamins A, B complex, B-17, C, E, & K. Additionally, it is an excellent source of calcium, potassium, iron, magnesium, phosphorus, sodium, sulfur, cobalt, zinc, as well as 17 forms of amino acids and enzymes." [apparently 'excellent source' doesn't mean much, since it's got 1% DV of calcium/magnesium/phosphorus but 413% DV zinc]
Here is where it gets good:
"Why is Chlorophyll important? [why did you capitalize it? why?]  
Chlorophyll, which makes up over 70% of the solid content of wheatgrass juice, is the basis of all plant life and closely resembles the molecular structure of human red blood cells. [...] Chlorophyll is the first product of light, containing more light energy than any other element. [make it stop. make it stop.] It can be extracted from any plant, but wheatgrass is superior because it has been found to have over 100 elements needed by the human body." [it has over 100 elements? I'm pretty sure you're obligated to include thallium and lead and stuff by that point...]

Chlorophyll A and human red blood cells
displaying remarkable structural similarity.
Credit: RBC Image is in the public domain.
Hey guys! Chlorophyll is THE BASIS of all plant life! Forget amino acids, carbohydrates, lipids, and nucleic acids.

And as depicted in the figure to the left, they're correct. Chlorophyll certainly does resemble human erythrocytes.

My favorite jam-packed sentence: "Chlorophylll is the first product of light, containing more light energy than any other element." Digest that one for a second. Pretty high cringe efficiency. Personally, I've never noticed the "element" chlorophyll on the periodic table, but then again--I'm an organic chemist, so if it's in the transition metals or lanthanides, I probably ignored it. And what is "light energy"? Photons? It has photons? In... a bucket? Where does it keep the photons? It's remarkable that chlorophyll is the "first product of light"; turning all those photons into carbon and nitrogen must be hard work.

Chlorophyll is important, of course, in the process of photosynthesis (which is a pretty cool process). It's what the authors are trying to hint at, though even if you fix the inaccuracies photosynthesis is irrelevant to human nutrition. We can't digest chlorophyll. So regardless what nice things you might say about it, it's useless as a supplement.

The website also proclaims the abundance of enzymes in wheatgrass:
"Enzymes play an important role in many bodily functions including vision, thought, reproduction, breathing, and digestion, just to mention a few. The enzymes found in wheatgrass have been found to supplement the indigenous enzymes manufactured in the human body."
This leaf also contains chlorophyll, and for $200 you can
probably make it into a trendy organic drink.
Source: my own work. I totally found that leaf.
This is, of course, nonsense. Enzymes are nature's catalysts, and with rare exceptions they are proteins. All organisms need enzymes to function--they catalyze diverse functions from translation of RNA to metabolism to immune responses to cell signaling. But we make our own diverse set of highly specialized enzymes, and each organism's enzymes are typically different from other species, genera, orders, and so on. So ingesting a bunch of wheatgrass enzymes doesn't give you mystical powers of wheatgrass. In fact, your body won't even use them. Since enzymes are proteins, they are digested indiscriminately in the stomach, along with all other protein. Congratulations: you've made some ordinary amino acids. Simply put, ingesting enzymes confers no health benefit.

I encourage you to read the rest of what they say; there's more delightful puzzles in there. The growers make a bunch of health claims, tell you that wheatgrass is so potent it'll give you nausea, and advise you to cleanse your palate with a lemon afterwards (maybe because grass is disgusting).

$3 worth of wheatgrass. Source:
Pure Intentions website
Like I said earlier, there's not a lot of scientific literature behind the wheatgrass juice phenomenon. So most of what is put out is hype--a mixture of novelty, optimism, and marketing. There may be health benefits (it's a vegetable, after all). But wrapping anything up in pseudoscience is dishonest and does a disservice to gullible customers. It's not the chlorophyll; in case your biology is rusty, humans can't photosynthesize or even digest the molecule. It's not the enzymes (hello, denaturing environment of the stomach).

Wheatgrass juice is an example of one of those areas where anecdotes carry more emotional weight than conventional medicine. This phenomenon has been written about before (see Denialism by Michael Specter for a good read in this area). It's interesting, and something we have to be aware of as scientists. As pitifully adorable as the glaring pseudoscience above is, it's actually effective in reaching people. We might have science on our side, but they have marketing.

Added note: check out their recently added "cat grass" (vets seem to support this) and "floral grass." I especially like the tagline: "Creat your own reality!"

Creat your own reality! Source: Pure Intentions website.

Descriptive notation

Drew, co-author of webcomic Married to the Sea, brings us a fine example of how to include qualitative observations in your lab notebook.

Science "Leadership" in Congress

It's common for prominent scientists or scientist/politicians (i.e. Bill Foster) to decry the lack of scientists in the US Congress. This lamentation is understandable, given the increasing dependence of our society on science-based issues (energy policy, climate change, reproductive rights, healthcare, STEM education, information freedom, telecommunications, biomedical research, pollution, and environmental regulation, to name a few).

The prospective leadership of the House Science Committee highlights this need.

This month, the House Republican Steering Committee will decide which of the members of the newly elected 113th Congress will lead each of the House’s committees, including the U.S. House of Representatives Committee on Science, Space, and Technology, come January.

There are three contenders for the chairman position: Lamar Smith (R-TX), Dana Rohrabacher (R-CA), and Jim Sensenbrenner (R-WI). The Committee has jurisdiction over several agencies chemists may be familiar with, including but not limited to NSF, NIST, NASA, the USGS, the DoE, EPA, NOAA, and ATSDR, and the power of the committee corresponds to large millions of dollars in funding. This is the same committee that included (until his recent defeat) Todd Akin (R-MO) and still includes just-reelected Paul Broun (R-GA), an M.D. (with, embarrassingly enough, a B.S. in chemistry) who this year denounced "evolution and embryology and the big bang theory" as "lies straight from the pit of Hell" (read more of what he said if you want to depress yourself a bit).

Current vice chair Jim Sensenbrenner, having served as the chair previously (1997-2001) isn’t likely to get the nomination. This will probably come as a relief to scientists, in light of Sensenbrenner’s public condemnation of the theory of anthropogenic climate change as “scientific fascism” and an “international conspiracy” and role in disbanding of the White House Office of Energy and Climate Policy. Lamar Smith has perhaps the most training in science of the three—he aspired to be a scientist at an early age but was deterred by a college introductory physics class. Dana Rohrabacher, an aggressively prominent climate change skeptic, stated in 2012: “my analysis is that in the global warming debate, [skeptics] won”. A paragraph later, he proclaimed “I love science.”

All three contenders are lawyers by training. The evaluation and use of scientific findings and allocation of funds should be – as scientists are taught but lawyers are loathe to accept – approached in as non-biased a way as possible. But the top leaders in the position to bolster or cripple our nation’s scientific abilities may not have objectivity at heart.

What to do? If we had more scientists or science-educated people go into politics the situation would probably improve.

But then again, Paul Broun has a chemistry degree.

Thursday, November 22, 2012

Mission statement

There are roughly 6 billion science-related blogs on the internet,1 so you might naturally wonder: what's the point of this one? I've got a couple ideas what to do with the space. Hopefully they'll come to something. Subscribe?

  1. Bring chemistry to the public. This will entail featuring research or areas of interest, presented in a manner suitable for non-chemists and chemists alike to find interesting. Public interest in science is crucial both for general enthusiasm, public support, and continued grant funding. People deserve to know what they're funding--and great science should be appreciated the way great art and great music are. 
  2. Bring ethical/social/political issues of science into focus. Scientists have a poor track record at engaging the public. Many of them have a poor track record at playing nice with each other. Chemistry culture has been described as toxic. There's lots of internal politics and fraud. And scientists are usually unwilling to dig into public policy and lawmaking. An important step towards fixing these issues is to discuss them and build awareness.
  3. Highlight interesting chemistry. I'm a chemist, and so I find chemistry interesting. As such, I'll find novel or useful topics in organic synthesis/catalysis/chemical biology/microbiology and share or comment on them. Hopefully it'll be interesting to other people too. This'll include articles, lab techniques, reviews, etc. of interest.
  4. Showcase valuable resources. This includes interesting databases, blogs, websites, journals, and the like that will be useful especially to chemists. 
It'll be slow (grad student here). For now it'll be pseudonymous blogging--that may change depending on other factors. 

Anyhow, that's about it for now. Next step: content.


1 +/- 6 billion, citation needed